Key files — per-file index (gbrain repo)

On-demand reference. CLAUDE.md (the always-loaded orientation file) routes here via its Reference map. Read a file's entry before editing that file.

Entries describe CURRENT behavior + load-bearing invariants only. Release history lives in CHANGELOG.md + git log / git blame, NOT here. Do not append per-release **vX.Y.Z:** narration — CI enforces this (scripts/check-key-files-current-state.sh).

• docs/operations/conversation-parser-llm-fallback.md — operator and maintainer contract for the default-off LLM parse fallback: exact config key, deterministic-first dispatch boundary, sampled data surface, untrusted-content prompt handling, page-date/cache-key coupling, timestamp validation, cache/checkpoint behavior, observability, limitations, and focused test commands.

• src/core/operations.ts — Contract-first operation contract, served through a ~300-line assembly façade: the op definitions live in the domain modules under src/core/ops/ (next entry) and are spread into the single exported operations array here; the shared contract types (src/core/ops/contract.ts) and the security/scope layer (src/core/ops/context.ts) are re-exported through this file, so every import path below resolves through the façade unchanged. The rest of this entry describes the surface as consumers see it. Exports upload validators validateUploadPath, validatePageSlug, validateFilename, plus matchesSlugAllowList(slug, prefixes) (glob matcher: <prefix>/* matches recursive children; bare <prefix> matches exact only). OperationContext.remote is a REQUIRED field flagging untrusted callers; OperationContext.allowedSlugPrefixes is the trusted-workspace allow-list set by the dream cycle; OperationContext.auth?: AuthInfo is threaded through HTTP dispatch for scope enforcement in serve-http.ts before the op runs. OAuth whoami exposes the authenticated AuthInfo.sourceId and AuthInfo.allowedSources grants as source_id and federated_read; absent grants serialize fail-closed as null and [], while local, legacy, and stdio response shapes stay unchanged. enforceSubagentSlugFence(ctx, slug, opName) is the shared fail-closed subagent write fence: when viaSubagent and allowedSlugPrefixes is set, the slug must match the allow-list; else the legacy wiki/agents/<id>/... namespace check applies. Both put_page and add_timeline_entry (subagent-allowlisted) route through it. Auto-link skipped only when remote=true && !trustedWorkspace. enforceClientSlugFence(ctx, slug, opName) is the OAuth-client write fence: when ctx.auth.boundSlugPrefixes is present (threaded from oauth_clients.bound_slug_prefixes at token-verification time), every direct slug-mutating write op — put_page, delete_page, restore_page, add_tag, remove_tag, add_link/remove_link (from endpoint only; linking TO a readable page is a reference), add_timeline_entry, revert_version, put_raw_data — rejects out-of-prefix slugs with permission_denied, BEFORE each op's dry-run short-circuit. Plain-startsWith semantics matching submit_agent's check for the same column (NOT the glob grammar of the subagent allow-list); empty-array binding is deny-all (fail-closed); no auth / no binding = no fence. The match rule itself lives in the exported slugUnderBoundPrefixes(prefixes, slug) so non-op write surfaces reuse it verbatim. It is BOUNDARY-AWARE (a prefix matches whole segments, so emp-alice does not admit emp-alice-2/…), lowercases both sides (stored slugs are lowercased by validateSlug, so comparing the caller's raw string let a mixed-case slug commit and only then trip the resolved-slug re-check), accepts BOTH the trailing-slash and the v85 <prefix>/* glob spelling via normalizeSlugPrefix (the column predates this fence as submit_agent's binding, so one stored value must mean one span of slugs on both paths), and ignores empty-string prefixes. assertValidSlugPrefixes (oauth-provider.ts) rejects empty, whitespace-bearing, non-lowercase, and boundary-less entries at registration and rescope. submit_agent applies the same boundary-aware rule when validating a requested prefix against the binding, normalizes trailing-slash prefixes to the glob form matchesSlugAllowList expects before handing them to the child job, and collapses an EXPLICIT empty allowed_tools/allowed_slug_prefixes to the binding (the worker reads empty as "full registry" / "legacy wiki/agents/<id>/ namespace", so ?? — which only substitutes null/undefined — left a vacuous-subset bypass). put_page additionally fences the RESOLVED slug when importFromContent's dedup pre-check redirects the write to a different page (same content_hash / frontmatter.id), since the disk write-through runs against that slug. That re-check applies whichever confinement the CALLER is under — OAuth binding and/or subagent allow-list/legacy namespace — via slugOutsideCallerFence(ctx, slug), which composes slugUnderBoundPrefixes with the subagent fence's own match rule: the delegated submit_agent → subagent context carries viaSubagent + allowedSlugPrefixes but NO auth, so an auth-only test let a slug-bound client holding agent scope reach an out-of-fence page simply by delegating the write. Denials never name the resolved slug (it would be a slug-enumeration oracle). Pinned by test/put-page-dedup-fence.test.ts. CLIENT_FENCED_WRITE_OPS + enforceBoundClientOpAllowList(auth, op) are the fail-closed companion, applied once in src/mcp/dispatch.ts (the choke point both MCP transports share): a slug-bound client calling ANY write/admin op not on the allow-list gets permission_denied. This covers the ops that write by a key other than a slug and therefore cannot be fenced — extract_entities/extract_facts (mutate people/*, companies/*), forget_fact (numeric fact id, crosses sources), ontology_propose — and makes a write op added later denied-by-default instead of silently unfenced. think is on the allow-list because remote callers cannot persist from it. Pinned by test/client-slug-fence.test.ts and over-the-wire by test/e2e/qm-provisioning.test.ts. Every Operation carries scope?: 'read' | 'write' | 'admin' + localOnly?: boolean; think is read-scoped for OAuth/MCP because remote callers have save/take forced off before persistence, while local CLI can still persist via remote:false; sync_brain, file_upload, file_list, file_url are admin + localOnly (rejected over HTTP). Four trust-boundary call sites (put_page allowlist, file_upload trust-narrowing, submit_job protected-name guard, auto-link skip) use FAIL-CLOSED semantics: ctx.remote === false for trusted-only sites, ctx.remote !== false for "untrust unless explicit-false" — anything not strictly false is treated as remote (closes the HTTP MCP shell-job RCE where a read+write OAuth token could submit shell jobs). sourceScopeOpts(ctx) encodes the source-scoped read precedence ladder — federated array (ctx.auth.allowedSources) wins over scalar (ctx.sourceId/ctx.auth.sourceId) over nothing; every read-side op handler routes through it so a source-bound OAuth client can't see neighboring sources via search/query/list_pages/get_page/find_experts/query's image path, plus the by-slug reads get_tags/get_links/get_backlinks/get_timeline/get_chunks (chunks follow the same ladder as get_page, so a federated grant that can open a page can read its chunks — and the chunk payload never carries embedding vectors) (and get_page's tag fetch, which resolves against the concrete page's own source_id). linkReadScopeOpts(ctx) is the link-read sibling for get_links/get_backlinks: a link row references three pages (from/to/origin), and the engine's federated (sourceIds[]) branch scopes ALL THREE while its scalar (sourceId) branch scopes only the near endpoint (by design — trusted internal callers like reconcileLinks and back-link validators call the engine with a scalar scope and need the cross-source view). For an UNTRUSTED remote caller (ctx.remote !== false) carrying only a scalar scope it promotes that scope to a single-element sourceIds:[id], routing them through the all-endpoint branch so a far/origin slug from outside the grant isn't disclosed; a federated array passes through unchanged and trusted local CLI (ctx.remote === false) keeps the scalar cross-source view. thinkSourceScopeOpts(ctx) maps the same precedence ladder onto runThink's public options (allowedSources/sourceId) so the think op's gather and trajectory stages inherit the caller's source grant. put_page's inline disk write-through is the shared writePageThrough helper (src/core/write-through.ts), ATOMIC via temp-sibling + rename so a crash or concurrent gbrain sync can't read a half-written .md; same helper backs gbrain brainstorm/lsd --save. Link provenance surface (#1941): add_link (gbrain link/link-add) + remove_link (gbrain unlink/link-rm) expose link_source/link_type; add_link rejects the reconciliation-managed built-ins via MANAGED_LINK_SOURCES (markdown/frontmatter/mentions/wikilink-resolved) and defaults omitted provenance to 'manual' (the engine's own default stays 'markdown' for internal callers); list_link_sources (gbrain link-sources, read) lists provenances via sourceScopeOpts. CLI aliases register through cliHints.aliases (collision-guarded in src/cli.ts).

• src/core/ops/ — the operations contract's module directory (the meat behind the operations.ts façade). contract.ts is the foundation contract: the error envelope (ErrorCode/OperationError/verbError), the shared param/logger/auth/context types, and the Operation interface — re-exported wholesale by the façade. context.ts carries the context validators + scope resolvers: the upload/slug/filename validators, the subagent and bound-client slug fences, and the source-scope resolution ladder (some internal helpers are exported only here and deliberately NOT re-exported from the façade — import those from context.ts directly). The remaining modules are one-per-op-domain (pages.ts, search.ts, takes.ts, tags.ts, links.ts, timeline.ts, admin.ts, skills-catalog.ts, sync-status.ts, raw-data.ts, chunks.ts, ingest-log.ts, files.ts, jobs.ts, orphans.ts, calibration.ts, salience.ts, facts.ts, sources.ts, transcripts.ts, insights.ts, image.ts, extraction.ts, code-intel.ts, chronicle.ts, embedding-migration.ts, request-tools.ts, schema-packs.ts, skillopt.ts), each exporting a <domain>Operations map that the façade spreads into the single operations export. Add a new op in the matching domain module — an existing domain needs no façade change; a brand-new domain module gets one spread line in operations.ts. facadeExpansion in scripts/generate-flag-registry.ts maps the façade to this whole directory so every module's --flag text stays on the command flag-scan surface.

• src/core/engine.ts — Pluggable engine interface (BrainEngine). clampSearchLimit(limit, default, cap) takes an explicit cap so per-operation caps can be tighter than MAX_SEARCH_LIMIT. Exports LinkBatchInput/TimelineBatchInput for the bulk-insert API (addLinksBatch/addTimelineEntriesBatch). readonly kind: 'postgres' | 'pglite' discriminator lets src/core/migrate.ts and others branch without instanceof + dynamic imports. Methods: batchLoadEmotionalInputs(slugs?) (CTE-shaped read with per-table aggregates so page × N tags × M takes never produces N×M rows), setEmotionalWeightBatch(rows) (UPDATE FROM unnest($1::text[],$2::text[],$3::real[]) composite-keyed on (slug, source_id)), getRecentSalience(opts), findAnomalies(opts). PageFilters has sort?: 'updated_desc'|'updated_asc'|'created_desc'|'slug' + PAGE_SORT_SQL whitelist consumed by both engines. listAllPageRefs(): Promise<Array<{slug, source_id}>> ordered by (source_id, slug) — cheap cross-source enumeration replacing the getAllSlugs()→getPage(slug) N+1 (which silently defaulted to source_id='default'); parity across postgres-engine.ts + pglite-engine.ts; Pinned by test/e2e/multi-source-bug-class.test.ts. SearchOpts+PageFilters add sourceIds?: string[] (federated read axis; both engines apply WHERE source_id = ANY($N::text[]) when set, preserve scalar sourceId fast path when unset); traverseGraph(slug, depth, opts?) and traversePaths(slug, opts?) accept opts.sourceId/opts.sourceIds. The by-slug read methods carry the same federated axis: getTags/getLinks/getBacklinks/getChunks opts and TimelineOpts (consumed by getTimeline) accept sourceIds?: string[] taking precedence over the scalar sourceId (source_id = ANY($::text[]) scoping the slug→page-id lookup); getChunks falls back to the 'default' source when neither is set (importCodeFile's incremental-embedding reuse relies on it) and SELECTs an explicit non-vector column list — embedding vectors never ride the payload since rowToChunk discards them (getChunksWithEmbeddings stays scalar-only by design: engine-internal, zero remote-reachable callers); the link reads (getLinks/getBacklinks) scope ALL THREE endpoints (from/to/origin) on the federated branch while the scalar branch scopes only the near endpoint for trusted internal cross-source callers. traverseGraph opts has frontierCap?: number (per-iteration recursive-CTE cap, approx per-BFS-layer); return type Promise<GraphNode[]> for MCP wire stability; export TraverseGraphOpts; Postgres uses parenthesized LIMIT N ORDER BY (slug, id) inside the recursive term, PGLite mirrors with positional params; Pinned by test/regressions/v0_36_frontier_cap.test.ts. Phantom-redirect methods: refreshPageBody(slug, sourceId, compiled_truth, timeline, content_hash) narrow-UPDATEs three columns + updated_at, skipping soft-deleted rows (content_hash refresh required so gbrain sync sees the canonical as unchanged after fence merge); migrateFactsToCanonical(phantomSlug, canonicalSlug, sourceId) UPDATEs entity_slug+source_markdown_slug on every active fact row keyed on the phantom, preserving embedding/validUntil/kind/status/source_session/confidence; parity at test/phantom-redirect-engine-parity.test.ts. getAdjacencyBoosts(pageIds): Promise<Map<number, AdjacencyRow>> powers the per-query graph-signals stage — one SQL query returning inbound-link counts among top-K plus a cross-source count (links from differing source_id); COALESCE(p.source_id,'default') null safety, HAVING >= 1, cross-source CASE-WHEN excludes the target's own source; parity SQL across both engines; SearchResult gains optional base_score, backlink_boost, salience_boost, recency_boost, exact_match_boost, graph_adjacency_boost, graph_cross_source_boost, session_demote_factor, reranker_delta + internal staging fields; Pinned by test/e2e/graph-signals-engine.test.ts. Two REQUIRED methods: deletePages(slugs, {sourceId}): Promise<string[]> (single-batch primitive returning slugs actually deleted) and resolveSlugsByPaths(paths, {sourceId}): Promise<Map<path,slug>> (batch path→slug lookup); sourceId REQUIRED on both at the type level (asymmetric with single-row deletePage which keeps optional/'default'); both short-circuit on empty input and throw when > DELETE_BATCH_SIZE. Embedding-signature stale-detection quartet: countStaleChunks(opts?) gains optional signature?: string widening the stale predicate from embedding IS NULL to ALSO include chunks whose JOINed page embedding_signature IS NOT NULL AND <> $signature (NULL signature is GRANDFATHERED, never counted; omit signature for the legacy NULL-only count); sumStaleChunkChars(opts?: {sourceId?, signature?}): Promise<number> = SUM(LENGTH(chunk_text)) over stale chunks (same predicate + embed_skip filter + optional sourceId scope), used by gbrain sync --all cost preview via estimateCostFromChars; setPageEmbeddingSignature(slug, {sourceId?, signature}) stamps pages.embedding_signature after a page's chunks (re)embed, idempotent no-op when page absent; invalidateStaleSignatureEmbeddings({signature, sourceId?}): Promise<number> NULLs embedding+embedded_at on every chunk whose page signature is set AND differs, returning the count, called BEFORE listStaleChunks so signature-drift pages flow through the NULL-embedding keyset cursor unchanged (NULL never invalidated). Widens findOrphanPages(opts?: {sourceId?, sourceIds?}) (candidate-side scoping only; inbound links counted from any source). Pinned by test/sum-stale-chunk-chars.test.ts, test/embedding-signature-stale.test.ts, test/e2e/engine-parity.test.ts. Free-text alias layer: resolveAliases(aliasNorms, opts?): Promise<Map<string, Array<{slug, source_id}>>> (READ; maps each normalized alias to declaring (slug, source_id) pairs, source-scoped) and setPageAliases(slug, sourceId, aliasNorms) (WRITE; replaces the full alias set, delete-then-insert, empty clears, idempotent on the unique triple), called by the importFromContent ingest projection and the reindex --aliases backfill; parity across both engines, Pinned by test/search/page-aliases-engine.test.ts. searchVector in both engines injects the shared buildBestPerPagePoolCte per-page max-pool so a page surfaces on its strongest chunk. executeRawDirect(sql, params?, opts?) is the lock-hot-path sibling of executeRaw: same single-statement contract, but routes to the direct session-mode pool when dual-pool is active (Postgres/Supabase port 5432) so a long-held lock heartbeat survives the transaction pooler's per-transaction connection recycling; PGLite delegates straight to executeRaw (no pooler). Both engines implement it; the Minion lock path (claim/renewLock) is the consumer. reconnect(ctx?: {error?}) is a REQUIRED lifecycle method on BOTH engines: it recovers a dropped connection using the config captured at the last connect(), so callers (autopilot health probe, batchRetry) never disconnect() + bare connect() (which loses the config and throws database_url undefined forever, and opens a null-connection window). PostgresEngine rebuilds its pool with a _reconnecting reentrancy guard and emits pool-recovery audit; PGLite is single-writer in-process so it just restores the saved data dir for parity. Plus two interface members: (1) optional findDuplicatePage?(sourceId, {hash, frontmatterId?}): Promise<{slug, id} | null> (identity precedence is content_hash OR frontmatter->>'id', both with deleted_at IS NULL); (2) resolveSlugs(partial, opts?) extended with {sourceId?, sourceIds?} so the MCP fuzzy get_page path scopes by source (field names match sourceScopeOpts(ctx) output so handlers spread directly; back-compatible — no opts gives prior behavior). Plus a stable tiebreaker ORDER BY score DESC, page_id ASC, chunk_id ASC in searchVector in both engines: on a score tie (basis-vector eval fixtures) older page_id wins, closing the planner-non-determinism class where a new index on pages could flip ranking on tied scores.

• src/core/engine-constants.ts — single source of truth for engine batch-sizing constants. Exports DELETE_BATCH_SIZE = 500 consumed by both engines' deletePages + resolveSlugsByPaths and by the sync delete + rename loops. Lives outside engine.ts (the interface module) to avoid circular-import worry — bounded per-statement work for predictable lock hold time + write amplification.

• src/core/background-work.ts (#1762/#1745/#1775) — process background-work registry: the single owner of "drain every fire-and-forget DB-write sink before the engine goes away," with TWO exit points. registerBackgroundWorkDrainer({name, order, drain(timeoutMs, mode), abort?}) over a Map<name, BackgroundWorkDrainer> (idempotent registration by name; __registerDrainerForTest returns an unregister handle); mode is 'exit' | 'disconnect' (#4143 — 'exit' = CLI teardown, engine still live, residual buffers may flush; 'disconnect' = an engine is mid-disconnect, sinks await only IN-FLIGHT work and never start new writes). drainAllBackgroundWorkForCliExit({timeoutMs}) runs mode 'exit' with abort allowed; drainBackgroundWorkBeforeDisconnect({timeoutMs}) (#4143) is called by BOTH engines' disconnect() so an in-flight statement settles before the underlying handle closes — PGLite's close() deadlocks PERMANENTLY with a statement in flight — and it NEVER calls abort() (permanent process state, wrong for a long-lived gbrain serve disconnecting one engine); a partial disconnect-drain warns once per sink to stderr. The module stays a zero-import leaf on purpose (both engines import it statically). Drains in explicit (order, name) order — facts FIRST (order 0) so its abort-path DB logIngest runs against the freshest live engine — and AWAITS abort() only when drain() reports unfinished>0 in 'exit' mode. Best-effort per drainer: one sink's failure never blocks the others or the disconnect. SIX sinks register at module import: facts/queue.ts (order 0; abort=shutdown() cancels a hung facts:absorb Haiku via internalAbort), last-retrieved.ts (order 1), search/hybrid.ts (order 2; awaitPendingSearchCacheWrites bounded via Promise.race), eval-capture.ts (order 3; captureEvalCandidate self-tracks its promise via awaitPendingEvalCaptures), context/volunteer-events.ts (order 4, #2095 — batched volunteer-event INSERTs, drained like the rest), search/telemetry.ts (order 5, #4143 — awaitPendingTelemetryFlush: awaits the in-flight flush in both modes, flushes residual buckets only in 'exit' mode so short-lived CLI calls land in search_telemetry on clean exit). Every cli.ts teardown site reaches it through finishCliTeardown (src/core/cli-force-exit.ts), which drains the registry before engine.disconnect() — closing the PGLite busy-loop where db.close() raced an in-flight job and pinned the single-writer lock (#1762). Exports backgroundWorkSinkCount() so the teardown helper computes its backstop deadline from the registered sink count, plus the shared teardown budgets (#4284): MAX_TIMER_DELAY_MS (the 2^31−1 setTimeout ceiling; process-watchdog.ts aliases it as MAX_WATCHDOG_TIMER_MS), SINK_DRAIN_TIMEOUT_MS (the per-sink drain bound, used as the runDrainers default), and pgliteCloseTimeoutMs() (the env-tunable in-loop close bound, defined here so cli-force-exit's computed deadline budgets the SAME bound the engine honors). CLI-EXIT-ONLY: the facts shutdown() abort is permanent process state, never call in a long-lived gbrain serve. Companion changes: src/core/ai/gateway.ts withDefaultTimeout(caller, ms) bounds every outbound AI call (chat 300s, embed+multimodal 60s; env GBRAIN_AI_{CHAT,EMBED,MULTIMODAL}_TIMEOUT_MS; composed with caller signals via AbortSignal.any) and the teardown backstop honors an errored op's exit code so a hung disconnect can't mask failure as success (see cli-force-exit.ts); src/core/postgres-engine.ts reconnect() module-mode branch re-establishes via idempotent db.connect() + connectionManager.setReadPool refresh instead of db.disconnect() (no null window for concurrent ops; fail-loud on real connect failure — #1745); src/core/search/hybrid.ts embedQueryBounded + a shared QueryEmbedDeadline (6s, floored 2s per embed via MIN_QUERY_EMBED_BUDGET_MS; env GBRAIN_QUERY_EMBED_TIMEOUT_MS) bounds the cache-lookup AND inner query embeds so a stalled provider falls back to keyword instead of stalling the whole op (#1775). Incorporates + hardens PR #1763 (@ElliotDrel). Pinned by test/core/background-work.test.ts, test/search/query-embed-deadline.test.ts, test/eval-capture-drain.test.ts, test/e2e/postgres-reconnect-singleton.test.ts, test/e2e/pglite-cli-exit.serial.test.ts, test/fix-wave-structural.test.ts.

• src/core/search/graph-signals.ts — per-query graph-signals helper. applyGraphSignals(results, engine, opts) runs as the 4th post-fusion stage (after backlink/salience/recency). Three boosts: ADJACENCY_BOOST=1.05 (page linked from 2+ OTHER top-K results — local hub for THIS query), CROSS_SOURCE_BOOST=1.10 (page linked from 2+ DIFFERENT sources — corroborated across team brains, dormant in single-source brains), SESSION_DEMOTE=0.95 (3+ results from same chat session — keep the highest-scoring at full score, demote the rest). All three inherit the floor-ratio gate preventing weak pages from being boosted past strong ones via popularity. computeScoreDistribution(results) emits min/p25/p50/p75/p95/max + reorder_band_width. sessionPrefix(slug) extracts the chat-session anchor (chat/2026-05-15-...). Pure pairedBootstrapPValue(deltas, resamples, rng) exported for eval gates. Test seam via adjacencyFn DI. Fail-open: any error logs via logGraphSignalsFailure (JSONL audit via audit-writer) and returns the input array unchanged. Pinned by test/search/graph-signals.test.ts (incl. the IRON-RULE floor-gate regression).

• src/core/search/explain-formatter.ts — renders SearchResult[] as a multi-line per-result breakdown for gbrain search --explain. Reads every boost-stamping field; also prints the raw query↔chunk cosine (SearchResult.cosine, the calibrated signal evidence keys off) next to the blended score when present — absent on keyword-only / no-embedding paths. Handles the "no boosts applied" empty path. 4-decimal precision with trailing-zero strip. Pinned by test/search/explain-formatter.test.ts.

• src/core/search/mode.ts — Named search-mode bundles + the search cache key. MODE_BUNDLES (conservative/balanced/tokenmax) and the resolution chain (per-call SearchOpts → per-key search.* config → bundle → balanced fallback) resolve every search knob; knobsHash folds every result-shaping knob into the query_cache key, and KNOBS_HASH_VERSION (exported from this file — the single source of truth for the current cache-key version) is bumped whenever a new knob shapes results so stale cache rows become unreachable. graph_signals: boolean knob in ModeBundle (defaults: conservative=false, balanced=true, tokenmax=true). KNOBS_HASH_VERSION appends a gs= parts entry per the cache-key contamination convention so a graph-on cache write can't be served to a graph-off lookup. SearchKeyOverrides + SearchPerCallOpts + loadOverridesFromConfig + SEARCH_MODE_CONFIG_KEYS + resolveSearchMode + attributeKnob all carry the field. Opt-out: gbrain config set search.graph_signals false. Mid-deploy query_cache rows from before the upgrade hash differently — natural row segregation, clears within cache.ttl_seconds (3600s default). title_boost: number | undefined knob in ModeBundle (default 1.25 for all three modes; multiplier for the post-fusion title-phrase boost). Override chain: per-call SearchOpts → search.title_boost config (clamped [1.0, 5.0]) → bundle. KNOBS_HASH_VERSION appends a tib= parts entry so a title-boost-on cache write can't be served to a title-boost-off lookup. SEARCH_MODE_CONFIG_KEYS gains search.title_boost. Cross-modal knobs in ModeBundle: cross_modal_both_text_weight/cross_modal_both_image_weight (weighted RRF for 'both' modality, defaults 0.6/0.4), image_query_text_refinement_weight/image_query_image_refinement_weight (hybrid intersect for searchByImage query refinement, defaults 0.4/0.6), unified_multimodal + unified_multimodal_only (unified-column routing flags), cross_modal_llm_intent (opt-in LLM escalation). SEARCH_MODE_CONFIG_KEYS carries the corresponding config keys, and the modality knobs participate in knobsHash so a cached text-mode result can't be served to an image-mode caller. Retrieval-quality knobs autocut_min_top (default 0.35 in all three bundles; config search.autocut_min_top; folds into knobsHash as an acm= part) and evidence_cosine_floor (default 0.8 in all three bundles; config search.evidence_cosine_floor; labels evidence — result-set-shape-neutral, so not hashed) ride the same bundle → config → per-call chain.

• src/core/context-engine.ts + src/openclaw-context-engine.ts — the deterministic context engine OpenClaw loads on every turn (assemble() injects the Live Context block, zero-LLM). createGBrainContextEngine({workspaceDir, resolveEntities?}) accepts an OPTIONAL host-injected resolver (ENGINE_API_VERSION 0.3.0, additive — older hosts work unchanged; the plugin entry maps ctx.resolveEntities/ctx.brainQuery onto it). Checkpoint compaction (cathedral 5): compact() runs a time-bounded (8s), fail-open, lazily-imported checkpoint step BEFORE delegating — spools the since-last-boundary window (openclaw tail reader over the exported adapter mapper, 40-turn cap = the no-prior-boundary fallback) as a content-addressed corpus segment + ledger entry, then rung 2 (PGLite: one bankOnly+flushCorpusFile IPC round trip to serve) or rung 3 (Postgres: inline harvest over the reflex ladder's exported getDirectPostgresEngine singleton, under sweep claim fencing + capability/kill-switch gates, abort post-check) — and rides an additive result.gbrain_checkpoint bag on the delegate's return (ownsCompaction stays false). assemble() consumes sessionId ?? sessionKey and splices a deterministic envelope-bearing Compaction-checkpoint block at parts[1] (after Live Context) from the banked manifest via an in-process memo + hash-keyed polls (≤5; stale manifests can't satisfy a poll for the new segment; no manifest ⇒ byte-identical output). assemble() runs the Retrieval Reflex after the Live Context block: extracts the current turn's user text, builds prior-context text (every message EXCEPT the current turn — suppression must not see the triggering mention), passes the rolling window (getWindowTurns, last 12 user/assistant turns; the reflex slices to its configured retrieval_reflex_window_turns), and appends the pointer block. warmReflex() fires at construction.

• src/core/context/ — Retrieval Reflex (Layer 1, issue #1981). entity-salience.ts: pure, zero-LLM, precision-biased extractCandidates(text) (capitalized runs + @handles, STOPWORDS + soft COMMON_WORDS + sentence-start guard, deterministic, capped; a lowercase weak pass additionally emits weak: true candidates — lowercase words ≥3 chars on a separate MAX_WEAK_CANDIDATES=32 budget that never evicts strong candidates — which downstream may resolve through the alias arm ONLY) + extractCandidatesFromWindow(turns) (#2095: merges per-turn extraction across the last N turns by normalizeAlias form with occurrence/newest-turn/user-mention metadata; salience-ordered — recency > frequency > user-role — so the cap drops stale assistant chatter first). retrieval-reflex.ts: resolveEntitiesToPointers(engine, sourceId, candidates, opts) — alias arm (resolveAliases, caught per-arm for pre-v110 brains) + exact title/slug-suffix arm (the recall fix: real slugs are namespaced people/x but slugify drops the prefix) + two lexical identity arms behind opts.lexicalArms (kill switch: config retrieval_reflex_lexical_arms / env GBRAIN_RETRIEVAL_REFLEX_LEXICAL_ARMS, default on): weak lowercase candidates probe the ALIAS arm ONLY (never title/slug-suffix, where ordinary lowercase words would fabricate pointers) and require GLOBAL uniqueness across all sources in play; the surname arm resolves a strong single capitalized token ≥3 chars via a lower(title) LIKE '% <token>' predicate on the same query, with exact-arm precedence and ambiguity counted over ALL person rows carrying the surname — ambiguity in either arm injects nothing; pointers carry source_id/arm/confidence/matchedNorm (#2095 — ARM_CONFIDENCE alias 0.9 / title 0.8 / title-surname 0.72 (deliberately above the volunteer layer's 0.70 gate, below title) / slug-suffix 0.6 lives next to the arm definitions; arm-2 provenance classified in JS since the combined OR can't report which predicate matched); opts: sourceIds? federated scope (alias arm loops per source, arm 2 uses source_id = ANY), suppression? ('slug-and-title' legacy default; 'slug-only' REQUIRED under windowing — the title rule would suppress every entity merely mentioned in a prior window turn), ambient-channel event logging is DELIVERY-side, not in-resolver — logDeliveredReflexPointers(engine, pointers) fires only once a block is actually handed to the consumer (serve's resolve-IPC onDelivered hook post-write; buildReflexAddition post-timeout on the direct rung), so abandoned/timed-out blocks never pollute the volunteered-vs-used stats; its event write is registered synchronously before return so the CLI background-work drain cannot miss it; synopsis runs through stripTakesFence/stripFactsFence (the same privacy boundary get_page applies) so private facts never reach the prompt; capped at MAX_POINTERS. reflex.ts: the orchestrator + engine-aware resolver ladder (host resolveEntities → PGLite serve IPC → Postgres cached process-singleton → disabled), zero-candidate fast path, fail-open + timeout, heartbeat write for the doctor check, reflexEnabled(cfg) (file/env gate, default ON; DB-plane does NOT gate — assemble() is sync); windowed extraction when windowTurns present and retrieval_reflex_window_turns (default 4; 1 = exact legacy behavior) > 1 — switches suppression to slug-only; accept-side reflex-channel logging fires after the per-turn timeout admits the block (direct-Postgres rung only — IPC logs server-side at delivery; host-injected resolvers are a documented gap). resolve-ipc.ts: local unix-socket resolve protocol (client + server) so PGLite resolves through the single connection gbrain serve holds (a second opener would hit the exclusive lock; a subprocess would force-steal it past the 5-min staleness window and crash). Wired into src/mcp/server.ts (serve binds <dataDir>/.gbrain-resolve.sock on PGLite, cleaned up on shutdown). Doctor surface: retrieval_reflex_health in src/commands/doctor.ts (reads the heartbeat for truthful runtime status; categorized in doctor-categories.ts) + volunteer_channels (engine-aware sibling: groups context_volunteer_events by channel over 7 days so operators see which push channels — reflex/op/watch/claude-code/codex — actually fire; info-only; the LOCAL doctor runs it brain-wide while the remote report path threads the caller's source scope, so a source-bound token never sees other sources' activity counts/timestamps; counts are reconciled against the hook heartbeat over the same 7-day window — a mostly-degraded week gets a CAUTION note, since a server-side delivery count isn't proof of injection; quiet-channel guidance is engine-aware — Postgres brains are told the hook lane is quiet by design rather than to chase registration — and walks both quiet classes (installed-but-unregistered vs registered-but-quiet; the check can't inspect registration itself); pre-v117 tolerant, and transient DB errors are reported as such, never as an old schema; pinned by test/doctor-volunteer-channels.test.ts). Config: retrieval_reflex + retrieval_reflex_max_pointers + retrieval_reflex_window_turns + retrieval_reflex_lexical_arms in src/core/config.ts (env GBRAIN_RETRIEVAL_REFLEX_WINDOW_TURNS, GBRAIN_RETRIEVAL_REFLEX_LEXICAL_ARMS). volunteer.ts (#2095): parseWindow (lenient user:/assistant: prefixes, unprefixed → one user turn), volunteerContext (extract → resolve → +0.05 multi-turn/newest-turn boost → min_confidence 0.7 gate → cap 3/5; deterministic rationale strings, never raw conversation text; slug-only suppression), volunteerUsageStats (per-arm/channel precision from the pages.last_retrieved_at > volunteered_at join — APPROXIMATE: the 5-min last-retrieved throttle causes false negatives, unrelated reads false positives). volunteer-events.ts (#2095): insertVolunteerEvents (ONE multi-row parameterized INSERT), logVolunteerEventsFireAndForget + bounded drain registered as the volunteer-events background-work sink (order 4), purgeStaleVolunteerEvents (90-day GC, called from the dream cycle's purge phase). Policy layer ships as the retrieval-reflex recipe (recipes/retrieval-reflex/). Pinned by test/context/entity-salience.test.ts, test/retrieval-reflex.test.ts, test/retrieval-reflex-pre-v110.test.ts, test/context/resolve-ipc.test.ts, test/doctor-retrieval-reflex.test.ts, test/volunteer-context.test.ts, test/e2e/volunteer-context-postgres.test.ts. Cathedral 5 additions in this dir: corpus-segments.ts — engine-free content-addressed compaction segments (<session>.seg-<hash24>.txt, idempotent by name; parsers accept 12–64 hex), the hash-keyed per-session ledger (atomic tmp+rename, fail-open, entry order = the only ordinal), sliceBoundaryWindow/splitByBoundaries, the redacted renderSegmentText (a segment is NEVER written unscanned — unlike the session-end full write, which degrades-and-writes), exact-set coverageComplete/decideCorpusMode (count equality can be fooled by a duplicated boundary), the compact-time bankCompactSegment step (per-step deadline degrades, segment-then-ledger crash order), the openclaw tail boundary reader (readOpenclawBoundaryTail, delegates mapping to the adapter's exported mapOpenclawLine), and orphan-sidecar/aged-ledger GC — pinned by test/corpus-segments.test.ts. checkpoint-harvest.ts — the serve-side prompt harvest of a segment: bounded FIFO (cap 8, 60s abort), sweep-shared claim fencing, capability-then-kill-switch gates, signal.aborted POST-check (the pipeline returns partials on abort; an aborted run writes nothing and stays retryable), receipt sidecar before idempotent manifest publish (source-scoped getPage verification — a link that resolves to nothing is never banked), .ingested last, explicit shutdownCheckpointHarvest() called by serve BEFORE engine.disconnect() (the background-work drain is CLI-exit-only by contract) — pinned by test/checkpoint-harvest.serial.test.ts. hook-heartbeat.ts — the hooks telemetry JSONL extracted from hook.ts (hook.ts re-exports; serve-side writers never import the command module); allowlist carries the cathedral-5 segment/inserted/duplicate/links count-only fields. session-state.ts also carries the v132 checkpoint_manifest helpers (getCheckpointManifest/appendCheckpointManifest: newest-first, dedup-by-slug, cap 20, seg-hash completion key, fail-open on pre-v132 schema) — pinned by test/checkpoint-manifest.test.ts. sensitivity-scan.ts + compile-view.ts — the compile-context stack: composed detector (secret-scan + ordered PII_PATTERNS + path/blocklist families + operator pattern file; uniform .gbrain-scan-allow fingerprint escape hatch; CONTENT hits drop an entry, CONFIG/loader failures THROW so the caller aborts without writing) and the deterministic compiled-view builder (recency decay anchored to the newest candidate updated_at, never wall-clock; total-order (score desc, slug asc); source-scoped listPages/getPage reads that skip op-layer write-backs; whole-file packToBudget math that never passes a <=0 budget) — pinned by test/sensitivity-scan.test.ts + test/compile-view.test.ts + test/e2e/compile-context-pglite.test.ts; the CLI shell is src/commands/compile-context.ts (targets claude-code|codex|openclaw, AGENTS.md managed-marker splice that throws on damaged markers, atomic writes, --check recompile-and-compare exit codes; the guide is docs/guides/checkpoint-compaction.md).

• src/commands/watch.ts — gbrain watch (#2095): the push transport. Reads turns from stdin as they arrive (user:/assistant: prefixes; unprefixed = user turn), keeps a rolling in-process window (--window-turns, default 4), calls volunteerContext per turn, streams pointers to stdout (--json for JSONL with turn attribution), logs channel: 'watch' events with a per-session id. Session dedupe feeds already-pushed slugs back as priorContext so the core's slug-only suppression dedupes. Blocks in the stdin iteration (interactive alive until Ctrl-C/Ctrl-D; piped ends at EOF) — deliberately NOT in DAEMON_COMMANDS; SIGINT closes the stream so teardown flows through finishCliTeardown. Per-turn resolution failures are fail-open. Registered in CLI_ONLY + CLI_ONLY_SELF_HELP + THIN_CLIENT_REFUSED_COMMANDS (thin clients use the volunteer_context MCP op). Pinned by test/watch-command.test.ts.

• src/commands/integrations.ts — recipe install. The resolver-row install fence is keyed by manifest.recipe (gbrain:<recipe>:resolver-rows), so a second copy-into-host-repo recipe no longer writes a block mislabeled with the first recipe's name. Pinned by test/integrations-install.test.ts. Health-check DSL includes the staleness-aware heartbeat_max_age type (#2787): declares the sense's expected cadence (max_age: 48h), and integrations doctor FAILS when the newest heartbeat event is older — the only check type that catches a green-but-dead sense (all others are point-in-time). Not embedded-gated (reads only the local heartbeat file). Recipe frontmatter carries output_paths (repo-relative dirs the collector writes, e.g. calendar-to-brain → daily/calendar/); getConfiguredCollectorOutputs() surfaces them for the #2788 db_only-collision check/warning. Pinned by test/integrations-heartbeat-max-age.test.ts. Standalone integration recipe management (no DB needed). Exports getRecipeDirs() (trust-tagged recipe sources), SSRF helpers (isInternalUrl, parseOctet, hostnameToOctets, isPrivateIpv4). Only package-bundled recipes are embedded=true; $GBRAIN_RECIPES_DIR and cwd ./recipes/ are untrusted and cannot run command/http/string health checks.

• src/core/audit/audit-writer.ts — shared JSONL audit primitive consolidating the hand-rolled audit modules. Exports createAuditWriter({kind, recordSchema}) returning {log, readRecent} plus shared helpers computeIsoWeekFilename(kind, now?) and resolveAuditDir() (honors GBRAIN_AUDIT_DIR). ISO-week file rotation; best-effort writes (stderr warn on failure, never throws); read-path scans current-week + previous-week files for boundary spans. Refactored onto it for parity: src/core/rerank-audit.ts, src/core/audit-slug-fallback.ts, src/core/minions/handlers/shell-audit.ts, src/core/minions/handlers/supervisor-audit.ts, src/core/facts/phantom-audit.ts (each module's public API preserved bit-for-bit). The graph-signals-failures audit (logGraphSignalsFailure) uses the same primitive. One hand-rolled audit remains at src/core/skillpack/audit.ts. Pinned by test/audit/audit-writer.test.ts.

• src/core/cli-force-exit.ts (#2084) — single owner of one-shot CLI exit + teardown, designed as a PAIR with the import.meta.main seam at the bottom of src/cli.ts. finishCliTeardown({engine, drainTimeoutMs?}) is teardown-ONLY (never exits on the clean path): arms a REF'D backstop (unref'd would let a hung teardown exit naturally, skipping the flush and exiting with whatever PGLite scribbled into process.exitCode) whose deadline is COMPUTED from the bounds it guards (computeTeardownDeadlineMs = sinks × drainTimeoutMs + sinks × SINK_DRAIN_TIMEOUT_MS disconnect-drain bound + the RESOLVED PGLite close bound (pgliteCloseTimeoutMs() from background-work.ts — an operator-raised GBRAIN_PGLITE_CLOSE_TIMEOUT_MS widens this backstop too, #4284, never a hardcoded copy of the default) + facts-abort grace + 2 × pool-end bound + slack, floor 10s — the #4143 terms budget engine.disconnect()'s own drain pass and bounded close so the backstop can't fire while every component honored its own bound; GBRAIN_TEARDOWN_DEADLINE_MS env override is the incident escape hatch), drains every background-work sink, disconnects the engine (a throw is warned + swallowed — the exit code reports the OPERATION, not the cleanup), then returns. The exit VERDICT lives in a gbrain-owned channel (setCliExitVerdict/currentExitCode; mirror-writes process.exitCode but NEVER reads it back) because PGLite's Emscripten runtime scribbles its own status into process.exitCode at arbitrary points mid-run — every writer that means to set the CLI exit code (op-dispatch catch, reindex, frontmatter, transcripts, brainstorm, autopilot, doctor's FAIL verdict, extract, and cli.ts's swept inner exits — friction, claw-test, smoke-test, the no-DB eval runners, status/status-thin, whoknows-thin) calls setCliExitVerdict; test/cli-exit-verdict-pin.test.ts greps src/ so the next raw process.exitCode = write fails CI instead of silently reporting success on failure. The deadline arms at TEARDOWN start, never before the op handler (the pre-#2084 placement measured handler + teardown combined, so PgBouncer deployments paid a flat 10s force-exit tax on every query and any >10s op was killed mid-run with exit 0). All nine cli.ts disconnect sites route through it; the ONE process exit happens in cli.ts's main().then/catch via flushThenExit(currentExitCode()), gated by shouldForceExitAfterMain() (daemon list: serve) — the CLI never waits for Bun's event loop to drain, because endPoolBounded deliberately races past stuck PgBouncer sockets that would keep it alive. flushThenExit(code) fences stdout+stderr (write('', cb) raced with an unref'd guard, EPIPE-safe both sync and async) then holds a REF'D aliveness grace for non-TTY stdio before process.exit — Bun delivers queued pipe writes only while the process is alive (no flush API reaches process.stdout's native queue; write callbacks fire on accept, not delivery), so the grace IS the flush (#1959 truncation class). Scope claim is deliberately cli.ts-only: command modules' mid-run engine lifecycles stay local (process-exit semantics inside them would be wrong) and are absorbed by the final explicit exit. Pinned by test/cli-finish-teardown.test.ts, test/flush-then-exit-harness.test.ts (real spawned-Bun pipe semantics), test/cli-should-force-exit.test.ts, test/cli-pipe-truncation.test.ts (real-CLI piped --tools-json byte-stable), test/cli-exit-verdict-pin.test.ts, the #2084 describes in test/fix-wave-structural.test.ts + test/e2e/pglite-cli-exit.serial.test.ts, and test/e2e/pgbouncer-teardown.test.ts (CI transaction-mode pooler — the #1972/#2015/#2084 class, finally reproducible in CI).

• src/commands/search.ts:gbrain search stats — graph_signals section (enabled/source/failures_count/failures_by_reason). JSON envelope adds a graph_signals sibling property; _meta.metric_glossary adds graph_signals.enabled + graph_signals.failures_by_reason. Human output prints the section after the existing block. Reads search.graph_signals config first, falls back to the mode default. Pinned by test/search/search-stats-graph-signals.test.ts. Both gbrain search stats and gbrain search tune also surface a coverage disclosure (JSON: {cli_invocations: 'recorded_on_clean_exit', reason}; human: a one-line caveat) sourced from telemetryCoverage()/TELEMETRY_COVERAGE_CAVEAT in src/core/search/telemetry.ts: since #4143 a short-lived CLI call's buffer flushes during the bounded CLI teardown drain, so a CLEAN exit is recorded; hard kills, drains that exceed their bound, and anything buffered when an engine disconnects outside the CLI teardown path still drop — the disclosure is display-only and reads its truth from the telemetry module's single-source constants. Pinned by the coverage-disclosure tests in test/commands-search.test.ts.

• src/core/engine-factory.ts — Engine factory with dynamic imports ('pglite' | 'postgres').

• src/core/pglite-engine.ts — PGLite (embedded Postgres 17.5 via WASM) implementation, all BrainEngine methods. The facts/takes/code-edges/salience method clusters are implemented in narrow-deps modules under src/core/pglite-engine/ (see the engine-module-dirs entry below); the class methods delegate to them and the façade keeps its full prior public surface. listLinkSources({sourceId?, sourceIds?}) returns distinct link_source provenances + counts (ORDER BY count DESC, link_source ASC NULLS LAST; scalar + federated scoped; parity with postgres-engine.ts) powering gbrain link-sources. addLinksBatch/addTimelineEntriesBatch/addTakesBatch pass the whole batch as one JSONB document via jsonb_to_recordset(($1::jsonb)->'rows') (bound through executeRawJsonb with a { rows } wrapper; rows built by the shared src/core/batch-rows.ts helpers, NUL-stripped), and are batchRetry-wrapped. connect() wraps PGlite.create() in a try/catch that classifies the failure and, for the wasm-abort verdict on a persistent data dir (torn WAL/checkpoint state after an unclean shutdown — the #223/#1670/#2575 class, historically misdiagnosed as a macOS WASM bug), runs in-place auto-repair via attemptWalRepairAndRetry (static import from pglite-repair.ts, #3596 engine-live rule; the retry create is preservingProcessExitCode-wrapped; success sets the public walRepairReceipt field + prints buildWalRepairNotice to stderr and returns with the lock held). The seam never throws, so every non-repaired path funnels through the single lock-release-then-throw site; repair refuses when the lock was acquired by reaping (LockHandle.reaped → 'possibly-live-writer'), when disabled (GBRAIN_PGLITE_WAL_REPAIR=off), on layout-validation failure, or inside the post-failure cooldown. disconnect() (#4143) early-nulls the handle (so no NEW statement can reach it), then runs drainBackgroundWorkBeforeDisconnect() so statements ALREADY in flight settle against the still-open handle — PGLite's close() deadlocks permanently (close's promise AND the in-flight query's promise never settle) with a statement in flight; the ordering is load-bearing (drain above the null would reopen the #1337 race). Teardown defense is layered and honestly scoped (#4284): the drain PREVENTS the known wedge; the in-loop close bound (GBRAIN_PGLITE_CLOSE_TIMEOUT_MS, default 5000ms, floor 1s, ceiling 2^31−1, read per call) covers ONLY a close that still yields to the event loop — armed BEFORE close() is called and deliberately ref'd, a timed-out close degrades to a once-per-process stderr warning naming both env knobs and teardown proceeds (an abandoned close's later rejection is swallowed; the WAL-repair path covers a zombie instance on next open); a close that WEDGES the loop (blocked or microtask-starved, the #1762 re-pump class) can never be caught by any same-loop timer and is observable/killable only by the opt-in out-of-band watchdog — a diagnostic/incident instrument, not ambient production protection: GBRAIN_PGLITE_CLOSE_WATCHDOG_MS (unset/0 = off; a positive value clamps UP to max(5000, registered-sink-count×2000 + close timeout + 2000) with a warn so a units typo never SIGKILLs a healthy slow teardown) + GBRAIN_PGLITE_CLOSE_WATCHDOG_GRACE_MS (default 30000) arm the shared process-watchdog.ts worker around a PGLite disconnect with a live handle (armed after the early-return, before the drain; disposed in a nested finally so a releaseLock throw can't leak it; SIGTERM at deadline, SIGKILL at deadline+grace; lock-only teardown and postgres pool teardown are out of scope). Pinned by test/pglite-engine-disconnect.serial.test.ts + test/search-telemetry-disconnect-hang.serial.test.ts + test/pglite-disconnect-watchdog.serial.test.ts (spawned fixture that genuinely starves the loop) + the #4284 structural pins in test/fix-wave-structural.test.ts. searchKeyword/searchKeywordChunks multiply ts_rank by the source-factor CASE at chunk grain; searchVector is a two-stage CTE — inner CTE keeps ORDER BY cc.embedding <=> vec so HNSW stays usable, outer SELECT re-ranks by raw_score * source_factor, inner LIMIT scales with offset to preserve pagination. searchTakes/searchTakesVector take full SearchOpts and apply the standard source-scope predicates (federated sourceIds[] wins over scalar sourceId, via the joined page's source_id) alongside the holder allow-list — parity SQL in postgres-engine.ts; pinned by test/e2e/think-source-isolation-pglite.test.ts. initSchema() calls applyForwardReferenceBootstrap() BEFORE replaying SCHEMA_SQL — probes for forward-referenced state the embedded blob needs (pages.source_id, links.link_source, links.origin_page_id, content_chunks.symbol_name, content_chunks.language, sources FK target, plus files.source_id, files.page_id, oauth_clients.source_id, oauth_clients.federated_read, sources.archived, sources.archived_at, sources.archive_expires_at, timeline_entries.event_page_id — column-only, migration v121 stays the source of truth for its FK + indexes) and adds only what's missing; threads the DDL connection from initSchema so probes run inside the advisory-lock scope; no-op on fresh installs and modern brains (closes the upgrade-wedge bug class #239/#243/#266/#357/#366/#374/#375/#378/#395/#396/#1018/#974/#820). getBrainScore returns 100/100 with full breakdown (35/25/15/15/10) when pageCount === 0 (vacuous truth — empty brain has no coverage problem); Pinned by test/brain-score-breakdown.test.ts empty-brain assertion + test/doctor-report-remote.serial.test.ts. disconnect() uses snapshot+early-null (snapshot _db/_lock, null instance fields BEFORE any await so a concurrent connect() can't see a partial mid-close state) wrapped in try/finally guaranteeing lock-release even if db.close() throws; KEEPS close-then-release order (release-then-close was rejected: it would widen the window where a sibling process connects to a still-closing brain); Pinned by test/pglite-engine-disconnect.serial.test.ts. PGlite.create() runs inside preservingProcessExitCode (#2084): PGLite's Emscripten runtime writes its own status into process.exitCode (99 at create; in-memory brains run initdb whose status lands on a later tick; the exit status at close — and assigning undefined cannot clear a prior value), which would otherwise silently clobber an errored op's exit 1 back to 0. The wrapper keeps the global tidy for external readers; db.close() stays unwrapped (its 0-write is baseline behavior test runners depend on). The CLI's exit verdict is immune either way — it lives in the gbrain-owned channel in cli-force-exit.ts and never reads process.exitCode back. Exports classifyPgliteInitError(message): 'bunfs' | 'wasm-abort' | 'corrupt' | 'unknown' + buildPgliteInitErrorMessage(verdict, original, platform?, ctx?) + stringifyPgliteInitError(err) + buildWalRepairNotice(receipt) + the PgliteInitRepairContext type, routing the catch-block hint by failure shape (bunfs matches literal $$bunfs OR ENOENT[\s\S]*pglite\.data co-occurrence, surfaces a paste-ready bun upgrade + Node fallback; corrupt — 58P01/internal_load_library/missing vector type, catalog corruption WAL repair can't fix — stays matched BEFORE the wasm arm and routes to reinit-pglite; wasm-abort matches the real production shapes Aborted()/RuntimeError/unreachable plus legacy signatures, names the corrupt-WAL root cause + the recovery ladder (pglite-repair → rebuild → engine switch) + what auto-repair did per ctx incl. the honesty-critical failed-not-restored arm, and keeps the #223 link; unknown is platform-gated per #2674). stringifyPgliteInitError also surfaces message-less Emscripten objects (ErrnoError (errno N)) instead of [object Object]. Pinned by test/pglite-init-classifier.test.ts + test/pglite-wal-repair.serial.test.ts + test/fix-wave-structural.test.ts. Implements deletePages(slugs, {sourceId}) + resolveSlugsByPaths(paths, {sourceId}) via slug = ANY($1::text[]) array-param binding, caller-chunking primitive throwing when input exceeds DELETE_BATCH_SIZE, deletePages returns RETURNING slug rows so callers filter pagesAffected to confirmed deletes. Implements the embedding-signature stale-detection quartet — sumStaleChunkChars({sourceId?, signature?}), setPageEmbeddingSignature(slug, {sourceId?, signature}), invalidateStaleSignatureEmbeddings({signature, sourceId?}), widened countStaleChunks({sourceId?, signature?}) (the signature opt widens via JOIN pages p ... WHERE cc.embedding IS NULL OR (p.embedding_signature IS NOT NULL AND p.embedding_signature <> $signature), NULL grandfathered); parity SQL with postgres-engine.ts. PGLite-specific DDL (pgvector, pg_trgm, triggers). Engine-path helper dependencies (retry, ontology, recency decay) avoid dynamic import(); the only lazy dynamic imports are ai/gateway.ts in initSchema and _upsertChunksOnce, line-marked because their local catches preserve compiled-default and stored-config fallbacks that eager module evaluation would bypass.

• src/core/pglite-embedded-assets.ts + src/core/pglite-embedded-asset-paths.ts — PGLite runtime-asset supply for every run mode (compiled binary, source checkout, bun-global install). pglite-embedded-asset-paths.ts is the bundler ANCHOR: five literal with { type: 'file' } imports of the wasm/data/extension-tarball assets via repo-relative node_modules paths (the package's exports map hides ./dist/*) — keep the specifiers literal and byte-stable, an expression or indirection silently stops the bytes embedding and the compiled binary regresses to the Bun-vfs ENOENT class (#1340). resolvePgliteAssetPaths() in pglite-embedded-assets.ts is the tiered resolver (#4116): tier 1 dynamically import()s the anchor (the rejection under a hoisted install — bun-global upgrades dedupe @electric-sql/pglite to the global root, making the anchor's specifiers unresolvable — is EXPECTED and routes to tier 2, which is why the anchor is not a static import); tier 2 derives the dist dir via module resolution of @electric-sql/pglite (import.meta.resolve then createRequire — the SAME specifier the engine imports, so assets can never come from a different pglite copy than the loaded JS); tier 3 throws one actionable error naming everything tried, with the canonical GitHub reinstall command (never the npm-registry name, which is squatted — see the README install warning). getEmbeddedPgliteOptions() memoizes one build per process and hands PGLite compiled WebAssembly.Modules + fs-bundle Blob + materialized extension tarballs via PGliteOptions. Pinned by test/pglite-embedded-assets.test.ts + test/pglite-hoisted-install.serial.test.ts (real bun add -g-shaped hoisted layout).

• src/core/pglite-lock.ts — advisory data-dir lock so two processes never open the same embedded PGLite (single-connection WASM Postgres) at once. Atomic mkdir of .gbrain-lock/ + a lock file carrying {pid, acquired_at, refreshed_at, command, subcommand}. A held lock HEARTBEATS its refreshed_at every 30s (.unref()ed timer; informational). A waiting acquirer reaps a holder ONLY when its PID is dead — a LIVE holder is NEVER stolen, regardless of how stale its heartbeat is (#2348). A live gbrain serve holder is identified from the parsed subcommand and reported immediately with separate CLI-retry and MCP-tool choices; other live holders keep the bounded wait. The heartbeat runs on the JS event loop, which is blocked during long synchronous WASM imports/CHECKPOINTs, so a working dream/embed holder can look stale while alive; the old steal-on-stale-heartbeat grace let a second OS process open the same data dir and corrupt the catalog + pgvector extension (58P01 / internal_load_library / type "vector" does not exist), recoverable only by wipe+restore. A wedged-but-alive or PID-reused holder is never stolen: serve-tagged holders report immediately, while other holders time out with a message naming the PID. Each holder carries an ownership token (<pid>:<acquired_at>); the heartbeat and releaseLock verify the on-disk lock is STILL theirs before touching it. In-memory engines take no lock. There is deliberately NO same-process reentrancy or same-PID special case: a second acquireLock from the process that already holds the lock waits out the timeout like any other live holder (#1963 was this shape — a command double-connecting a second engine on the same data dir; the fix is to reuse the connected engine at the dispatch layer, never to soften the lock). LockHandle.reaped marks an acquisition that reaped a prior holder's lock (dead-PID reap or corrupt-lock-file removal — the only reaps that exist post-#2348); the WAL auto-repair gate refuses to run surgery on a reaped acquisition since a corrupt lock file cannot prove its holder is dead. A corrupt-lock reap ALSO writes a persisted marker (<dataDir>.lock-reap.json, read via exported msSinceLastReap) so the NEXT process's clean acquisition is still repair-quarantined for 10 minutes — the in-process flag alone let the reaper's successor run surgery under a possibly-live writer; dead-PID reaps (affirmative ESRCH verdict; EPERM reads as ALIVE) deliberately skip the marker so dead-holder recovery stays one-failed-command-plus-one-re-run. Heartbeat refreshes write via tmp+rename (a torn in-place write could be read mid-flight by a polling acquirer and misclassify a HEALTHY live holder as a corrupt lock). Pinned by test/pglite-lock.test.ts. A corrupted store surfaces a reinit-pglite recovery hint via classifyPgliteInitError's corrupt verdict in pglite-engine.ts.

• src/core/pglite-resetwal.ts — pg_resetwal for PGLite NodeFS data dirs, in TypeScript (ported from electric-sql/pglite PR #994 by @yestheboxer, Apache-2.0, rejected upstream as "should be a separate tool" — gbrain is that tool). Validates the PG17 pg_control layout fail-closed (WalResetUnsupportedError on any unsupported shape — PG_VERSION ≠ 17, control ≠ 8192 bytes, control version ≠ 1700, bad seg/block size), removes stale postmaster.pid + old WAL segments + archive_status/summaries entries, writes a replacement shutdown-checkpoint WAL segment + CRC32C'd pg_control. Both file writes are atomic + durable (tmp cleared then opened 'wx' so a pre-planted symlink at the predictable tmp name can never redirect the write, + fsync(tmp) + rename + fsync(parent dir)); write order is segment-first/control-last so a mid-write kill leaves a state that still fails startup and the next attempt re-runs (idempotent — a torn pair can never claim success). WAL segment size is capped at 64MB (pglite ships 16MB; the Postgres-general 1GB bound would let a corrupt-but-plausible control field drive a 1GB allocation on the repair path). Exports the shared PG17 layout literals (PG_CONTROL_FILE_SIZE, isWalSegmentName) consumed by pglite-repair.ts. LAYOUT COUPLING: any pglite bump past PG17 must revisit this file together with the ./vector export blocker (TODOS.md "pglite upgrade blocker" entry). Pinned by test/pglite-resetwal.test.ts.

• src/core/pglite-repair.ts — WAL-repair orchestrator wrapping the resetWal port with the safety layers that make it runnable automatically from connect(): validateWalRepairTarget (read-only, fail-closed; refuses symlinked dataDir/pg_wal/global/pg_control — lstat follows INTERMEDIATE symlinks, so global/ itself must be checked or surgery would write pg_control through it into a foreign dir; tolerates the in-dir .gbrain-lock), rename-based backup (the ENTIRE pg_wal/ dir + postmaster.pid renamed into a sibling <dataDir>.wal-repair-backup-<ts>/, only the 8KB pg_control copied — zero transient disk cost), restoreWalBackup (overwrite order: control first via atomic tmp+rename, then a pg_wal dir swap with the reset dir set ASIDE inside the backup — nothing is ever deleted during restore; mtime guard refuses when a foreign segment is newer than the backup; a missing/empty backup NEVER reports restored:true), WalRepairError (thrown when resetWal fails AFTER the backup — carries the receipt + the best-effort restore's REAL result so the seam's restored flag and the failed-restored/failed-not-restored message arms never lie), a cooldown sidecar <dataDir>.wal-repair-attempt.json (skip 'recently-failed' inside GBRAIN_PGLITE_WAL_REPAIR_COOLDOWN_SECONDS, default 3600 — bounds the autopilot/supervisor reconnect loops) with episode-scoped backups (attempts within one corruption episode REUSE the episode's first backup — the pre-damage forensic state, honored only when the sidecar's path is a real non-symlink <dataDir>.wal-repair-backup-* sibling since the sidecar is user-writable JSON; retention keeps the newest 3 episodes, never pruning the open episode's), and attemptWalRepairAndRetry — the engine seam that NEVER throws (gates: kill-switch → reaped-lock 'possibly-live-writer' → 10-minute reap-marker quarantine (msSinceLastReap, cross-process) → validation → cooldown; then repair → retry create once → restore-and-record on failure; prints a repair-start stderr line so a timeout-killed attempt is self-explaining). inspectPgliteDataDir is the read-only diagnosis for gbrain doctor + pglite-repair --dry-run. Imports runtime values only from pglite-lock.ts/pglite-resetwal.ts/node:fs — never from pglite-engine.ts (no cycle; the engine statically imports THIS file per the #3596 engine-live rule). Pinned by test/pglite-repair.test.ts + test/pglite-wal-repair.serial.test.ts.

• src/commands/pglite-repair.ts — gbrain pglite-repair: the manual surface for WAL repair (--dry-run | --yes | --json | --path <dir>; CLI_ONLY + SELF_HELP; returns an exit code via setCliExitVerdict, never process.exit). Never connects an engine — works when the DB won't open and when auto-repair is disabled. --dry-run is strictly read-only. Its confirmation prompt (and src/commands/reinit-pglite.ts's) writes to stderr so --json stdout stays clean, refuses non-TTY stdin in-prompt (defense-in-depth behind the caller-side "Non-TTY environment requires --yes" guard), resolves false on EOF/close instead of parking forever on a closed or piped stdin, and cleans up its listeners; --yes/-y stays the non-interactive path. The real run validates BEFORE locking (acquireLock mkdirs the data dir — a typo'd --path must not create directories), refuses a live lock holder (pre-lock diagnosis names the PID; a live gbrain serve is called out), refuses a reaped acquisition (refused_reaped_lock — no --force by design: force-removing .gbrain-lock would reopen the #2348 concurrent-writer hole), re-validates under the lock, repairs with episode-backup reuse, and records the attempt in the sidecar. Pinned by test/pglite-repair-command.serial.test.ts.

• src/commands/doctor.ts — gbrain doctor [--json] [--fast] [--fix] [--dry-run] [--index-audit]: health checks. The file is a façade carrying buildChecks/runDoctor and output rendering; the check-function library lives in bundles under src/commands/doctor/checks/ plus four tail-cluster modules under src/commands/doctor/ (see that entry), all re-exported here so the full prior surface is unchanged — structural guards pin its source text via test/helpers/doctor-source.ts, never by reading this file alone. Checks include jsonb_integrity + markdown_body_completeness (reliability), schema_version (fails loudly when version=0, routes to gbrain apply-migrations --yes), queue_health (Postgres-only: stalled-forever active jobs started_at > 1h, waiting-depth-per-name > threshold default 10 via GBRAIN_QUEUE_WAITING_THRESHOLD, and dead-lettered subagent jobs with last_error matching the prompt_too_long classifier in last 24h), sync_failures ([CODE=N, ...] breakdown for unacked-warn + acked-ok; severity comes from the shared decideSyncFailureSeverity in src/core/sync-failure-ledger.ts so the LOCAL and REMOTE/thin-client doctor surfaces can never drift — a stuck bookmark escalates to FAIL once an OPEN failure has blocked past the staleness window or ≥10 files block, while already auto_skipped rows stay a visible WARN), rls_event_trigger (healthy evtenabled set is ('O','A') only; fix hint gbrain apply-migrations --force-retry 35), graph_coverage (short-circuits to ok when SELECT COUNT(*) FROM pages WHERE type IN ('entity','person','company','organization') returns 0; WARN hint is gbrain extract all), embedding_column_registry (probes each declared column via Postgres format_type(atttypid, atttypmod) to catch dim mismatch with a paste-ready gbrain config set embedding_columns '{...}' hint, probes HNSW index presence via pg_indexes, computes default-column population via COUNT(*) FILTER (WHERE <col> IS NOT NULL) / COUNT(*) warning below 90% except empty brains where chunk_count=0 short-circuits to ok; PGLite parity via executeRaw), and skill_brain_first (walks SKILL.md via autoDetectSkillsDirReadOnly, calls analyzeSkillBrainFirst() from src/core/skill-brain-first.ts per file with structured Check.issues[]; warn states missing_brain_first/brain_first_typo, ok states compliant_callout/compliant_phase/compliant_position/exempt_frontmatter/no_external; snapshot+diff audit at ~/.gbrain/audit/skill-brain-first-YYYY-Www.jsonl). --fix delegates inlined cross-cutting rules to > **Convention:** see [path](path). callouts via src/core/dry-fix.ts (and MISSING_RULE_PATTERNS for the brain-first callout); --fix --dry-run previews. --index-audit (Postgres-only, informational, no auto-drop) reports zero-scan indexes from pg_stat_user_indexes. Every DB check runs under a progress phase; markdown_body_completeness runs under a 1s heartbeat. runDoctor uses autoDetectSkillsDirReadOnly (from src/core/repo-root.ts; install-path fallback so cd ~ && gbrain doctor finds bundled skills); --fix carries a D6 install-path safety gate that refuses auto-repair when detected.source === 'install_path' (would rewrite the bundled tree). The Lane D supervisor check at doctor.ts:1011-1043 consumes summarizeCrashes(events) from src/core/minions/handlers/supervisor-audit.ts (warn at >=1 real crash; ok message has clean_exits_24h=N; warn message has runtime=A oom=B unknown=C legacy=D per-cause breakdown) so OOM/runtime/unknown crashes are distinguishable from clean code=0 worker drains; cross-surface parity with gbrain jobs supervisor status is pinned by source-grep wiring assertions requiring the breakdown substrings in BOTH doctor.ts and jobs.ts. checkSyncFreshness (exported, in runDoctor local + doctorReportRemote thin-client) is a staleness probe: warns at 24h, fails at 72h or never-synced; future-last_sync_at warns ("clock skew") instead of falling through ok; env overrides GBRAIN_SYNC_FRESHNESS_WARN_HOURS/GBRAIN_SYNC_FRESHNESS_FAIL_HOURS (invalid fall back with once-per-process stderr warn via _resolveSyncFreshnessHours); failure messages embed source.id so the printed gbrain sync --source <id> matches. A source holding a LIVE, non-expired per-source sync lock (inspectLock(engine, syncLockId(source.id)) from src/core/db-lock.ts) is reported as actively syncing (the message names the holder pid + host) and counted in synced_recently_count, NOT flagged stale — the live lock is the only honest in-progress signal (checkpoint banking can't distinguish in-progress from wedged: a blocked sync banks its files but writes no anchor). A blocked/failed sync's process has exited (no lock row) and a wedged holder stops refreshing (TTL lapses), so either falls through to the stale path and is never masked; the dynamic db-lock import is swallowed to a no-op on a stub engine or pre-lock-table brain, so this can only ADD an in-progress verdict, never suppress a real stale one. The in-progress note is appended to whatever verdict the buckets produce and is empty when nothing is syncing, so steady-state messages stay byte-for-byte unchanged. It has a localOnly-gated git short-circuit (runDoctor passes localOnly: true; doctorReportRemote runs in the HTTP MCP server src/commands/serve-http.ts and keeps default false so that path never walks DB-supplied local_path via subprocess — trust boundary). The local predicate mirrors sync's "do work?" gate (HEAD == last_commit AND working tree clean via requireCleanWorkingTree: 'ignore-untracked' so a quiet repo with only untracked dirs is unchanged not SEVERE, AND chunker_version === CURRENT); the inline SELECT carries last_commit + chunker_version + newest_content_at. The REMOTE path computes lag via lagFromContentMs(newest_content_at, lastSync, now) from the stored column, NO git subprocess; LOCAL fall-through and the < 0 clock-skew check stay on raw wall-clock. Three-bucket count math populates Check.details = {unchanged_count, synced_recently_count, stale_count} with the invariant sum === sources.length. checkCycleFreshness is DELIBERATELY NOT git-short-circuited or content-relativized (last_commit == HEAD can't answer "did the full cycle complete?"; a sync can succeed while later cycle phases fail; different axis last_full_cycle_at). Pinned by test/doctor.test.ts (incl. IRON-RULE regression banning stale verb names, the sync_freshness boundary matrix, the D4 regression guard verifying git probes are NEVER called when localOnly is unset/false, the three-bucket invariant, and the untracked-folders / remote-never-shells-out trust-boundary cases). pglite_data_dir check: fs-only check that runs when a PGLite brain FAILS to connect (!fastMode && !engine && config.engine === 'pglite', placed after orphan_clones, before the DB-checks gate): computePgliteDataDirCheck(dataDir, diagnosis) (exported pure fn, computeWorkerOomLoopCheck convention) maps the inspectPgliteDataDir verdict to a Check — corruption-likely/looks-healthy-but-unopenable/unsupported-layout → fail naming gbrain pglite-repair --dry-run/--yes or the rebuild path, live-lock/missing-dir → warn; all remediation_status: 'human_only' (Minion remediation needs the DB that is down). Escalates when ≥2 repair attempts failed inside 7 days (unclean-shutdown genesis still active → engine-switch pointer) and reports retained backup-dir inventory (orphan_clones disk-visibility class). Registered in doctor-categories.ts OPS_CHECK_NAMES. Pinned by test/doctor-pglite-datadir.test.ts. silent-failure batch (#2250/#2784/#2788): content_hash_duplicates (single GROUP BY over (source_id, content_hash) with FILTER aggregates — never N² — flagging hash groups that hold BOTH a bare and a path-prefixed slug, the wrong-import-root pattern; warn carries sample pairs + the pages delete → purge-deleted --older-than 0 remediation); undeclared_db_only_pages (per source with a local repo: markdown pages with no backing file outside every declared + derive-phase-default db_only prefix — the one check deliberately allowed to stat the repo); db_only_collector_collision (configured recipe output_paths inside a declared db_only dir — auto-gitignore means sync AND import silently skip the collector's files; same warning fires in sync's manageGitignore at config-write time). All warn-level, engine-parity pinned by test/e2e/doctor-silent-death-parity.test.ts; units in test/doctor-silent-death-checks.test.ts. graph_signals_coverage check wired into both runDoctor (local) and doctorReportRemote (HTTP/JSON thin-client path). Reads search.graph_signals config first, falls back to mode default; silent ok when disabled. Computes inbound link coverage on the page set; warns at <10% with gbrain extract all fix hint; ok at ≥30% ("fire on most queries") and 10-29% ("fire occasionally"), each with the percentage embedded. Pinned by cases in test/doctor.test.ts. subagent_provider check (layer 3 of 3). Resolves subagent model config in runtime order (models.subagent > models.default > models.tier.subagent > built-in default) and warns when the selected model lacks native tool-loop capability (message names the bad value + paste-ready fix gbrain config set models.tier.subagent anthropic:claude-sonnet-4-6); also warns when models.default would sneak subagent into a non-Anthropic provider via tier inheritance. OK when subagent tier resolves to Anthropic. Tests in test/doctor.test.ts. computeWorkerOomLoopCheck(engine) is the single authoritative OOM-loop signal, unioning supervised summarizeCrashes(readRecentSupervisorEvents(24)).by_cause.rss_watchdog (cross-week read via readRecentSupervisorEvents so a Monday window can't lose Sunday) + bare-worker minion_jobs error_text='aborted: watchdog' count (Postgres-only; the same source queue_health subcheck 3 reads). Cap comes from the latest rss_watchdog_loop breaker alert's max_rss_mb, else resolveDefaultMaxRssMb() fallback. fail at breaker-tripped or oomKills≥5, warn at ≥1, null otherwise. computePoolReapHealthCheck(engine) is the Postgres-only pool_reap_health check reading readRecentPoolRecoveries(1) — fail when reconnect failures>0 (reconnect throwing is the actionable signal), warn at ≥10 reaps/hr (pooler thrash), null otherwise. Both registered in buildChecks after the supervisor block. The supervisor causeStr carries rss=N (see worker_oom_loop) and queue_health's watchdog message cross-references worker_oom_loop. DoctorReport.top_issues + the cause-ranked render header. worker_oom_loop + pool_reap_health registered under ops in doctor-categories.ts. Pinned by test/doctor-worker-oom-loop.test.ts, test/doctor-pool-reap-health.test.ts. supervisor_singleton check (#1849), a SEPARATE check from supervisor (same split precedent as the niceness check) so a singleton-divergence warn can't clobber the crash/liveness precedence. Runs only when a started supervisor event was seen in the last 24h and a live engine is available. Reads the queue-scoped DB lock row (gbrain_cycle_locks WHERE id = supervisorLockId(queue)) and compares the lock holder (holder_host:holder_pid) against the local pidfile holder via the pure classifySupervisorSingleton. mismatch → warn (a second supervisor may be running with a different --max-rss; message names both holders, the effective cap from the started event's max_rss_mb, and the fix gbrain jobs supervisor stop); single → ok (names holder + cap); no_lock → no check emitted. Best-effort try/catch (silent skip on brains without the lock table). Registered under ops in doctor-categories.ts as supervisor_singleton. Pinned by test/supervisor-db-lock.test.ts + test/doctor.test.ts. checkBatchRetryHealth: batch_retry_health check surfacing Supavisor circuit-breaker incidents. Wired into both runDoctor (local) and doctorReportRemote (thin-client). Reads last 24h. States: ok (zero exhausted in 24h OR <3 from a single site), warn (>=3 same-site OR >=5 cross-site), fail (>=20 sustained breaker). Surfaces bad GBRAIN_BULK_* env at doctor startup. Corrupt-JSONL tolerant. Paste-ready fix hints in every warn/fail message. Also reads readRecentDbDisconnects(24) and appends Disconnect-call audit: N call(s) in 24h (most recent caller: <frame>). to ALL three message paths so connection-incident signal is greppable from one gbrain doctor --json call (module-import wrapped in try/catch so older brains without the audit file degrade silently). Pinned by test/doctor-batch-retry.test.ts (10 cases). three checks wired into runDoctor() and the JSON envelope, all warn-only with paste-ready fix hints. (1) checkSourceRoutingHealth(engine) scans up to 200 pages on federated brains and flags pages whose source_id doesn't match what resolveSourceWithTier() would have picked for their source_path; single-source brains short-circuit to ok; the 200-page cap is total across the brain so doctor stays under 5s. (2) checkOauthConfidentialHealth(engine) probes registered confidential clients for /token reachability. (3) checkAutopilotLockScope() (pure, no engine) compares the resolved lock path to $GBRAIN_HOME; warns when set but the lock lives elsewhere, with a PID-safe inspection hint (kill -0 <pid> before deletion). Pinned by test/doctor-v0_37_7_checks.test.ts. buildChecks(engine, args, dbSource): Promise<Check[]> exported as a test seam. runDoctor is a thin wrapper: buildChecks → computeDoctorReport → render + process.exit. All 10 process.exit sites stay in the wrapper; the two early-return paths (no engine, connection failure) return partial check lists instead of inline exits (observable output identical). Pinned by test/doctor-behavioral.test.ts (13 cases: pure aggregation math over computeDoctorReport, orchestrator cases for --fast skip set + --json flag + no-engine partial path + snapshot of load-bearing check names) and test/doctor-cli-smoke.serial.test.ts (1 subprocess case spawning bun run src/cli.ts doctor --json against a fresh PGLite tempdir, asserting schema_version=2 envelope, status enum, non-empty checks array — the render-path coverage buildChecks-only tests miss; quarantined .serial because PGLite write-locks don't play with parallel runners). three checks wired into runDoctor() and the JSON envelope: oversized_pages (warns on pages exceeding content_sanity.bytes_warn), scraper_junk_pages (warns on live DB pages matching any junk pattern that escaped ingest), and content_sanity_audit_recent (reads the last 7 days of audit events, aggregates by pattern+source). Default scans the 1000 most-recent pages; --content-audit opts into a full scan. All three warn-only with paste-ready fix hints (junk → gbrain sources audit <id> + git rm source-of-truth, oversize → split or accept). two checks wired into runDoctor() + the JSON envelope: quarantined_pages (counts pages carrying the quarantine marker via engine.executeRaw JSONB ? existence, works on PGLite + Postgres; warn-only with a gbrain quarantine list hint) and flagged_pages (counts content_flag pages — searchable but odd; warn-only). Both skip gracefully (status ok, "Skipped") on engines/brains where the probe errors. Pinned by test/doctor.test.ts. home_dir_in_worktree: filesystem check walking up from gbrainPath() toward $HOME looking for a .git directory (main repo) or .git file (linked worktree pointer; Conductor + git-worktrees topology). Walk terminates at $HOME so a .git above the user's home doesn't false-positive. Honors GBRAIN_HOME (appends .gbrain to the override). Warn (not fail) with worktree-root path + paste-ready fix pointing at GBRAIN_HOME override or moving the brain. --remediation-plan [--json] [--target-score N] prints what would run (stable id, idempotency_key, severity, est_seconds, est_usd_cost, depends_on); --remediate [--yes] [--target-score N] [--max-usd N] submits each plan step as a Minion job in dependency order, re-checking score between steps. --target-score N defaults to 90; refuses to start when target exceeds maxReachableScore() and lists what's missing. --max-usd N is the cron-safety guard — submission refuses when the plan's est_total_usd_cost exceeds the cap. JSON envelope adds a Check.remediation field (additive, schema_version unchanged). Pinned by tests in test/doctor.test.ts. 4 checks: abandoned_threads, calibration_freshness, grade_confidence_drift (mitigation surface; math ships later), voice_gate_health.

• src/commands/doctor/ — the doctor module directory (the meat behind the doctor.ts façade). checks/ holds the check-function library in bundles grouped by concern (core-health.ts, queue-jobs.ts, extraction-sync.ts, graph-embedding.ts, search-eval.ts, calibration.ts, consolidation-cycle.ts, pglite-worker.ts, routing-federation.ts, verbs-reflex.ts); schema-pack-checks.ts, report-remote.ts, bootstrap-checks.ts, and skill-checks.ts are the four tail-cluster modules (schema-pack checks, the remote/thin-client doctor report, bootstrap checks, skill checks). All are re-exported by the façade. Structural guards that pin doctor source text load it through test/helpers/doctor-source.ts: doctorSource() concatenates the façade plus every src/commands/doctor/**/*.ts (façade first, then sorted) so a module move can never take a pinned string out of a guard's sight; doctorFileSource(rel) reads one named file for positional/ordering assertions; the helper also feeds the doctor-source-helper detector in scripts/classify-tests.ts. facadeExpansion in scripts/generate-flag-registry.ts keeps this directory on the doctor command's flag-scan surface.

• src/core/postgres-engine.ts — Postgres + pgvector implementation (Supabase / self-hosted). The facts/takes/code-edges/salience method clusters are implemented in narrow-deps modules under src/core/postgres-engine/ (see the engine-module-dirs entry below); the class methods delegate to them and the façade keeps its full prior public surface. addLinksBatch/addTimelineEntriesBatch/addTakesBatch pass the batch as one JSONB document — INSERT ... SELECT FROM jsonb_to_recordset(($1::jsonb)->'rows') AS v(...) JOIN pages ... bound through executeRawJsonb({ rows }) — which encodes arbitrary free text safely (the old unnest(${arr}::text[]) array-literal path crashed Postgres with "malformed array literal" on calendar/Zoom context, gbrain#1861) and sidesteps the 65535-parameter cap; takes declares native recordset column types (page_id int, weight real, active boolean, …) so no per-element casts; all three are batchRetry-wrapped. disconnect() runs drainBackgroundWorkBeforeDisconnect() before pool teardown (#4143 engine parity with PGLiteEngine — mode 'disconnect', so residual telemetry buffers drop symmetrically on both engines; guarded so a never-connected/already-torn-down engine skips the drain). searchKeyword/searchVector scope statement_timeout via sql.begin + SET LOCAL so the GUC dies with the transaction instead of leaking across the pooled postgres.js connection. getEmbeddingsByChunkIds uses tryParseEmbedding so one corrupt row skips+warns instead of killing the query. searchKeyword/searchKeywordChunks/searchVector apply source-aware ranking by inlining the source-factor CASE and NOT (col LIKE …) hard-exclude from src/core/search/sql-ranking.ts; searchVector is a two-stage CTE (HNSW-safe inner ORDER BY, source-boost re-rank in outer SELECT) carrying p.source_id inner→outer. _savedConfig retains the connect config; reconnect() tears down + recreates the pool from saved config (called by supervisor watchdog after 3 consecutive health-check failures, and by batchRetry on a retryable connection error). Concurrent callers share one in-flight _reconnectPromise (they await the single reconnect rather than racing a half-rebuilt pool); ownership re-samples through the atomic db.connect() token on the connect leg. reconnect(ctx?) accepts the triggering error and records a pool-recovery audit event (reap_detected/reconnect_other/reconnect_succeeded/reconnect_failed) for the pool_reap_health doctor check. executeRaw is a single-statement passthrough — no per-call retry (unsound for non-idempotent statements; recovery is supervisor-driven). connect() applies resolveSessionTimeouts() from db.ts as connection-time startup parameters (statement_timeout, idle_in_transaction_session_timeout) so orphan pgbouncer backends can't hold locks for hours. countStaleChunks()+listStaleChunks() server-side-filter on embedding IS NULL for embed --stale (eliminates ~76 MB/call client-side pull); upsertChunks() resets both embedding AND embedded_at to NULL when chunk_text changes without a new embedding. initSchema() calls applyForwardReferenceBootstrap() BEFORE replaying SCHEMA_SQL on the same probe set as PGLite (extended for column-only forward-reference cases: files.source_id, files.page_id, oauth_clients.source_id, oauth_clients.federated_read, sources.archived/archived_at/archive_expires_at, timeline_entries.event_page_id); the entire probe path runs on the DDL connection threaded from initSchema (closing a concurrent-bootstrap race for Supabase pooler users); closes #1018/#974/#820. disconnect() is idempotent — _connectionStyle tracks whether the engine owns its pool (worker engines) or shares the module-level singleton; second call on an instance-pool engine is a no-op rather than clobbering the singleton; and a module-style engine only calls db.disconnect() when it owns the singleton (_ownsModuleSingleton, set from the db.connect() creation token), so a borrower probe engine's teardown leaves the cycle owner's connection intact. Pinned by test/e2e/postgres-engine-disconnect-idempotency.test.ts + test/postgres-engine-singleton-ownership.test.ts. getBrainScore empty-brain parity with PGLite — 100/100 with breakdown 35/25/15/15/10 when pageCount === 0 (both engines must agree to keep doctor-report-remote.serial.test.ts deterministic). Implements deletePages(slugs, {sourceId}): Promise<string[]> via DELETE FROM pages WHERE slug = ANY($1::text[]) AND source_id = $2 RETURNING slug (single round-trip; caller chunks); resolveSlugsByPaths does SELECT slug, source_path FROM pages WHERE source_path = ANY($1::text[]) AND source_id = $2; FK cascades through content_chunks/links/tags/raw_data/timeline_entries/page_versions, files.page_id+links.origin_page_id go SET NULL; throws when input exceeds DELETE_BATCH_SIZE (from src/core/engine-constants.ts); both short-circuit on empty input. Implements the embedding-signature stale-detection quartet (sumStaleChunkChars, setPageEmbeddingSignature, invalidateStaleSignatureEmbeddings, widened countStaleChunks, all accept optional signature extending "stale" to model/dims-swap drift via the pages.embedding_signature JOIN, NULL grandfathered; the embedding IS NULL server-side filter is preserved as the no-signature fast path); Pinned by test/e2e/engine-parity.test.ts. Retry classifiers, ontology/recency helpers, and disconnect/pool-recovery audit writers bind statically; only the two ai/gateway.ts fallback lookups stay lazy and line-marked, in parity with PGLite. insertFact + insertFacts no longer hardcode tx.unsafe(\'${embedLit}'::vector`)for the embedding column.resolveFactsEmbeddingCast()(private) probespg_attributeonce per engine instance (cached in_factsEmbeddingCastSuffix) and returns '::halfvec'when migration v40 created the column as halfvec, else'::vector'; both insert paths use the cached suffix so the cast matches the actual column type (works on older pgvector that lacks implicit auto-cast). Test seam __resetFactsEmbeddingCastCacheForTest()clears the per-engine cache.withReservedConnectionroutes long-hold reserved work (CREATE INDEX CONCURRENTLY,transaction: falsemigration DDL, backfill write batches) to the DIRECT session lane when dual-pool is active, so multi-minute holds stop pinning the worker's shared read pool (the issue #6 starvation class) — never rerouted inside an open transaction (same guard shape asexecuteRawDirect), semaphore-capped below direct_pool_sizewith deliberately NO minimum-1 floor (atdirect_pool_size=1a floor would let one long reserve consume the only direct session and starve the claim/renewLock heartbeats — the same starvation class reintroduced on the direct lane), overflowing to the shared read pool when the direct lane has no spare capacity or is unavailable; the permit is released on both fn throw and reserve failure.getPoolDiagnostics()(duck-typed, no BrainEngine change) surfaces theCheckoutGaugein-flight counters fromsrc/core/pool-gauge.tsat the raw/direct/reserved/tx seams — a tracked SUBSET (tagged-template traffic is untracked) thatdb-probe.tslabels honestly in health-probe failure lines. Pinned bytest/postgres-engine-reserved-routing.test.ts`.

• src/core/postgres-engine/ + src/core/pglite-engine/ — narrow-deps engine module directories, mirrored in lockstep (the engine-parity discipline applies to these dirs exactly as to the façades). Each holds facts.ts, takes.ts, code-edges.ts, and salience.ts: the corresponding BrainEngine method clusters implemented as free functions over a typed deps interface (e.g. PgliteFactsDeps) that the engine class satisfies, so each module depends only on the narrow slice it uses. The façade methods delegate to them via static top-level imports (the engine-live no-runtime-dynamic-import rule applies) and keep the full prior public surface.

• src/core/cjk.ts — Single source of truth for CJK detection. Exports CJK_RANGES_REGEX, CJK_SLUG_CHARS (character-class fragment for embedding inside other regexes), CJK_SENTENCE_DELIMITERS (。！？), CJK_CLAUSE_DELIMITERS (；：，、), CJK_DENSITY_THRESHOLD = 0.30, hasCJK(s), countCJKAwareWords(s) (30% density threshold — English docs with one Japanese term stay whitespace-tokenized; Chinese-dominant docs get char-counted), and escapeLikePattern(s) (escapes %, _, \\ for ILIKE ... ESCAPE '\\'). BMP-only ranges (Han / Hiragana / Katakana / Hangul Syllables). Consumers: expansion.ts, sync.ts:slugifySegment, operations.ts:validatePageSlug + validateFilename, chunkers/recursive.ts:countWords + DELIMITERS, pglite-engine.ts:searchKeyword + searchKeywordChunks.

• src/core/chunkers/recursive.ts — base chunker: 300-word chunks, 50-word sentence-aware overlap, 5-level delimiter hierarchy. Lossless invariant: non-overlapping portions reassemble to the original. Also strips the facts fence via stripFactsFence({keepVisibility:['world']}) so private fact visibility tiers never reach embeddings.

• src/core/chunkers/semantic.ts — embedding-based topic-boundary detection: embeds sentences, computes cosine-similarity valleys, smooths with a Savitzky-Golay filter (5-window, 3rd-order polynomial) to find chunk boundaries.

• src/core/chunkers/llm.ts — LLM-guided chunking: pre-splits into 128-word candidates via the recursive chunker, then asks a Haiku-class model "where does the FIRST topic shift occur?" per window.

• src/core/search/dedup.ts — 4-layer result dedup + compiled-truth guarantee: (1) top 3 chunks per page by score, (2) drop chunks >0.85 Jaccard-similar to already-kept chunks of the SAME page (cross-page near-dups survive — two legitimately similar pages both return), (3) no page type exceeds 60% of results, (4) max 2 chunks per page (default; the two-pass structural expansion in hybrid.ts widens it), (5) ensure at least 1 compiled_truth chunk per page. Page identity is the composite pageKey() (source_id, slug) — the one canonical key helper every layer uses, so slug collisions across sources can't collapse recall.

• src/core/audit-slug-fallback.ts — Weekly ISO-week-rotated audit JSONL at ~/.gbrain/audit/slug-fallback-YYYY-Www.jsonl. logSlugFallback(slug, sourcePath) fires when importFromFile falls back to a frontmatter slug because slugifyPath returned empty (emoji / Thai / Arabic / non-CJK exotic-script filenames). readRecentSlugFallbacks(days) reads the last N days for gbrain doctor's slug_fallback_audit check. Honors GBRAIN_AUDIT_DIR via the shared resolveAuditDir(). Separate surface from sync-failures.jsonl — that file carries bookmark-gating semantics that info events shouldn't trigger.

• src/core/embedding-pricing.ts — EMBEDDING_PRICING map keyed provider:model for the post-upgrade reindex cost estimate. Sibling to anthropic-pricing.ts; EMBEDDINGS only — chat/completion pricing lives in model-pricing.ts (different unit) and is never mixed in. Every entry carries its official source URL + the date it was last read. Entries: OpenAI text-embedding-3-large ($0.13/1M), 3-small ($0.02/1M), ada-002 ($0.10/1M); Voyage 4-large ($0.12/1M), 4 ($0.06/1M), 4-lite ($0.02/1M), legacy 3-large ($0.18/1M), 3 ($0.06/1M); ZeroEntropy zembed-1 ($0.05/1M), zerank-2 ($0.025/1M); Mistral mistral-embed ($0.10/1M); Perplexity pplx-embed-v1-4b ($0.03/1M), 0.6b ($0.004/1M). voyage-4-nano is deliberately unpriced (open-weight variant, no published hosted rate) so it degrades to "estimate unavailable" rather than a fabricated 0. lookupEmbeddingPrice(modelString) returns a tagged union (known with price + unknown with provider name); estimateCostFromChars(charCount, pricePerMTok) uses 3.5 chars/token. Unknown providers degrade to "estimate unavailable" instead of fabricating numbers.

• src/core/post-upgrade-reembed.ts — Pure functions backing the gbrain upgrade chunker-bump cost prompt. computeReembedEstimate(engine, model) queries real SQL (COUNT(*) + COALESCE(SUM(LENGTH(compiled_truth)) + SUM(LENGTH(timeline)), 0)) on pages WHERE chunker_version < MARKDOWN_CHUNKER_VERSION. formatReembedPrompt(est, graceSeconds) is the stderr-line formatter. runPostUpgradeReembedPrompt(engine, model, opts) orchestrates the 10-second Ctrl-C window; TTY-only wait (non-TTY auto-proceeds for CI / cron); GBRAIN_NO_REEMBED=1 bails with a doctor-warning marker; GBRAIN_REEMBED_GRACE_SECONDS=0 skips the wait.

• src/commands/reindex.ts — gbrain reindex --markdown [--type PAGE_TYPE] [--limit N] [--dry-run] [--json] [--no-embed] [--repo PATH]. Walks markdown pages with stale chunker_version (plus unstamped contextual-retrieval mode when embedding is enabled) in 100-row id-keyset batches; a failed row cannot starve later batches in the same invocation. --type adds a bound-parameter pages.type = $N scope for focused backfills such as atom pages and is rejected by reindex modes that do not consume it. Current-version chunkless healing deliberately remains owned by the native, bounded embed --stale path. Rows with non-null source_path re-import via importFromFile; rows without fall back to importFromContent. Both paths pass forceRechunk: true to bypass importFromContent's content_hash short-circuit — without it the chunker version bump never reaches pages whose source content hasn't changed, AND the stripFactsFence privacy strip never applies to pre-strip chunks. Wired into src/commands/upgrade.ts:runPostUpgrade after apply-migrations. The DB-only fallback (no source file on disk) does NOT pass body-only compiled_truth to importFromContent (that path re-parses with EMPTY frontmatter and OVERWRITES the page's real frontmatter/title/timeline); it getPage+getTags, reconstructs FULL markdown via serializeMarkdown(frontmatter, compiled_truth, timeline, {type, title, tags}), and re-imports THAT so re-chunking a DB-only page preserves everything while bumping chunker_version. Pinned by test/reindex-preserve-tags.test.ts and test/reindex.test.ts.

• src/commands/reindex-code.ts — gbrain reindex --code [--source ID] [--dry-run] [--yes] [--json] [--force] [--no-embed]. Walks pages WHERE type = 'code' in 100-row batches, replays through importCodeFile for chunk + embed + content_hash folding. Idempotent unless --force bypasses the content_hash early-return. Cost-preview model field reads getEmbeddingModelName() from the gateway so preview reflects what the gateway will actually embed with. An informational stderr nudge inside runReindexCode (so dry-run + execute both surface it): when the configured embedding model isn't code-tuned (allowlist {'voyage-code-3'}, case-insensitive bare match), prints a recommendation to switch to voyage:voyage-code-3; suppress with GBRAIN_NO_CODE_MODEL_NUDGE=1, --no-embed, or --json. Pure shouldNudgeCodeModel(bareName) returns a tagged NudgeDecision union (takes the bare model name, emits qualified voyage:voyage-code-3 for the paste-ready gbrain config set line). When --yes is absent and the caller is non-TTY or passed --json, the cost gate refuses (exit 2, no spend) via the pure exported buildCostRefusal({json, previewMsg, preview, costUsd, model}): {stdout?, stderr?} — JSON envelope only when --json is explicit, otherwise a human refusal on stderr (the spend guardrail is independent of the output format). spend.posture=tokenmax OR an explicit --max-cost off/unlimited makes the gate informational and proceeds (#2139); --max-cost off also disables the runtime BudgetTracker cap. Pinned by test/ai/voyage-code-3-recipe.test.ts, test/reindex-code-nudge.serial.test.ts, test/reindex-code-model-source.serial.test.ts (IRON-RULE regression for the cost-preview fix), test/reindex-cost-refusal.test.ts.

• src/core/fts-language.ts — Single source for the Postgres text-search configuration name used by FTS. getFtsLanguage() resolves GBRAIN_FTS_LANGUAGE (default english), validates against /^[a-z][a-z0-9_]*$/ (tsvector config names can't be bound as parameters, so the value is interpolated into raw SQL — the allowlist regex is the injection guard; invalid values warn once and fall back to english), and caches on first read (resetFtsLanguageCache() is test-only). Consumed by both engines' searchKeyword/searchKeywordChunks (websearch_to_tsquery query side), the configurable_fts_language migration, and reindex-search-vector (write-side trigger functions). Pinned by test/fts-language.serial.test.ts + test/fts-language-migration.serial.test.ts (includes the '; DROP TABLE pages; -- injection cases).

• src/commands/reindex-search-vector.ts — gbrain reindex-search-vector [--dry-run] [--yes] [--json]. Escape hatch for changing GBRAIN_FTS_LANGUAGE after the configurable_fts_language migration has run (the migration shows applied and is skipped): recreates update_page_search_vector + update_chunk_search_vector with the configured language — bodies mirror the migration's and KEEP the SET search_path = pg_catalog, public hardening (CREATE OR REPLACE resets proconfig) — then backfills pages (UPDATE-to-self re-fires the trigger) and content_chunks (direct vector recompute) in id-keyset batches of BACKFILL_BATCH_SIZE (5000) via UPDATE … WHERE id IN (SELECT … LIMIT n) RETURNING id, streaming phases reindex_search_vector.pages/.chunks through the shared progress reporter (stderr). Confirmation gate: --yes, or an interactive TTY [y/N]; --json does NOT bypass the gate (non-TTY without --yes refuses with a ConfirmationRequired envelope, exit 2). Idempotent. Pinned by test/reindex-search-vector.serial.test.ts.

• src/commands/sync.ts — gbrain sync CLI + the performSync / performFullSync library entrypoints (consumed by the autopilot cycle and the Minion sync handler). Six pure-function clusters live in src/core/sync-{cost-gate,git,anchor,lock,reconcile,status-report}.ts (see the grouped entry below) and are re-exported through this façade, so the full prior import surface is unchanged. performSync runs under a writer lock: per-source gbrain-sync:<sourceId> whenever opts.sourceId is set, wrapped in withRefreshingLock from src/core/db-lock.ts so long-running sources (250K+ chunks) don't lose the lock at the 30-min TTL mid-run; the bare no-source path uses the SAME refreshing lock (#1794 — it was previously a non-refreshing tryAcquireDbLock, stealable mid-run during an incident); SyncOpts.lockId?: string is the explicit override. The lock refresh AND its health probe route through the DIRECT session pool so Supavisor transaction-pool exhaustion (EMAXCONNSESSION) can't kill renewal; takeover is heartbeat-aware (it will NOT steal a holder whose last_refreshed_at is within GBRAIN_LOCK_STEAL_GRACE_SECONDS, defending an alive-but-starved holder); the import loop yields the event loop every GBRAIN_SYNC_YIELD_EVERY files (setTimeout(0), not setImmediate — Bun starves the timers phase) so the refresh setInterval heartbeat fires mid-import. This lock-identity invariant prevents a sync --all per-source worker racing sync --source foo on the global lock from corrupting the same source. performSync throws a typed SyncLockBusyError when the writer lock is held; the Minion sync handler (src/commands/jobs.ts) catches it and marks the job SKIPPED (not failed) so a cron/autopilot tick defers to the holder without polluting crash metrics. performSyncInner is RESUMABLE (incremental path): it drains a PINNED target commit (lastCommit..pin), banking drained file paths via appendCompleted (append-only delta into the op_checkpoint_paths child table, migration v115 — one row per path, O(delta) not the old O(N²) full-array rewrite), keyed by syncFingerprint({sourceId, lastCommit}) from src/core/op-checkpoint.ts (paths under op:'sync'; the pinned target under op:'sync-target'), and advances last_commit/last_sync_at ONLY at full import completion. Checkpoint writes route through the DIRECT session pool + bounded retry so they survive EMAXCONNSESSION; the flush cadence is first-file then every GBRAIN_SYNC_CHECKPOINT_EVERY (default 1000) files OR GBRAIN_SYNC_CHECKPOINT_SECONDS (default 10s), with a race-safe pendingCheckpointPaths delta (single-flight swap, re-merge on failure) under parallel workers; a SIGTERM banks the in-flight delta via a no-retry one-shot (appendCompletedOnce, ordered before lock release through registerCleanup); and sustained flush failure aborts the run with reason:'checkpoint_unavailable' after GBRAIN_SYNC_MAX_CHECKPOINT_FAILURES consecutive fails rather than importing work it can never bank (every partial/blocked exit logs the banked-file count). A sync killed mid-import banks its progress, leaves the anchor unmoved (the source stays correctly stale to the autopilot scheduler — last_sync_at is never bumped on a partial), and the next run resumeFilters the same fixed diff to skip done files. The pin is the checkpoint's stored target when still reachable from HEAD, else live HEAD (a history rewrite / reset re-pins); completion advances to the pin, NOT live HEAD, so commits landing past the pin are a clean next-sync diff — this closes the cross-run staleness window. After import a pin-reachability gate (git merge-base --is-ancestor pin HEAD) replaces the old strict head-drift gate: forward commits on top of the pin (e.g. a background enrich process committing to the same repo every ~2 min) are SAFE and no longer block the run; only a real rewrite (pin not an ancestor of HEAD) blocks and discards the checkpoint. A file added in lastCommit..pin but gone from disk (deleted by a commit after the pin) is SKIPPED and marked completed, not recorded as a failure. Downstream extract/facts/embed are size-gated: inline only for totalChanges <= 100; large syncs defer to the resumable extract --stale watermark + embed --stale/backfill + the facts cycle phases, so a 44K-page facts/embed pass never re-blocks import convergence (sync convergence == import convergence). Worker engines wrap in try/finally so disconnect always fires; both PGLite-detection sites use engine.kind === 'pglite'. CLI accepts --workers N (alias --concurrency N) validated via parseWorkers (explicit bypasses the file-count floor; auto path defers to autoConcurrency()). The newest-first descending-lex order uses sortNewestFirst(addsAndMods) from src/core/sort-newest-first.ts (shared with gbrain import). gbrain sync --all runs a continuous worker pool: parseWorkers-validated --parallel N (default min(sourceCount, --workers, DEFAULT_PARALLEL_SOURCES=4)), long-lived async workers pulling from a shared FIFO queue (no head-of-line blocking), per-source withSourcePrefix(src.id, ...) so every slog/serr line carries [<source-id>]; --skip-failed/--retry-failed are scoped per source (acknowledgeFailures(sourceId); --all acks every source, single-source acks only its own) and run UNDER parallel — the #1939 failure ledger is per-(source_id, path) and serialized through withLedgerLock, so the old "not supported under parallel, re-run with --serial" refusal is lifted (#2139, which also removed the forcing-function that pushed recovery syncs to --serial and thus armed the inline cost gate); a connection-budget stderr warning fires when parallel × workers × 2 > 16 (the × 2 per-file pool factor: each per-file worker opens its own PostgresEngine with poolSize=2). Exports resolveParallelism, syncOneSource, buildSyncStatusReport, printSyncStatusReport, SyncStatusReport back the gbrain sources status dashboard. --json envelope {schema_version: 1, sources, parallel, ok_count, error_count, skipped_count} on stdout; human banners route to stderr via humanSink so jq parses cleanly. Exit matrix: 0 all ok (sources skipped by --missing-path skip count as ok), 1 any error. --missing-path <fail|skip> (default fail) handles sources whose local_path does not exist on this machine — machine-specific state in a brain-wide table, so a brain registered from several machines fails every foreign source on every run; skip classifies them skipped_missing_path (⊘ line, envelope entry with local_path, excluded from error_count and the rc gate) via the exported pure helpers parseMissingPathMode + partitionMissingPathSources, pinned by test/sync-all-missing-path.test.ts; default fail stays loud because on a single-machine brain a missing path usually means an unmounted volume. (The non-TTY cost gate no longer exits 2 — it auto-defers; #2139.) The dashboard SQL is content_chunks ch JOIN pages pg ON pg.id = ch.page_id WHERE pg.deleted_at IS NULL with archived = false at the caller; embedding column resolved via resolveEmbeddingColumn(undefined, cfg) from src/core/search/embedding-column.ts so Voyage/multimodal/non-default-column brains count against the column they use; errors propagate (no swallow-catch). The sync delete loop is interleaved per-batch resolve+delete using engine.resolveSlugsByPaths + engine.deletePages from src/core/engine.ts (73K-delete commit: ~146K SQL round-trips → ~292, closing the cascade-staleness class where one big-delete commit jammed every other source's sync); per-batch try-catch decomposes batch DELETE failures to per-slug deletePage fallback, unrecoverable per-slug failures land in failedFiles; pagesAffected filters to confirmed-deleted slugs. The rename loop gets the same batched slug-resolve; a rename whose destination is un-syncable folds the source path into the delete set so the old page can't orphan (#1970). An entry-time bookmark-reachability guard distinguishes a gc'd anchor (cat-file fails → performFullSync) from a history-rewrite anchor that is merely no-longer-an-ancestor but still on disk: the latter is diffed tree-to-tree directly (git diff lastCommit..pin is an endpoint-tree compare, ancestry not required) so a force-push / master→main consolidation imports only the real delta instead of re-walking the whole tree forever (#1970); an oversized or failed diff degrades to performFullSync. performFullSync is itself authoritative for deletes — after an advancing full import it purges file-backed pages (source_path != null AND strategy-aware isSyncable) whose source file no longer exists, sparing put_page/manual pages (null source_path) and metafiles. The stale-file decision routes through the pure, exported planReconcileDeletes(rows, currentFiles, isSyncablePath): it normalizes path separators on both sides of the membership test (a Windows path.relative backslash path vs a git-derived forward-slash source_path would otherwise mark every page stale and wipe the source) and computes a mass-delete signal — when the reconcile would delete more than MASS_RECONCILE_RATIO (50%) of the file-backed pages the strategy manages, on a source holding more than MASS_RECONCILE_MIN_PAGES (20) of them, the delete is REFUSED with a loud stderr warning (that shape is almost always a path-comparison bug or the wrong repo path, not a genuine bulk deletion); GBRAIN_ALLOW_MASS_RECONCILE=1 restores the unguarded delete for genuinely intended bulk removals. Pinned by test/sync-reconcile-mass-delete.test.ts. Below the valve, stale pages are partitioned by git history via exported listEverCommittedPaths(repoPath) (one git log --all --no-renames --diff-filter=A --name-only pass; null on non-git dirs → unchanged behavior): a stale path that EVER existed in history was genuinely deleted → reconciled; a path with NO history is DB-only write-through (never committed/pushed, e.g. lost to a fresh clone) → the page is KEPT and its markdown re-exported to the working tree via writePageThrough, with a stderr hint to commit it (#2426 — "absent from git" is the symptom of the missing write-through commit, not evidence the content is disposable). Pinned by test/sync-reconcile-db-only.serial.test.ts. resolveSlugByPathOrSourcePath at sync.ts:267 delegates to engine.resolveSlugsByPaths when sourceId is set, keeping legacy executeRaw fallback for the no-sourceId path. failedFiles is hoisted to the top of performSyncInner so both delete-decompose and import loops feed the same bookmark gate. The cost gate is the shared runInlineCostGate (one implementation on BOTH the --all and single-source paths; runs at the command layer, never inside performSync), mode-aware via willEmbedSynchronously + posture-aware shouldBlockSync from src/core/embedding.ts (#2139). The DEFERRED path (v2 on, parallel) is INFORMATIONAL (embedding goes to per-source embed-backfill jobs with their own $X/source/24h cap, default $25 via SPEND_CAP_CONFIG_KEY from embed-backfill-submit.ts; prints the cap + backlog + queued-job count, NEVER exits 2). The INLINE path (v2 off, or --serial) gates on the DELTA estimate vs sync.cost_gate_min_usd (default $0.50): below floor proceeds; above floor in a TTY prompts [y/N]; above floor in a non-TTY/--json session AUTO-DEFERS embeds to capped backfill jobs and exits 0 (NEVER exit 2 — the wedged-cron fix); spend.posture=tokenmax makes it informational and proceeds inline. The estimate MIRRORS EXECUTION instead of pricing the whole tree: estimateInlineNewTokens routes through the shared computeSyncDelta (src/core/sync-delta.ts) — fetch-first against origin/<branch>, prices only the committed delta (a dirty-but-caught-up tree → $0), with a full-tree CEILING only on the fail-open rungs (chunker drift, first sync, git-unavailable) honestly labeled; --full adds the stale backlog (full sync sweeps it inline). Return shape carries estimateKind: 'delta'|'ceiling'|'mixed'|'unchanged' + ceilingReasons. Helpers resolveCostGateFloorUsd(engine) + resolveBackfillCapUsd(engine) resolve via parseUsdLimit (off/unlimited → Infinity; floor accepts 0 = block-on-any-spend). JSON envelopes carry mode + gate discriminators (dry_run | deferred_notice | below_floor | auto_deferred_embeds | posture_tokenmax) + a paste-ready hint; Infinity floors/caps render as the string 'unlimited' (never raw, which JSON-serializes to null); SyncStatusReportSource gains backfill_queued/backfill_active/backfill_last_completed_at; cost previews read getEmbeddingModelName() (no hardcoded OpenAI). Format splits on the explicit --json flag only (human text otherwise). SyncOpts.noSchemaPack (CLI --no-schema-pack, threaded through performSync AND syncOneSource) skips loadActivePack so pages fall back to legacy prefix typing — an escape hatch when a suspect pack regex wedges a sync. A per-file BEGIN heartbeat if (process.env.GBRAIN_SYNC_TRACE) serr('[sync] begin import: <path>') fires BEFORE importFile (the progress.tick fires only AFTER) so a stuck file is a begin-line with no matching completion. Triage doc: docs/architecture/serve-sync-concurrency.md (PGLite single-writer serve↔sync contention + the GBRAIN_SYNC_TRACE + --no-schema-pack recipes). Pinned by test/e2e/sync-status-pglite.test.ts (IRON-RULE: PGLite seeds 2 sources × pages × chunks, soft-deletes 1 page, archives 1 source, validates the SQL excludes both AND uses the active embedding column), test/sync-cost-gate.serial.test.ts, test/sync-cost-preview.test.ts. Runaway-sync protection: resolveSyncHardDeadline(args, {isTty, env, defaultNonTtySec?}) resolves a wall-clock hard deadline (precedence --no-hard-deadline > --hard-deadline <s> > --timeout <s>(non---all, which auto-arms the backstop) > GBRAIN_SYNC_MAX_RUNTIME_SECONDS env > non-TTY default 3600s > none; HARD_DEADLINE_GRACE_SEC=30). src/cli.ts installs the out-of-band watchdog (see src/core/process-watchdog.ts) for the sync command BEFORE connectEngine and disposes it in the dispatch finally, so even an event-loop-starved sync — or a connect-phase hang — is SIGTERM-then-SIGKILLed by the deadline instead of orphaning under cron. runSync registers a SIGINT handler that aborts an interrupt AbortController composed via composeAbortSignals(...) (an AbortSignal.any wrapper over the defined signals) with the per-source --timeout signal, so Ctrl-C returns a clean partial and releases the lock through the normal finally (process-cleanup.ts owns SIGTERM lock-release; the watchdog owns the hard kill). withRefreshingLock unref()s its refresh setInterval. The spin's own root cause is not yet pinned (leading lead is catastrophic-backtracking in a pack link-inference regex, bounded by the redos-guard); the watchdog heartbeat plus the existing [gbrain phase] breadcrumbs are the diagnosis surface. Pinned by test/sync-hard-deadline.test.ts (resolution precedence + composeAbortSignals). Monorepo subdir sources (#753/#774): --src-subpath <dir> (or a repo path that IS a subdir — auto-discovery via discoverGitRoot, i.e. git rev-parse --show-toplevel) splits the repo path into gitContextRoot (all git ops: pull/diff/rev-parse/cat-file) and syncScopeRoot (walk/import/delete/rename scope); scoped syncs use git-root-relative slugs + source_path (full sync threads slugRoot into runImport) so full and incremental agree; NAV-1/NAV-2 realpath containment rejects ../-traversal and symlinked scopes resolving outside the repo BEFORE any git op, and a per-file realpath guard (isPathSafe) refuses symlink-escape files in the incremental drain and rename reimport (fail-closed into failedFiles, so the bookmark can't advance past an escape); the full-sync reconcile is scope-restricted so a scoped sync never sweeps out-of-scope pages. --exclude <glob> (repeatable) filters scope-relative paths in both full and incremental paths; exclusion never deletes previously-imported pages (conservative, matching the #1433 metafile posture); an all-excluded run warns loudly (NAV-4). A warn-and-continue internal git pull failure (non-timeout class — e.g. a local-path origin rejected by protocol.file.allow=never) still falls through to sync the local working tree, but a ZERO-import run after a failed pull returns partial with reason: 'pull_failed' instead of up_to_date: last_commit AND the last_sync_at heartbeat stay frozen (so doctor sync_freshness / sources status staleness fires), the single-source CLI exits non-zero, sync --all exits non-zero if any source hit it (JSON envelope carries the per-source reason), and the autopilot cycle's sync phase maps it to warn. Timeout-class partials keep their pre-existing exit-0 / phase-ok semantics (they converge on retry; a failing pull does not). Pinned by test/sync-pull-failed-anchor.serial.test.ts. resolveSlugByPathOrSourcePath: Resolves a slug by pages.source_path first (returns the stored slug for frontmatter-fallback pages whose path doesn't derive a slug), then falls back to resolveSlugForPath(path). Threaded into all 4 delete/rename call sites (performSync's un-syncable cleanup at ~:531, deletes at ~:603, rename oldSlug at ~:622). Without this, emoji-only / Thai / Arabic filenames whose slug came from frontmatter would orphan on delete/rename (the delete path would compute the wrong path-derived slug). Best-effort query — pre-migration brains fall through to the legacy path. #2849: above the size gate (totalChanges > 100) the deferred link/timeline extraction is DURABLY QUEUED, not just hinted — the defer branch submits an extract Minion job {stale: true, sourceId?, deferred_commit: pin} keyed extract-stale:<sourceId|default>:<pin> (repeat submissions toward the same drained pin coalesce; deliberately NO maxWaiting — an unscoped payload's coalesce filter matches ANY waiting extract job and would silently drop the sweep), timeout_ms derived from extract.ts's exported STALE_TIME_BUDGET_MS + headroom. The returned row is verified to be a live {stale:true} job (waiting/delayed/active) before the log claims "queued"; a finished row occupying the key slot (a prior sweep toward the same pin that completed before this run's pages landed — the checkpoint-resume / blocked-advance re-sync case) triggers a fresh submission under a run-unique key so those pages never strand stale. Submission is best-effort (failure falls back to the hint; pages stay stale + doctor-visible, never mis-stamped). Pinned by test/sync-deferred-extract-queue.serial.test.ts.

• src/core/sources-ops.ts — Multi-source registration + clone-lifecycle ops (addSource, recloneIfMissing, defaultCloneDir, isOwnedClone, unownedHint). Reclone-ownership invariant (must-never-violate): gbrain may only delete/re-clone a clone it created, NEVER a user working tree. recloneIfMissing deletes local_path, so it gates on isOwnedClone(src) and throws a SourceOpError('unmanaged_path', ...) BEFORE any filesystem op when ownership is unprovable — fail-closed. Ownership is proven by config.managed_clone === true (written by addSource's --url path, covering default-location and --clone-dir clones) OR local_path === defaultCloneDir(id) (back-compat for pre-marker clones, via exact normalized-path equality, symlink-free). A row with remote_url + an unowned local_path (a user-registered working tree, e.g. sources add --path) is refused untouched; re-add with --url to regain auto-reclone. The reclone is EXDEV-safe: clone into a SIBLING temp of local_path (not the shared clones/.tmp, which may sit on a different mount than a --clone-dir target), then swap (move old aside → move new in → drop old) so local_path is never left missing-and-unrecoverable; on swap failure the original is restored, and if restore fails the error names the aside path so it's never reflexively deleted. A TOCTOU re-check re-confirms ownership immediately before the destructive move and rejects a symlink leaf swapped in after the entry check (symlink_escape). unownedHint(src, state) is the shared recovery message used by both the core error and the gbrain sync --source CLI error; gbrain sources restore special-cases unmanaged_path to print "DB row restored; gbrain syncs this path read-only" instead of the misleading "try sync to recover" guidance. SourceOpErrorCode includes unmanaged_path. Pinned by test/sources-ops.test.ts, test/sources-resync-recovery.test.ts.

• src/core/utils.ts — Shared SQL utilities extracted from postgres-engine.ts. Exports parseEmbedding(value) (throws on unknown input, used by migration + ingest paths where data integrity matters) and tryParseEmbedding(value) (returns null + warns once per process, used by search/rescore paths where availability matters more than strictness). isUndefinedColumnError(err) predicate — pattern-matches Postgres SQLSTATE 42703 / "column ... does not exist" with engine-driver shape variation tolerated; replaces bare catch {} blocks in oauth-provider.ts so genuine errors (lock timeout, network blip, permission denied) propagate while column-missing falls through to the legacy fallback. validateSourceId(id) throws on anything outside ^[a-z0-9_-]+$, used by the per-source disk-layout fix in patterns.ts/synthesize.ts before any join(brainDir, '.sources', source_id, slug+'.md') so source_id can't traverse out of brainDir. rowToSearchResult projects email message_id / thread_id metadata and exposes source_subject only when a non-empty Message-ID proves the page is an email, so generated page titles never become authoritative email subjects. rowToPage populates the required Page.source_id from the SELECT projection (scripts/check-source-id-projection.sh enforces every projection feeding rowToPage includes the column).

• src/core/db.ts — Connection management, schema initialization. resolveSessionTimeouts() returns statement_timeout + idle_in_transaction_session_timeout (defaults 5min each, env-overridable via GBRAIN_STATEMENT_TIMEOUT/GBRAIN_IDLE_TX_TIMEOUT/GBRAIN_CLIENT_CHECK_INTERVAL). Both connect() (module singleton) and PostgresEngine.connect() (worker pool) consume the result via postgres.js's connection option, sending GUCs as startup parameters that survive PgBouncer transaction mode (setSessionDefaults kept as a back-compat no-op shim). connect() returns Promise<boolean> — true iff THIS call created the module singleton, false if it joined an existing one; the decision is atomic (no await between the if (sql) null-check and the synchronous sql = postgres(...) assignment), so two concurrent module connects can't both claim creation. PostgresEngine stores the return as its _ownsModuleSingleton token and only the creating engine may db.disconnect() the singleton — a borrower probe engine (lint/doctor config-lift) no-ops its disconnect, so its teardown can't null the connection the long-lived cycle owner is still using (the dream-cycle "connect() has not been called" failure). The module sql is only ever nulled by db.disconnect() (postgres.js auto-reconnects its own internal pool and never touches our reference). disconnect() snapshots + nulls sql before awaiting the pool end so a concurrent connect can't join a pool that's already closing. The end routes through endPoolBounded(pool) (#1972) — a gbrain-owned Promise.race of pool.end({ timeout: POOL_END_TIMEOUT_SECONDS }) against a hard timer — so a PgBouncer transaction-mode drain that never settles can't hang teardown — the #2084 contract (finishCliTeardown's computed-deadline backstop + flushThenExit's fence-and-grace exit in cli-force-exit.ts) bounds it and delivers pending stdout before exit. connection-manager.ts ends its direct + read pools concurrently through the same helper so the per-pool bounds don't stack. resolveMaxLifetimeSeconds(env?) — explicit client-pool max_lifetime for all four postgres() call sites (matches the postgres.js implicit 30-60min jittered default; GBRAIN_POOL_MAX_LIFETIME_S overrides, 0 disables; warn-once on invalid). Pinned by test/db-pool-max-lifetime.test.ts.

• src/core/pool-gauge.ts — CheckoutGauge: approximate in-flight counters at the engine's raw/direct/reserved/tx seams, surfaced via duck-typed PostgresEngine.getPoolDiagnostics() (no BrainEngine change, no PGLite stub). HONESTY CONTRACT in the module doc: tagged-template traffic is untracked; consumers must label counts as a subset and never derive waiter/available figures. Fail-open (clamped release, try/finally around sync-throwing runUnsafe). Consumed by db-probe.ts. Pinned by test/pool-gauge.test.ts.

• src/commands/migrate-engine.ts — Bidirectional engine migration (gbrain migrate --to supabase/pglite). Copies the complete source catalog FIRST (copyMigrationSources — every sources row incl. archived rows and sync/routing metadata, ON CONFLICT (id) DO UPDATE, default ordered first) so every page write has a valid pages.source_id FK parent and the target preserves per-source behavior; pages copy afterward, tracked in the resume manifest by composite (source_id, slug) key. Link copy preserves each row's to_source_id (falling back to the origin source only for legacy rows without it), and failed-target filtering uses that same target composite key, so cross-source links migrate without being rebound to the origin source. The resume manifest is target-aware: migrationTargetId(config) hashes (engine, locator) (database_url for Postgres, resolved database_path for PGLite) and manifestMatchesTarget requires schema_version === 2 plus a matching target_id — a legacy engine-only manifest, or one from a DIFFERENT target of the same engine kind, starts fresh instead of skipping "completed" pages the new target never received. Pinned by test/migrate-engine-resume.test.ts (manifest identity) + test/e2e/migrate-engine-sources-postgres.test.ts (source catalog lands before overlapping-slug pages, PGLite → real Postgres) + test/e2e/multi-source-bug-class.test.ts (cross-source links).

• src/core/import-file.ts — importFromFile + importFromContent (chunk + embed + tags). importFromContent and importCodeFile stamp pages.embedding_signature via setPageEmbeddingSignature(slug, {sourceId, signature: currentEmbeddingSignature()}) when the import actually embedded (not --no-embed) so a model/dims swap is detectable as stale; importCodeFile only stamps when every chunk was freshly embedded this call (needsEmbedIndexes.length === chunks.length), mixed reuse-by-hash pages stay unstamped (reindex --code --force / embed --stale handle those). importFromContent's tag reconciliation is ADD-ONLY: it only addTag (idempotent, ON CONFLICT DO NOTHING). The tags table has no provenance column and frontmatter tags are stripped from stored pages.frontmatter (markdown.ts:118), so a frontmatter-origin tag can't be distinguished from a DB-enrichment tag (auto-tag / dream synthesize / signal-detector) at re-import — deletion is unsafe (would wipe enrichment under gbrain reindex --markdown). Accepted trade-off: removing a tag from frontmatter no longer removes it from the DB on next sync (needs a tag_source provenance column). Pinned by test/reindex-preserve-tags.test.ts + test/import-file.test.ts. identity-based dedup pre-check at :427-490. Calls engine.findDuplicatePage?.(sourceId, {hash, frontmatterId}) (optional ? so test doubles compile). Posture: SKIP when frontmatter.id matches (true external duplicate from overlapping ingest roots), WARN-ALWAYS on content_hash collision with different/missing frontmatter.id (templates and daily logs may legitimately share text), FAIL CLOSED on lookup error, bypass via --force-rechunk. Soft-deleted pages excluded at the engine layer so tombstones don't block legitimate re-imports under new slugs. Pinned by test/import-dedup-frontmatter-id.test.ts (11 cases). importFromContent is the narrow waist every ingest path passes through (gbrain import, gbrain sync, put_page MCP, /ingest webhook). It runs a three-tier content-quality disposition via assessContentSanity from src/core/content-sanity.ts BEFORE chunking: (1) high-confidence junk (built-in Cloudflare/CAPTCHA interstitial patterns + operator literals) → QUARANTINE (stamps the quarantine frontmatter marker, writes ZERO chunks, hides the page from search) OR REJECT (throw → sync-failure) when content_sanity.junk_disposition is reject; (2) fuzzy markup-heavy (prose-vs-markup ratio above content_sanity.max_markup_ratio, warn-tier byte window, code pages exempt) → content_flag:markup_heavy marker (page stays fully searchable, marker rides search results + get_page to warn the agent); (3) oversize → embed_skip soft-block via buildEmbedSkipMarker() PLUS a content_flag:oversized marker, AND deletes any pre-existing chunks in the same transaction so search can't surface stale chunks. Gate-owned markers (quarantine, content_flag) are STRIPPED from untrusted (remote MCP, ctx.remote !== false) frontmatter so a write-scoped client can't hide pages or forge the warning channel; markers are excluded from content_hash so a flagged page doesn't re-embed every sync. gbrain import honors errors > 0 for non-zero exit. classifyErrorCode in src/core/sync.ts recognizes the PAGE_JUNK_PATTERN code so sync-failures.jsonl grouping bins these. extractEntityRefs (canonical; matches both [Name](people/slug) markdown links and Obsidian [[people/slug|Name]] wikilinks), extractPageLinks, inferLinkType heuristics (attended/works_at/invested_in/founded/advises/source/mentions), parseTimelineEntries, isAutoLinkEnabled config helper. Link candidates match any dir-shaped path (#2576; existence-checked at persist). Used by extract.ts, operations.ts auto-link post-hook, and backlinks.ts. Pinned by test/import-file-content-sanity.test.ts.

• src/core/sync.ts — Pure sync functions (manifest parsing, filtering, slug conversion). Exported pruneDir(name: string): boolean is the single source of truth for descent-time directory exclusion across walkers — blocks node_modules (no leading dot, so naive walkers slipped through and inflated MISSING_OPEN counts via vendor packages), vendor/dist/build/venv, dot-prefix dirs, and *.raw sidecars — NOT ops/, which is ordinary user content (#2404; the bundled daily-task-manager stores ops/tasks there); isSyncable applies it per path segment, and walkMarkdownFiles in src/commands/extract.ts + listTextFiles in src/core/cycle/transcript-discovery.ts consult it BEFORE recursing to save the IO of walking thousands of vendor files (closes #923 + #202). manageGitignore worktree discriminator matches the gitdir path segment (/modules/<name> = submodule, /worktrees/<name> = worktree, per Git's documented layout) so Conductor worktrees (first-class repos) get .gitignore management for storage-tiering (closes #889). The sync-failure ledger (failure store, error classifier, the shared bookmark gate, and the doctor severity rule) lives in src/core/sync-failure-ledger.ts; sync.ts re-exports classifyErrorCode, summarizeFailuresByCode, loadSyncFailures, unacknowledgedSyncFailures, acknowledgeSyncFailures, recordSyncFailures, decideSyncFailureSeverity, applySyncFailureGate, and the SyncFailure type for backward-compatible imports — see its entry below. isSyncable factored through private classifySync(path, opts): SyncableReason | null; exported companion unsyncableReason(path, opts) returns the same tagged reason or null when syncable. SYNC_SKIP_FILES is a named export (the four canonical metafile basenames schema.md, index.md, log.md, README.md). SyncableReason union: 'metafile' | 'strategy' | 'pruned-dir' | 'include-glob-miss' | 'exclude-glob-hit' | 'malformed-path'. Malformed filenames are TWO-TIER: hasMalformedPathSegment (ADMISSION — control chars on any path; square brackets on .md/.mdx paths only, so code-strategy lanes keep indexing app/[id]/page.tsx framework layouts) vs isPoisonedPath (DESTRUCTION — only the injection signature ]( or control chars; sync's row-DELETING lanes gate on this so a bare-bracket markdown row imported by a pre-gate release survives reconcile while its file exists). sanitizePathForDisplay scrubs control bytes + caps length before echoing such paths. The commands/sync.ts cleanup loop guards on unsyncableReason(path) being 'metafile' OR 'pruned-dir' (#2404) so previously-indexed metafile pages AND deliberately put-created pages under pruned dirs survive every re-sync. Does NOT cover manifest.deleted (the upstream filter already strips metafiles). Pinned by test/sync-isSyncable-shape.test.ts (15 cases, duality contract) + test/sync-metafile-skip.serial.test.ts (3 PGLite cases incl. the renamed .md → .txt negative). pruneDir: pruneDir(name, parentDir?) extended with optional parentDir. When provided, additionally rejects directories containing .git as a FILE — the git submodule gitfile pattern (regular repos have .git as a DIRECTORY; submodules as a file pointing into the parent's .git/modules/). Sync + extract walkers thread parentDir so the gitfile-as-FILE check fires per descend step. Best-effort: statSync failures fall through and treat as a normal dir. Closes the phantom-import bug class where syncing a worktree-with-submodules walked into submodule trees. Pinned by test/sync-walker-submodule.test.ts.

• src/core/sync-failure-ledger.ts — the bounded auto-skip sync failure ledger (issue #1939; formerly inline "Bug 9" in sync.ts). A LEAF module (imports only fs/path/crypto/config) so sync.ts can re-export it without a circular dependency. State lives in ~/.gbrain/sync-failures.jsonl, one JSON object per line, keyed by (source_id, path) with a per-key attempts count and a 3-state machine: open (fresh/blocking) → auto_skipped (chronic, still doctor-visible) or acknowledged (human resolved via gbrain sync --skip-failed from either unresolved state). classifyErrorCode(errorMsg) regex classifier with 12 codes (SLUG_MISMATCH, YAML_PARSE, YAML_DUPLICATE_KEY, MISSING_OPEN, MISSING_CLOSE, NESTED_QUOTES, EMPTY_FRONTMATTER, NULL_BYTES, INVALID_UTF8, STATEMENT_TIMEOUT, FILE_TOO_LARGE, SYMLINK_NOT_ALLOWED) plus UNKNOWN (also recognizes PAGE_JUNK_PATTERN from the content-sanity gate); summarizeFailuresByCode(failures) returns sorted [{code, count}]; MISSING_OPEN/MISSING_CLOSE/EMPTY_FRONTMATTER regexes match the markdown.ts validator strings, FILE_TOO_LARGE covers import-file.ts:199, 352, 401, SYMLINK_NOT_ALLOWED covers :347. All mutations run under withLedgerLock (cross-process file lock) with an atomic rename write. The auto-skip threshold resolves via resolveAutoSkipThreshold() from GBRAIN_SYNC_AUTOSKIP_AFTER (default DEFAULT_AUTOSKIP_AFTER = 3; 0 disables the valve = pure fail-closed). Two pure decision functions are the unit-test surface: decideGateAction({fileFailures, sentinels, attemptsByPath, threshold, skipFailed}) returns hard_block | block | advance | advance_then_autoskip (sentinels like <head> ALWAYS hard-block, even with --skip-failed, so a history rewrite can't auto-skip; any FRESH failure with attempts < threshold blocks fail-closed; only when ALL failures are chronic does it advance_then_autoskip), and decideSyncFailureSeverity({entries, nowMs, failHours}) returns the sync_failures doctor status (ok when zero unresolved; fail when ≥10 OPEN-blocking or the oldest OPEN failure has blocked the bookmark past failHours; otherwise warn — auto_skipped-only rows stay WARN-visible regardless of count because the bookmark already advanced). applySyncFailureGate(input) is the one orchestrator BOTH sync paths (incremental + full/runImport) call: it records/clears ledger rows, runs decideGateAction, then executes effects in the crash-safe order (advance the bookmark FIRST via the injected advance() callback, THEN auto-skip the chronic set) so a crash can never mark a file skipped while leaving sync wedged. isSkippablePath rejects <…> sentinels. Pinned by test/sync-failure-ledger.serial.test.ts + test/sync-failures.test.ts.

• src/core/sync-cost-gate.ts + sync-git.ts + sync-anchor.ts + sync-lock.ts + sync-reconcile.ts + sync-status-report.ts — six pure-function clusters relocated out of src/commands/sync.ts as a pure move; the façade re-exports them, and facadeExpansion in scripts/generate-flag-registry.ts keeps exactly these six (NOT the pre-existing sync-* siblings, which are ordinary deps) on the sync command's flag-scan surface. sync-cost-gate.ts: the inline-embed cost gate + token estimation for gbrain sync. sync-git.ts: git plumbing — invocation building, repo discovery, baseline-commit self-heal, path-containment guards. sync-anchor.ts: sync anchor + chunker-version state helpers (source-scoped vs legacy global-config storage). sync-lock.ts: the lock layer — typed lock-busy error, the rich busy message, --break-lock handling, the partial-result envelope (performSync itself stays in the façade). sync-reconcile.ts: full-sync reconcile planning (the mass-delete valve and ever-committed gate) + sync deadline/stall resolution. sync-status-report.ts: the per-source sync status report backing gbrain sources status and the get_status_snapshot op.

• src/core/storage.ts — Pluggable storage interface (S3, Supabase Storage, local).

• src/core/storage-config.ts — Storage tiering: loadStorageConfig reads gbrain.yml, normalizes deprecated keys (git_tracked/supabase_only) to canonical (db_tracked/db_only) with once-per-process deprecation warning, and runs normalizeAndValidateStorageConfig (auto-fixes missing trailing /, throws StorageConfigError on tier overlap). Path-segment matcher: media/x/ does NOT match media/xerox/foo. Uses a dedicated parser for the gbrain.yml shape rather than gray-matter (broken on delimiter-less YAML). Also carries DERIVE_PHASE_DB_ONLY_DEFAULTS (life/events/, atoms/, extracts/, dream-cycle-summaries/) + effectiveDbOnlyDirs — the engine's derive-phase output prefixes treated as implicitly-declared db_only by the undeclared_db_only_pages doctor check but deliberately NOT merged into loadStorageConfig (a global merge would auto-gitignore those dirs and silently kill ingestion for brains that file-back them, the #2788 class) — and findDbOnlyCollisions (pure collector-output vs db_only overlap detector shared by the db_only_collector_collision doctor check and sync's manageGitignore warning). Pinned by test/storage-config.test.ts + test/doctor-silent-death-checks.test.ts.

• src/core/disk-walk.ts — walkBrainRepo(repoPath) returns Map<slug, {size, mtimeMs}> from one recursive readdirSync. Skips dot-dirs, node_modules, non-.md files. Used by gbrain storage status to replace per-page existsSync + statSync (~400K syscalls on 200K-page brains → tens).

• src/core/git-head.ts — local git HEAD freshness probe for gbrain doctor. isSourceUnchangedSinceSync(localPath, lastCommit, opts?) returns true iff localPath is a git repo whose current HEAD matches lastCommit; when opts.requireCleanWorkingTree is true also requires a clean working tree (mirrors gbrain sync's force-walk gate at sync.ts:1075 so doctor and sync agree on "is there work to do?"). requireCleanWorkingTree is boolean | 'ignore-untracked' — in 'ignore-untracked' mode the clean probe runs git status --porcelain --untracked-files=no so a quiet repo with stray untracked dirs (?? companies/, ?? media/) is still "unchanged" (sync's incremental path keys off the commit diff and never imports untracked files); GitCleanProbe gains an ignoreUntracked? second arg. Two probe seams (_setGitHeadProbeForTests, _setGitCleanProbeForTests) keep unit tests R2-compliant (no mock.module). Uses execFileSync with array args so shell metachars in local_path cannot escape to a shell (the regression test runs real execFileSync against '/nonexistent/$(touch <sentinel>)/repo' and asserts the sentinel is never created). Fail-open on every error (missing path, not a git repo, git not installed, timeout, NULL inputs, dirty-probe errored → false) preserving the caller's prior time-based behavior. The chunker-version-match check lives in the caller (doctor.ts) because it depends on engine state (sources.chunker_version vs CHUNKER_VERSION from src/core/chunkers/code.ts). Pinned by test/core/git-head.test.ts (incl. the shell-injection regression guard).

• src/core/source-health.ts — per-source health metrics for gbrain sources status + doctor's federation_health. Commit-relative staleness: newestCommitMs(localPath) = HEAD committer time via git log -1 --format=%ct (fail-open null; NO working-tree mtime parsing — committed content only, robust against the porcelain-mtime bug farm); pure lagFromContentMs(contentMs|null, lastSyncMs|null, nowMs) = remote/column comparator (null lastSync → null; negative wall-clock → skew passthrough; contentMs <= lastSync → 0; else/null-content → wall-clock). computeAllSourceMetrics(engine, sources, {probeContent?}): LOCAL (probeContent:true, gbrain sources status) → isSourceUnchangedSinceSync(..., {requireCleanWorkingTree:'ignore-untracked'}) ? 0 : wall-clock (live commit-hash catches HEAD moving to an old-dated commit a timestamp compare would miss); REMOTE (default, federation_health on the HTTP MCP path) → lagFromContentMs(row.newest_content_at, ...), NO git subprocess (trust boundary). commitTimeMs(localPath, sha) is the newestCommitMs sibling pinned to an arbitrary commit (committer time via git show -s --format=%ct <sha>, fail-open null, execFileSync array args) — the resumable sync stamps newest_content_at against its pinned target commit, not whatever HEAD raced to. Pinned by test/source-health.test.ts.

• src/core/npm-squat-check.ts — classifies gbrain PATH entries as real, foreign npm package, broken, or unknown for doctor's npm_squat check. On Windows it normalizes Git Bash/MSYS drive paths (/c/... → C:/...) and tries the native .exe suffix before reporting a broken entry; non-Windows classification keeps the original single-candidate behavior. Pinned by test/npm-squat-check.test.ts.

• src/core/git-remote.ts — SSRF-hardened git invocations for remote-source cloneRepo, pullRepo, and fetchRemote(repoPath, branch) (the last added for the sync cost-estimator's fetch-first path, #2139, so a cost preview / dry-run fetches through the same hardened flags + GIT_TERMINAL_PROMPT=0 as real sync rather than a less-protected route). Exports two distinct flag constants because git's argv grammar treats them differently: GIT_SSRF_FLAGS (3 -c config flags — protocol.allow=user, protocol.file.allow=never, http.allowRedirects=false) is global config, spread BEFORE the subcommand verb; GIT_SSRF_SUBCOMMAND_FLAGS = ['--no-recurse-submodules'] is subcommand-scoped, spread AFTER the verb (a combined array would spread --no-recurse-submodules before the verb where real git rejects it exit 129). cloneRepo argv: git <GIT_SSRF_FLAGS> clone <GIT_SSRF_SUBCOMMAND_FLAGS> --depth=1 [--branch X] -- <url> <dir>. pullRepo argv: git <GIT_SSRF_FLAGS> -C <dir> pull <GIT_SSRF_SUBCOMMAND_FLAGS> --ff-only. Pinned by test/git-remote.test.ts position-anchored regression guard (argv.indexOf('--no-recurse-submodules') > argv.indexOf(verb)). Also exports the durability-side helpers that power gbrain sources harden/pull: GIT_ENV_AUTH (the no-prompt env minus the askpass /bin/false overrides, so an auth'd push/fetch can consult the repo's configured credential helper while GIT_TERMINAL_PROMPT=0 still fails fast on a missing credential), divergenceSafePull(repoPath, branch) (fetch + pull --rebase; returns skipped_dirty on a dirty tree, conflict_aborted on a rebase conflict after rebase --abort so the tree is never left mid-rebase, else up_to_date/advanced), detectDefaultBranch (origin/HEAD → current branch → main), pushProbe(repoPath, branch) (authenticated push --dry-run that proves push access and classifies auth/protected/unreachable), and isWorkingTreeDirty. These auth'd paths route their protocol.file.allow through GBRAIN_GIT_ALLOW_FILE_TRANSPORT (default never; set =1 for self-hosted filesystem remotes), unlike clone/pull which stay strict.

• src/core/brain-repo-durability.ts + src/commands/sources-harden.ts — brain-repo git durability. hardenBrainRepo(opts) makes a brain's working tree durable, idempotently: divergence-safe pull, a LOCAL untracked .git/hooks/post-commit auto-push safety net (never committed — a pulled commit can't rewrite executed code next to the token; installed into the active core.hooksPath dir and excluded via .git/info/exclude when that dir is tracked), a committed scripts/brain-commit-push.sh that refuses to exit 0 without a confirmed push and stages+commits BEFORE any pull so a dirty tree of modified pages (the write-through shape) can still be committed — the push-retry's rebase-on-reject handles a remote that advanced (#2426; hook + helper render from ONE bash push-retry template — DRY at the TS source, not by the hook sourcing a repo-controlled script), durability rules patched into the active resolver file (findResolverFile → RESOLVER.md > AGENTS.md; taxonomy rendered from the bundled _brain-filing-rules.json), a minimal DB-free pull cron (launchd/crontab running gbrain sources pull --path <dir> so it never opens the PGLite single-writer lock), and a push-probe verify (no heartbeat commit). Credential is REPO-scoped (acceptPat from --pat-file/GBRAIN_GITHUB_PAT, warns on loose perms; reuses an existing repo-local credential.helper, else a 0600 store wired via repo-local config); the token is redacted everywhere via redactSecretsInText and never enters the repo, remote URL, logs, or DurabilityReport. unhardenBrainRepo removes the cron/hook/credential wiring (ownership-fingerprinted); sources remove runs it only AFTER the source row's DELETE commits (a refused or raced delete leaves the scaffolding intact; post-commit teardown failure is loud but non-fatal). CLI: gbrain sources harden <id|--all> / pull <id>|--path <dir> / unharden <id>; auto-harden fires on sources add --url ... --pat-file for managed clones (--no-harden opts out). sources pull --path is dispatched in src/cli.ts BEFORE connectEngine so the cron stays DB-free. CLI-only (writes executables + an OS cron + a credential helper on the host); never exposed over MCP. Tests: test/brain-repo-durability.serial.test.ts, test/git-remote-durable.serial.test.ts, test/brain-durability-hook.serial.test.ts, test/durability-cron.test.ts.

• src/commands/storage.ts — gbrain storage status [--repo P] [--json]. Split into pure data (getStorageStatus) + JSON formatter + human formatter (ASCII-only) matching the orphans.ts pattern. PageCountsByTier and DiskUsageByTier are distinct nominal types so swaps fail at compile time.

• gbrain.yml (brain repo root) — Optional storage tiering config. Top-level storage: section with db_tracked: and db_only: array-valued keys. gbrain sync auto-manages .gitignore for db_only paths on successful sync (skips on dry-run, blocked-by-failures, submodule context, or GBRAIN_NO_GITIGNORE=1). gbrain export --restore-only [--repo P] [--type T] [--slug-prefix S] repopulates missing db_only files from the database.

• src/core/supabase-admin.ts — Supabase admin API (project discovery, pgvector check).

• src/core/file-resolver.ts — File resolution with fallback chain (local -> .redirect.yaml -> .redirect -> .supabase).

• src/core/chunkers/ — 3-tier chunking (recursive, semantic, LLM-guided). code.ts is a tree-sitter-based semantic chunker for 30 languages (plus SQL via DerekStride/tree-sitter-sql) with embedded-asset WASMs (src/assets/wasm/), @dqbd/tiktoken cl100k_base tokenizer, small-sibling merging. CHUNKER_VERSION is folded into importCodeFile's content_hash so chunker shape changes force clean re-chunks across releases. extractSymbolName has an inline SQL branch (extractSqlSymbolName) diving through DerekStride's statement wrapper into the inner DDL child (create_table/create_function/create_view/create_index/create_procedure/create_type/create_schema/create_database/create_trigger/alter_table/alter_view) and extracting the target identifier via the name field with identifier-shaped fallback; DML kinds (select/insert/update/delete/merge/with) deliberately return null so chunks emit unnamed (code-def is a DDL signal). normalizeSymbolType has parallel SQL branches mapping create_table → 'table', create_view → 'view', etc. src/commands/code-def.ts:DEF_TYPES is extended with 'table' | 'view' | 'index' | 'procedure' | 'schema' | 'database' | 'trigger' so the new chunks surface in gbrain code-def <name> queries.

• src/core/errors.ts — StructuredAgentError + buildError + serializeError. Every agent-facing surface (code-def, code-refs, usage errors) uses this envelope; matches the CycleReport.PhaseResult.error shape.

• src/assets/wasm/ — 37 tree-sitter grammar WASMs + tree-sitter runtime. Committed to the repo so bun --compile embeds them deterministically via import path from ... with { type: 'file' }. The CI guard scripts/check-wasm-embedded.sh fails the build if the compiled binary ever silently falls through to recursive chunks. tree-sitter-sql.wasm (DerekStride/tree-sitter-sql @ c2e1e08db1ea20dc23bdb8d228a81a8756e9c450, built with tree-sitter-cli@v0.26.3 --abi 14) adds SQL coverage at 11 MB — larger than peers because the grammar covers PostgreSQL + MySQL + SQLite + T-SQL basics (40 MB generated parser.c); the compiled binary grows ~6%.

• src/commands/code-def.ts + src/commands/code-refs.ts — symbol definition + references lookup. Query content_chunks.symbol_name or chunk_text ILIKE with page_kind='code' filter. Auto-JSON when stdout is not a TTY (gh-CLI convention). Bypass the standard searchKeyword DISTINCT ON (slug) collapse so multiple call-sites from the same file surface. The JSON envelope (CLI + the code_def/code_refs MCP ops) carries status + ready from src/core/code-graph-readiness.ts so a count:0 result is distinguishable as not_built (no code indexed) vs ready (genuinely no match); human output prints a one-line hint when not ready.

• src/core/code-graph-readiness.ts — typed readiness signal shared by the four code-* surfaces (code-def/code-refs/code-callers/code-callees). resolveCodeReadiness(engine, {kind:'symbol'|'edge', count, sourceId?, allSources?}) returns {status:'not_built'|'indexing'|'ready'|'unknown', ready, has_code, pending_edges}. count>0 short-circuits to ready with no query; on empty it runs EXISTS probes against content_chunks JOIN pages (page_kind='code') — no page_kind index needed, and the pending probe rides the partial idx_content_chunks_edges_backfill. kind:'symbol' (code-def/refs) is 2-state + brain-wide because symbol metadata is set at chunk time; kind:'edge' (code-callers/callees) is 3-state + source-scoped, with the pending predicate mirroring the resolver (edges_backfilled_at IS NULL OR < EDGE_EXTRACTOR_VERSION_TS from src/core/chunkers/symbol-resolver.ts) so a resolver-version bump never falsely reports ready. Probe scope matches each command's result-query deleted_at posture (def/refs don't filter deleted_at, so neither do the probes). Any DB error returns status:'unknown' (fail-open; never breaks the command). readinessHint(r) renders the human one-liner. Wired into code-def.ts/code-refs.ts (brain-wide), code-callers.ts/code-callees.ts (resolved sourceId/allSources), and all four code_* MCP op handlers in src/core/operations.ts. Pinned by test/code-graph-readiness.test.ts + readiness-envelope cases in test/e2e/code-intel-mcp-ops-pglite.test.ts.

• src/core/search/ — Hybrid search: vector + keyword + RRF + multi-query expansion + dedup. searchKeyword/searchKeywordChunks/searchVector apply source-aware ranking at the SQL layer (curated content like originals/, concepts/, writing/ outranks bulk content like <fork>/chat/, daily/, media/x/). searchVector uses a two-stage CTE so source-boost re-ranking doesn't kill the HNSW index. Hard-exclude prefixes (test/, archive/, attachments/, .raw/ by default) filter at retrieval, not post-rank. Both gates honor detail !== 'high' so temporal queries surface chat pages normally.

• src/core/search/query-intent.ts — Deterministic query classifiers (pure, no LLM): classifyQuery/classifyQueryIntent (entity/temporal/event/concept/general → auto-selects detail level, salience/recency/modality axes; concept fires on definitional-paraphrase OR landscape/quantifier cues with a proper-noun name-guard — capitalized names, quoted phrases, slugs, and sub-3-word queries never trigger — and ranks vector-lean via the RRF-k tilt in intent-weights.ts), isAmbiguousModalityQuery (LLM-escalation gate), and the #2416 concept-shape pair — looksConceptShaped (fuzzy-quantifier/landscape cues minus exact-identifier anti-signals, tuned to favor false-negatives; cues owned by other routers like "who are the"/find_experts and bare "anything"/salience are deliberately excluded) + conceptNudge (full one-line CLI hint string steering a concept-shaped search toward query; consumed by maybePrintConceptNudge in src/cli.ts on BOTH the local-engine and thin-client result paths, stderr-only, --quiet-gated). Pinned by test/query-intent-concept.test.ts + test/cli-concept-nudge.test.ts.

• src/core/search/llm-intent.ts — opt-in LLM modality tie-break. classifyModalityWithLLM(query, fallback) routes through gateway.chat() with a fixed single-word-output system prompt; 1s timeout via AbortController. parseModality(raw, fallback) is the pure parser (tolerates trailing punctuation + casing). Fail-open on every error (gateway unavailable, timeout, parse failure, unrecognized output) — returns the fallback so a misbehaving LLM can never break search. Cost-bounded by isAmbiguousModalityQuery in query-intent.ts so the LLM call fires on only a small fraction of queries when on.

• src/core/search/image-loader.ts — loadImageInput(input, opts) accepts a local path, data: URI, or http(s):// URL. Magic-byte sniff for PNG/JPEG/WebP. Hard size cap (default 10 MB, configurable via search.image_query.max_bytes). URLs route through fetchWithSSRFGuard so DNS rebinding + redirect chains are defeated; pre-flight Content-Length check + post-fetch size guard for lying servers. ImageLoadError with discriminated code (INVALID_FORMAT / OVERSIZED / INVALID_URL / FETCH_FAILED / TIMEOUT / SSRF_BLOCKED / NOT_FOUND).

• src/core/search/by-image.ts — searchByImage(engine, input, opts). Always runs the image branch (embedQueryMultimodalImage + searchVector(embedding_image)). Hybrid intersect: when the caller provides an optional query, runs a parallel text branch via embedQueryMultimodal(query) and merges via rrfFusionWeighted with effectiveRrfK(baseRrfK, weight) from the resolved mode's refinement weights. Widens to the unified column when search.unified_multimodal=true (transparently upgrades retrieval quality post-reindex).

• src/core/ssrf-validate.ts — DNS-rebinding-defended URL validation. validateAndResolveUrl(url) resolves the hostname via dns.lookup({all: true, family: 0}), checks EVERY A and AAAA record against the internal-IP deny list, and returns the resolved IP so callers fetch by IP (validation IP === fetch IP defeats DNS rebinding). fetchWithSSRFGuard(url, opts) does redirect-aware fetching with per-hop re-validation (max 3 hops by default). Reusable across all URL-fetching features. Test seam __setDnsLookupForTests for hermetic tests.

• src/core/spend-log.ts — per-OAuth-client paid-API spend tracking against the mcp_spend_log table. checkBudget(engine, clientId, capCents) is the pre-flight gate; throws BudgetExceededError when today's spend has hit the cap. recordSpend(engine, entry) is best-effort post-call. UTC day-aligned aggregation so caps roll over deterministically regardless of server timezone. Local CLI callers (no clientId) bypass the gate; brains without the table fail open to spend=0. VOYAGE_MULTIMODAL_3_PER_IMAGE_CENTS = 0.12 cents per image embed.

• src/commands/reindex-multimodal.ts — gbrain reindex --multimodal [--limit N] [--dry-run] [--cost-estimate] [--no-embed] [--yes] [--json]. Walks content_chunks WHERE embedding_multimodal IS NULL, batches via embedMultimodalSafe (partial-failure-aware), persists. Lock via tryAcquireDbLock (360min) so a concurrent autopilot embed phase can't race it. Cost prompt + Ctrl-C grace window in TTY. GBRAIN_NO_REEMBED=1 bypass. Checkpoint at ~/.gbrain/reindex-multimodal-checkpoint.json for resume. Auto-flip prompt at coverage=100% completion (TTY: interactive; non-TTY: stderr hint with a paste-ready command).

• src/core/backfill-registry.ts — registry of idempotent data backfills. The modality backfill flips modality to 'image' on image-asset chunks the ingest path missed; its SQL filter requires chunk_source='image_asset' AND embedding_image IS NOT NULL AND (modality IS NULL OR modality != 'image') — the chunk_source guard ensures a non-image chunk that happens to have embedding_image populated is never flagged. A second run finds zero rows.

• src/core/search/eval.ts — Retrieval eval harness: P@k, R@k, MRR, nDCG@k metrics + runEval() orchestrator.

• src/core/search/source-boost.ts — Source-type boost map keyed by slug prefix. DEFAULT_SOURCE_BOOSTS (originals/ 1.5, concepts/ 1.3, writing/ 1.4, people/companies/deals/ 1.2, daily/ 0.8, media/x/ 0.7, <fork>/chat/ 0.5, archive/ 0.5, extracts/ 0.3) and DEFAULT_HARD_EXCLUDES (test/, attachments/, .raw/). archive/ is DEMOTED (findable, ranked below curated), not hard-excluded — archive holds high-signal history users expect to retrieve; the demote is a prior at the SQL/fusion layer and the cross-encoder reranker can still promote a strongly-matching archive page. parseSourceBoostEnv/parseHardExcludesEnv parse comma-separated prefix:factor pairs from GBRAIN_SOURCE_BOOST/GBRAIN_SEARCH_EXCLUDE. resolveBoostMap and resolveHardExcludes merge defaults + env + caller SearchOpts.exclude_slug_prefixes/include_slug_prefixes. The surviving exclude policy is auditable via the hidden_by_search_policy doctor check (src/commands/doctor.ts, local + remote paths) which counts chunked pages withheld per active exclude prefix, reusing resolveHardExcludes + buildVisibilityClause + the exported escapeLikePattern.

• src/core/search/sql-ranking.ts — Pure SQL string builders. buildSourceFactorCase(slugColumn, boostMap, detail) emits a CASE with longest-prefix-match wins (returns literal '1.0' when detail === 'high' for temporal-bypass parity with COMPILED_TRUTH_BOOST). buildHardExcludeClause(slugColumn, prefixes) emits NOT (col LIKE 'p1%' OR col LIKE 'p2%') — OR-chain wrapped in NOT, NOT NOT LIKE ALL/ANY (those quantifiers don't express set-exclusion). LIKE meta-character escape covers all three of %, _, AND \ (backslash is Postgres LIKE's default escape char). Single-quote doubling on SQL string literals so injection-style inputs are inert text. buildBestPerPagePoolCte(...) is the shared per-page max-pool CTE both engines' searchVector inject — instead of returning the single best chunk per page from an inner ORDER BY embedding <=> vec LIMIT N (which let a page lose to a neighbor on ONE weak chunk while its strong chunk sat just below the inner cut), the CTE pools the BEST chunk score per (source_id, slug) composite key so a page surfaces on its strongest evidence; composite key (not bare slug) keeps multi-source brains correct; single source of truth so the two engines can't drift.

• src/core/search/title-match.ts — pure, zero-I/O title-phrase matcher shared by the production title boost AND NamedThingBench (no drift). isTitlePhraseMatch(query, title) returns true when the normalized query is a contiguous token run inside the title with >= MIN_CONTENT_TOKENS=2 non-stopword tokens, OR an exact full-title match (covers deliberate 1-word chosen names like "Helios"). Token-boundary matching (never raw substring, so "art" doesn't match "Bartholomew"); small conservative English stopword set excluded from the content-token floor (guards against promoting generic pages on stopword-y queries); NFKC normalize so CJK / width variants converge. Exports tokenizeTitle + __test__ internals.

• src/core/search/alias-normalize.ts — ONE normalizer shared by the WRITE path (ingest projects frontmatter aliases: into page_aliases) and the READ path (search matches query against page_aliases), so stored aliases can't silently fail to match queries via divergent normalization (same single-source posture as cjk.ts). normalizeAlias(raw) does NFKC + lowercase + whitespace-collapse + trim + strip one layer of wrapping quotes/brackets; returns '' for empty (callers MUST skip empty aliases). normalizeAliasList(value) coerces a frontmatter scalar / array / comma-list / garbage into a deduped list of normalized non-empty aliases — used by both the ingest projection and the reindex --aliases backfill.

• src/core/search/evidence.ts — the agent-facing why-it-matched contract (closes the root behavior where an agent read one blended score, decided "no strong match, safe to create", and wrote a duplicate over a fully-developed page). classifyEvidence(r, opts?) names the strongest signal (precedence: alias_hit > exact_title_match > high_vector_match (real query↔chunk cosine SearchResult.cosine ≥ DEFAULT_HIGH_COSINE_FLOOR=0.8, overridable via EvidenceOpts.cosineFloor / config search.evidence_cosine_floor — never the blended score, so a keyword+boost pile-up can't earn the label; keyless/hermetic runs have no cosine and degrade to keyword-based labels; legacy HIGH_MATCH_FLOOR=0.85 stays exported for back-compat only) > keyword_exact (base ≥ SOLID_MATCH_FLOOR=0.6) > weak_semantic). createSafetyFor(evidence) derives the don't-duplicate hint (exists/probable/unknown) the agent keys off INSTEAD of a raw threshold (a blended RRF/cosine score is not a calibrated probability). stampEvidence(results, opts?) stamps evidence + create_safety in place once at pipeline end (after the alias hop, before slice); idempotent.

• src/commands/search-diagnose.ts — gbrain search diagnose "<query>" --target <slug> [--json] [--source <id>]: Phase-0 retrieval diagnostic. Traces WHERE a target page surfaces (or fails to) across keyword / vector (per-page max-pool) / alias / hybrid layers and names the layer responsible for an incident, so an operator can pin whether the fix is max-pool/innerLimit (vector) vs title/alias. The verdict names the layer that DOES surface the target (or "none"). Pinned by test/search/search-diagnose.test.ts.

• src/commands/reindex-aliases.ts — gbrain reindex --aliases [--limit N] [--dry-run] [--json] [--source <id>]: backfills the free-text alias layer for EXISTING pages whose frontmatter aliases: predate the alias table (the import-time projection covers new + changed pages). Reads each page's frontmatter aliases:, writes via engine.setPageAliases. Idempotent + convergent (setPageAliases replaces a page's alias set) so no op-checkpoint needed; walks listAllPageRefs (cheap cross-source enumeration), --source narrows. Pinned by test/search/reindex-aliases.test.ts.

• src/eval/retrieval-quality/harness.ts + src/commands/eval-retrieval-quality.ts + test/fixtures/retrieval-quality/namedthing.jsonl — NamedThingBench, the retrieval-quality eval that makes the named-thing-miss incident impossible to reintroduce silently. Seven query families, each a distinct failure class: title-substring (the direct regression), generic-to-named (tourist label → named thing), alias-synonym (declared alias / romanization → canonical), multi-chunk-dilution (one strong chunk among many weak — stresses max-pool), short-vs-rich, graph-relationship (guardrail), hard-negative (precision guard, must NOT return a page). gbrain eval retrieval-quality <fixture.jsonl> runs it with hard gates (e.g. title-substring Hit@1 ≥ 0.95, alias Hit@1 ≥ 0.98, multi-chunk-dilution Hit@3 = 1.0). Pure: caller injects a SearchFn (CLI uses hybridSearch, tests stub) so it's engine-agnostic. Metric glossary entries (hit@1/hit@3) added to src/core/eval/metric-glossary.ts. Pinned by test/eval-retrieval-quality.test.ts + test/retrieval-quality-harness.test.ts.

• docs/architecture/RETRIEVAL.md + docs/architecture/RETRIEVAL_MAXPOOL_INCIDENT.md — retrieval-pipeline architecture reference + the named-thing-miss incident write-up (root cause, the five-layer fix, the eval that pins it).

• src/eval/brainbench/ + src/commands/eval-brainbench.ts — BrainBench, the cross-harness memory conformance suite (gbrain eval brainbench; methodology in docs/eval/BRAINBENCH.md). types.ts carries the PUBLISHED interchange shapes (fixture/gold/result/baseline — mirrored as JSON Schemas in evals/brainbench/schema/; breaking changes bump the schema versions). fixtures.ts: strict loader/validator + corpus fixtures_hash (covers fixture AND gold files); a gold key inside a fixture turn is a validation error — gold is SEALED in the gold dir and adapters only ever see sanitized PublicTurns. seed.ts: fail-fast hermetic seeding (importFromContent noEmbed + NULL-embedding insertFact; any non-imported status ⇒ SeedError ⇒ fixture seed_failed ⇒ run exit 2). adapters/shared.ts: ONE runReflexPipeline all three adapters drive with declarative config (pointer budget, suppression mode) — cross-harness comparability is structural; openclaw.ts (seam production, the shipped pipeline), claude-code.ts (seam production; drives the shipped gbrain hook user-prompt path end-to-end — fixture turns become UserPromptSubmit stdin JSON, synthesized Claude Code JSONL transcripts feed the real window parse + cross-turn dedupe, and resolution rides a run-scoped resolve-IPC server with the real shared secret; bench-pinned deviations disclosed in docs/eval/BRAINBENCH.md: generous userPromptDeadlineMs, push-failure banner suppressed), codex.ts (seam contract; static entity-index preamble whose slugs deliberately don't count as injections + ≤1 per-turn fragment; fixture conversations round-trip through the real rollout format + the shipped parser src/core/transcripts/codex.ts for turn selection — fragment DELIVERY remains harness-shaped until a shipped codex injection path lands). metrics/: know-to-ask (+false-fire anti-gaming companion), push (micro-averaged P/R), write-back (drives the PRODUCTION conversation→facts pipeline via the injectable-extractor seam; gold extractor in CI, real extractor under --llm), continuity (writer→reader pairs on a shared brain through DIFFERENT adapters; pointer-injection OR stored-fact keyword probe). harness.ts: ONE in-memory PGLite per run + resetTables between fixtures (longmemeval engine-sharing pattern); read-only suites share one seeding across all adapters; emits per-(harness×suite) cells + re-scoreable turn rows; source_isolation_violations counted per turn and gated at zero. scoreboard.ts: markdown render, canonical diff-stable committed baseline (4-decimal rounding, sorted keys, receipts excluded), compareBaselines with main-baseline governance — same-hash count-aware gate vs corpus-bless mode (the committed baseline must byte-match the run; regressions vs main require a justification). The CLI brings its own PGLite (cli.ts routes before connectEngine), writes --out as the canonical CI artifact, and terminates via an explicit grace-tick process.exit(verdict) (0 pass / 1 regression / 2 error) because PGLite stomps process.exitCode and Bun discards queued stdout on exit. runBrainBenchCore() is the in-process entry eval run-all uses (one record per sweep, EvalRunRecord schema_version 3, mode: 'n/a'). Pinned by test/brainbench-*.test.ts + test/eval-brainbench-e2e.test.ts.

• evals/brainbench/ — the committed BrainBench corpus: 141 fixtures (135 generated + 6 hand-authored spike) / 241 gold-annotated turns across 7 categories (kta-pos/kta-neg/push/write-back/continuity/multi-source/adversarial), ~15% holdout (excluded from the CI gate, scored in published --include-holdout runs). generator/gen.ts rebuilds the corpus byte-identically (Mulberry32, seed 42; whole-cloth fictional universe from curated synthetic name pools so scenario privacy is structural; prose is template-synthesized with PRNG-selected variants — deliberately no LLM pass, difficulty stays controlled; several know-to-ask variants intentionally exercise documented v1 reflex limits so the baseline measures the roadmap). gold/ is sealed; schema/ is the foreign-runner contract (gbrain-evals drives the suite as a subprocess via --fixtures DIR --gold DIR --json --out FILE); baselines/main.json is the committed gate baseline; _ledger.json records counts/seed/rebuild command. CI: the .github/workflows/test.yml brainbench job + scripts/ci-brainbench-gate.sh (fetches MAIN's baseline via git show origin/master:… — a PR cannot rewrite what it's compared against; first-landing path runs ungated) + scripts/render-brainbench-delta.ts (compact step-summary/PR-body delta block from the --out artifact). Privacy: scripts/check-synthetic-corpus-privacy.sh scans evals/brainbench/{fixtures,gold} in bun run verify.

• src/core/types.ts extension + src/core/operations.ts:search + src/core/import-file.ts + src/cli.ts + src/core/search/telemetry.ts — the wiring layer for the retrieval cathedral. SearchResult gains evidence, create_safety, title_match_boost, alias_hit (all optional; evidence/create_safety reference the union types in evidence.ts). The search MCP op uses a cheap-hybrid path by default and accepts a per-call mode (conservative|balanced|tokenmax) honored ONLY for trusted/local callers (resolvePerCallMode(ctx, ...) — remote callers use the configured mode so a remote provider can't force tokenmax spend); every search path stamps evidence fail-soft. importFromContent projects frontmatter aliases: into page_aliases via normalizeAliasList + engine.setPageAliases so new + changed pages register aliases at ingest. src/cli.ts adds the gbrain search diagnose dispatch (lazy import) and reconciles the search CLI path with the cheap-hybrid op. src/core/search/telemetry.ts extends the rollup with the rank-1 base_score drift signal (sum/count + 3 coarse buckets, aggregate not per-query), surfaced via gbrain search stats, backed by migration v111's search_telemetry columns. Tests: test/cli-search-dispatch.test.ts, test/search/per-call-mode.test.ts, test/search/telemetry-rank1.test.ts, test/search/title-boost-stage.test.ts, test/search/alias-hop.test.ts, test/search/evidence.test.ts, test/search/searchvector-maxpool.test.ts, test/search/pre-migration-failopen.test.ts.

• src/commands/eval.ts — gbrain eval command: single-run table + A/B config comparison. Sub-subcommand dispatch on args[0] routes gbrain eval export + gbrain eval prune + gbrain eval replay into session-capture handlers; bare gbrain eval --qrels … fall-through preserves the legacy IR-metrics flow. gbrain eval cross-modal is in the dispatch (the user-facing path is the cli.ts no-DB branch — src/commands/eval.ts:cross-modal only fires when callers re-enter with an existing engine).

• src/commands/eval-cross-modal.ts — multi-model quality gate. Three different-provider frontier models score the OUTPUT against the TASK on a 5-dim list. Verdict pass (exit 0) / fail (exit 1) / inconclusive (exit 2; <2/3 model successes). Reuses src/core/ai/gateway.ts:chat() so config/auth/aliasing comes from the gateway recipe registry — no parallel provider stack. Self-configures the gateway (configureGateway(loadConfig() + process.env)) since the cli.ts dispatch bypasses connectEngine(). Default cycles 3 in TTY, 1 in non-TTY (partial cost guardrail) via the shared resolveCycleDefault(explicit, isTty) in src/core/eval/cycle-default.ts; the cost-estimate banner appends cycleDefaultSuffix(...) (for 1 cycle(s) (non-interactive default; --cycles N for more)) when the value is the silent non-TTY fallback, so the 1-vs-3 difference isn't hidden. Receipts land at gbrainPath('eval-receipts')/<slug>-<sha8-of-output>.json. --batch <jsonl> [--limit N] [--concurrent N] [--max-usd FLOAT] [--yes] fans out cross-modal scoring across a LongMemEval-shape JSONL; mutually exclusive with --task (fail-fast usage error if both set); filters kind: "by_type_summary" rows; pre-flight cost estimate refuses if > --max-usd without --yes (default cap 5.00 USD). Semaphore-bounded fan-out via inline runWithLimit<T>(items, limit, fn) (exported for unit tests): max N questions in-flight × 3 model slots = ceiling of 3N parallel API calls (default --concurrent 3 → 9). Per-question receipts land in a per-batch tempdir and are deleted at end of run; the summary receipt inlines per-question verdicts as JSON, not file paths. Exit precedence (batch-level policy, NOT inherited from aggregate.ts): ERROR > FAIL > INCONCLUSIVE > PASS. DI seam: runEvalCrossModal(args, opts?: {runEval?: typeof runEval}) mirrors runEvalLongMemEval(args, {client?}); tests pass opts.runEval to bypass real LLM calls AND the gateway availability check. Pinned by test/eval-cross-modal-batch.test.ts.

• src/core/eval/cycle-default.ts — single source of truth for the eval cycle-count default. Exports DEFAULT_CYCLES_TTY = 3, DEFAULT_CYCLES_NONTTY = 1, resolveCycleDefault(explicit, isTty): {cycles, usedNonTtyDefault}, and cycleDefaultSuffix(r) (returns (non-interactive default; --cycles N for more) only when the non-TTY default was applied, else ''). Consumed by eval-cross-modal.ts, eval-takes-quality.ts (run + regress), and takes-quality-eval/runner.ts (core uses only the constant — library stays TTY-agnostic; the CLI owns the TTY=3 upgrade + banner annotation). eval-suspected-contradictions.ts applies the same transparency to its $5/$1 budget default via a budgetUsdExplicit flag (the budget is overwritten in-place so explicitness can't be inferred post-hoc). Not shared with resolveWorkersWithClamp (different domain, no engine, no dedup). Pinned by test/eval/cycle-default.test.ts, test/eval-suspected-contradictions-budget-default.test.ts.

• src/core/cross-modal-eval/json-repair.ts — parseModelJSON(raw) named export with a 4-strategy fallback chain (direct parse → fence-strip → trailing-comma + single-quote + embedded-newline repair → regex nuclear option). Adversarial input throws rather than fabricating scores — the aggregator treats a throw as "this model contributed nothing this cycle" so the gate stays correct at >=2/3 successes.

• src/core/cross-modal-eval/aggregate.ts — pure verdict logic. Pass criterion: (successes >= 2) AND (every dim mean >= 7) AND (every dim min across models >= 5). Inconclusive when <2/3 models returned parseable scores (regression guard for the v1 Object.values({}).every(...) === true empty-array PASS bug).

• src/core/cross-modal-eval/runner.ts — orchestrator. Each cycle runs Promise.allSettled([gwChat(slotA), gwChat(slotB), gwChat(slotC)]) (bare allSettled, no rate-leases for the CLI path). Stops early on PASS or INCONCLUSIVE; runs up to 3 cycles. Default slots: openai:gpt-5.2 / anthropic:claude-opus-4-7 / deepseek:deepseek-v4-pro. estimateCost() prices via the canonical model-pricing table; test/cross-modal-default-slots.test.ts pins recipe support, pricing coverage, and three distinct providers.

• src/core/cross-modal-eval/receipt-name.ts — receipt filename binds (slug, SKILL.md sha-8). findReceiptForSkill(skillPath, receiptDir) returns 'found' | 'stale' | 'missing'. Skillify-check surfaces the status as informational; the audit does NOT fail on missing/stale receipts.

• src/core/cross-modal-eval/receipt-write.ts — wraps fs.writeFileSync with mkdirSync({recursive:true}) ahead of every write (gbrainPath() does NOT auto-mkdir).

• src/commands/eval-export.ts — streams eval_candidates rows as NDJSON to stdout with schema_version: 1 prefix on every line. EPIPE-safe, progress heartbeats on stderr, stable id-desc tiebreaker so --since windows never dupe/miss rows.

• src/commands/eval-prune.ts — explicit retention cleanup. Requires --older-than DUR. --dry-run reports would-delete count.

• src/commands/eval-replay.ts — contributor-facing replay tool. Reads NDJSON from gbrain eval export, re-runs each captured query / search op against the current brain, computes set-Jaccard@k between captured + current retrieved_slugs, top-1 stability rate, and latency Δ. Stable JSON shape (schema_version: 1) for CI gating; human mode prints a regression table. Pure Bun, zero new deps. The dev-loop half of BrainBench-Real. See docs/eval-bench.md. parseNdjson skips lines where _kind === 'baseline_metadata' so gbrain bench publish baselines parse cleanly without the metadata header polluting row counts. Exports replayCore(engine, opts): Promise<{summary, results}> + ReplaySummary type so gbrain eval gate calls replay in-process (NOT subprocess — avoids gbrain-version-drift for source-tree CI). CLI runEvalReplay wraps replayCore.

• src/core/bench/baseline-file.ts + src/core/bench/qrels-file.ts + src/core/bench/correctness-gate.ts + src/commands/bench-publish.ts + src/commands/eval-gate.ts — the eval-loop wave. gbrain bench publish --from <captured.ndjson> --to <X.baseline.ndjson> writes a baseline (stamps stable query_hash per row; metadata header carries _kind: 'baseline_metadata' + thresholds + source_hash + baseline_mean_latency_ms; deterministic sort by (tool_name, query_hash); strict: empty=fail, dupes=fail with paste-ready hint, --to exists=refuse without --force). gbrain eval gate [--baseline X] [--qrels Y] is the two-gate dispatcher (regression gate via in-process replayCore, correctness gate via bare hybridSearch for determinism, both must pass when both flags set, exit 0 PASS / 1 FAIL / 2 USAGE). Source-id-aware: bench publish dedup key is (tool_name, source_ids, query_hash); qrels compare keys are ${source_id}::${slug} everywhere (closes the multi-source bug class at the file-shape layer). Latency math: (baseline + delta) / baseline <= multiplier. Fail-closed: ANY in-process throw flips verdict to fail with named breach in breaches[] — never silently exit 0. .qrels.json preserves the 12-row test/fixtures/eval-baselines/qrels-search.json fixture (slug-only relevant_slugs + first_relevant_slug auto-promote to source_id='default') AND supports the federated shape (explicit relevant: [{source_id, slug}] + expected_top1). correctness-gate.ts runs each qrels query via bare hybridSearch; per-query throw recorded as errored: true and flagged as gate failure. Audit JSONL at ~/.gbrain/audit/bench-publish-YYYY-Www.jsonl. Hermetic mode: --embedder deterministic (correctness gate ONLY — rejected with --baseline, requires --qrels) embeds each query as the qrels fixture's basis vector via src/eval/deterministic-embed.ts (basisEmbedding unit vectors; FNV-1a-derived fallback dim for off-fixture query texts) and threads it into bare hybridSearch through the queryEmbedFn seam — no API keys, no network; bare hybridSearch neither reads nor writes the semantic query cache (both live in hybridSearchCached), so deterministic runs cannot poison cached production results. scripts/run-eval-canary.ts (check:eval-canary, wired into bun run verify + CI) is the hermetic CLI retrieval canary built on it: boots a throwaway PGLite brain under a temp GBRAIN_HOME, seeds the qrels fixture corpus (the expected-top1 page carries its query text in timeline too — page-grain FTS indexes title(A) + timeline(C) only, compiled_truth is deliberately unindexed), spawns the REAL CLI with engine-reroute/provider env stripped, and asserts exit 0 + metric floors; --record additionally appends an EvalRunRecord-shaped line to .gbrain-evals/eval-results.jsonl. Honest scope: the canary gates the hybrid ranking pipeline (keyword/title/alias arms + RRF against gold qrels) with synthetic vectors — semantic-embedding regressions remain the keyed eval suites' job. Pinned by test/bench/baseline-file.test.ts, test/bench/qrels-file.test.ts, test/bench/correctness-gate.test.ts, test/bench-publish.test.ts, test/eval-gate.test.ts, test/eval-canary.test.ts, test/eval-replay-metadata-skip.test.ts, test/cycle/nightly-probe-adapters.test.ts, test/autopilot-nightly-probe-wiring.test.ts, test/e2e/eval-loop.test.ts.

• src/core/cycle/nightly-probe-adapters.ts — bridges the autopilot's object-shape NightlyProbeDeps to the argv-shape runEvalLongMemEval + runEvalCrossModal CLI functions. Cross-modal adapter argv MUST include --output summaryPath (without it the summary lands at the default receipt path and the adapter reads nothing from summaryPath). In-process invocation (NOT subprocess) — avoids gbrain-version-drift for source-tree CI. Pinned by test/cycle/nightly-probe-adapters.test.ts (incl. argv-shape regression for the --output requirement).

• test/eval-replay-gate.test.ts + test/fixtures/eval-baselines/qrels-search.json — hermetic retrieval qrels gate running in the standard PR unit-shard CI matrix (.github/workflows/test.yml, NOT the fixed-file E2E workflow). Uses the canonical PGLite block (test-isolation R3+R4) and the basis-vector embedding pattern from test/e2e/search-quality.test.ts:23-28 for fully hermetic retrieval. The qrels fixture (12 queries) uses PLACEHOLDER names only (alice-example, widget-co-example, etc. — privacy rule) and embeds each query at a deterministic basis dimension so retrieval is reproducible. Each query lists relevant_slugs[] + first_relevant_slug; the test computes top1_match_rate (top-1 == first_relevant) and recall@10 (fraction of relevant_slugs in top-10), asserting both meet floors (defaults >= 0.80 and >= 0.85). Env-overridable floors GBRAIN_REPLAY_GATE_TOP1_FLOOR / GBRAIN_REPLAY_GATE_RECALL_FLOOR (via withEnv() per R1). Refresh discipline: when ranking changes intentionally move expected slugs, edit qrels-search.json directly with a Why: line in the commit body or the gate degrades to rubber-stamp. Pinned by test/eval-replay-gate.test.ts (incl. a privacy-grep regression guard against real-name reintroduction).

• src/core/cycle/nightly-quality-probe.ts + src/core/audit-quality-probe.ts + test/fixtures/longmemeval-nightly.jsonl + test/nightly-quality-probe.test.ts — opt-in nightly cross-modal quality probe. The phase runs gbrain eval longmemeval --by-type against the committed 10-question placeholder fixture, pipes output through gbrain eval cross-modal --batch --max-usd 5 --yes, and writes one event per run to ~/.gbrain/audit/quality-probe-YYYY-Www.jsonl (ISO-week-rotated, mirrors audit-slug-fallback.ts; honors GBRAIN_AUDIT_DIR). Default DISABLED — opt-in via gbrain config set autopilot.nightly_quality_probe.enabled true (prevents surprise API spend). 24h rate limit (pure shouldRunNightly(now, recentEvents, windowMs?)) skips with audit row outcome: rate_limited. Embedding-key short-circuit: longmemeval needs gateway.embedQuery(), so the phase exits early with outcome: no_embedding_key + stderr warn when no provider configured. Full DI surface via NightlyProbeDeps (isEnabled, hasEmbeddingProvider, resolveMaxUsd, resolveRepoRoot, runLongMemEval, runCrossModalBatch, now) so the unit test stubs every external effect. Cost ceiling: $5/run × 30 nights ≈ $150/month worst-case; expected ~$10.50/month. New nightly_quality_probe_health doctor check (src/commands/doctor.ts, right after slug_fallback_audit) reads last 7 days: SKIPPED when flag off (with enable command); OK when enabled + all PASS; WARN on any FAIL / ERROR / BUDGET_EXCEEDED with per-outcome counts. Pinned by test/nightly-quality-probe.test.ts.

• src/commands/eval-trajectory.ts + src/commands/founder-scorecard.ts + src/core/trajectory.ts — temporal trajectory + founder scorecard. gbrain eval trajectory <entity> shows the chronological typed-claim history (mrr/arr/team_size/etc) with regressions auto-flagged inline; gbrain founder scorecard <entity> rolls up claim_accuracy / consistency / growth_trajectory / red_flags into one JSON. Pure-function math in trajectory.ts: detectRegressions(points, threshold) walks consecutive metric-value pairs per metric (10% drop default, env override GBRAIN_TRAJECTORY_REGRESSION_THRESHOLD); computeDriftScore(points) returns 1 - mean(cosine(emb[i], emb[i-1])) over existing embeddings (null when <3 embedded points). Backed by BrainEngine.findTrajectory(opts) — both Postgres and PGLite, single SQL query, deterministic ORDER BY valid_from ASC, id ASC. Source-scoped via the sourceId scalar / sourceIds array dual pattern; visibility-filtered for remote callers. MCP op find_trajectory (read scope, NOT localOnly) registered after find_experts. Migration v67 adds optional typed-claim columns (claim_metric, claim_value, claim_unit, claim_period) + a partial index on (entity_slug, claim_metric, valid_from) WHERE claim_metric IS NOT NULL. Fence widens from 10 to 14 cells when any row has typed data; renderer stays at 10 cells when none do (no churn diff on existing fences). Metric labels normalize to lowercase snake_case via normalizeMetricLabel (15-entry seed map). The consolidate cycle phase does semantic upsert keyed on (page_id, claim, since_date) (fixes the duplicate-takes bug where re-running the cycle after extract_facts cleared consolidated_at appended duplicates via MAX(row_num)+1) and writes chronological valid_until on each cluster's older facts. The extract_facts cycle phase batch-embeds via gateway.embed() before insert AND threads pages.effective_date as the pageEffectiveDate fallback for valid_from (precedence: fence-row > pageEffectiveDate > now()). The contradiction probe MUST NOT write valid_until — grep guard at test/eval-contradictions/no-valid-until-write.test.ts. Haiku extraction lives in src/core/facts/extract.ts (not the extract-facts.ts cycle phase); its output cap is config facts.extraction_max_tokens (default 4000), a stopReason: 'length' response retries once at 2× the cap, and persistent truncation warns loudly on stderr instead of silently extracting zero facts. Mixed extractor arrays salvage valid candidates and warn with the dropped malformed count; all-malformed output still fails retryably, while an explicitly empty facts array remains a successful empty result. pageEffectiveDate is OPTIONAL because fence-write.ts callers have no Page object. Migration v89 adds a nullable event_type TEXT column on facts so the substrate carries event-shaped rows (event_type='meeting' / 'job_change' / 'location_change') alongside metric rows. TrajectoryPoint.event_type: string | null projected by both engines. TrajectoryOpts.kind?: 'metric' | 'event' | 'all' filter (default 'all'); founder-scorecard + eval-trajectory pass kind: 'metric' explicitly. Back-compat pinned by test/regressions/v0_40_2_0-trajectory-backcompat.test.ts (byte-identical computeFounderScorecard + computeTrajectoryStats with and without event rows); engine parity in test/engine-parity-event-type.test.ts.

• src/core/trajectory-format.ts — shared formatTrajectoryBlock(points, entitySlug, opts) consumed by both gbrain think (production) and the LongMemEval harness (benchmark). Groups by (metric ?? event_type), per-metric cap 20, total cap 100, knowledge_update intent annotates value-change rows with (superseded prior). Emits a <trajectory entity="..."> XML envelope — INJECTION_PATTERNS in src/core/think/sanitize.ts escapes </trajectory>, <trajectory ...> open tags, and attribute injection so adversarial fact text can't break out. Pinned by test/trajectory-format.test.ts.

• src/core/think/intent.ts + src/core/think/entity-extract.ts — pure classifyIntent(question) returns 'temporal' | 'knowledge_update' | 'other' (regex-first, no LLM, 'other' fast path short-circuits with zero SQL). extractCandidateEntities(question, retrievedSlugs) pulls high-precision candidates from retrieved entity-prefix slugs (people/, companies/, organizations/) and medium-precision noun phrases. Stop-word boundaries + leading-verb stripper handle "When did I last meet Marco" → marco. Both consumed by runThink and the LongMemEval harness so the two paths cannot drift. Pinned by test/think-intent.test.ts and test/think-entity-extract.test.ts.

• src/commands/eval-suspected-contradictions.ts + src/core/eval-contradictions/{judge,runner,types,date-filter,cost-tracker,cache,severity-classify,cross-source,trends,calibration,judge-errors,auto-supersession,fixture-redact}.ts — gbrain eval suspected-contradictions [run|trend|review]. Probe samples top-K retrieval pairs per query (cross-slug + intra-page chunk-vs-take), date pre-filters (3-rule layered — same-paragraph-dual-date overrides separation rule), LLM judge (query-conditioned; UTF-8-safe truncation; confidence-floor double-enforcement; resolution_kind output drives paste-ready commands), persistent cache keyed on (chunk_a_hash, chunk_b_hash, model_id, prompt_version, truncation_policy) (prompt edits cleanly invalidate prior verdicts), Wilson 95% CI calibration on the headline percentage with small_sample_note when n<30, judge_errors as first-class typed counters (parse_fail/refusal/timeout/http_5xx/unknown — avoids bias from silent skip), trend writes to eval_contradictions_runs, source-tier breakdown reuses DEFAULT_SOURCE_BOOSTS prefix logic, deterministic sampling (combined_score DESC + lex tiebreaker for stable cache hit-rate). Hermetic via judgeFn + searchFn DI in the runner; never touches the real gateway in tests. Engine surface: BrainEngine.listActiveTakesForPages (batched), writeContradictionsRun + loadContradictionsTrend, getContradictionCacheEntry + putContradictionCacheEntry + sweepContradictionCache. Schema migrations v51 + v52. MCP op find_contradictions (read scope, NOT localOnly, NOT in subagent allowlist — user-initiated only). Doctor check surfaces high-severity findings with paste-ready resolution commands; synthesize phase pre-fetches the latest probe's top-5-by-severity findings and threads them into buildSynthesisPrompt as an informational block. Architecture doc: docs/contradictions.md.

• src/core/think/index.ts — runThink builds its internal LLMClient via a small adapter wrapping gateway.chat() from src/core/ai/gateway.ts (not new Anthropic() directly) so stdio MCP launches (Claude Desktop, Cursor) that don't inherit shell env still find a key set via gbrain config set anthropic_api_key (the gateway reads ~/.gbrain/config.json AND env). Test seam: opts.client?: ThinkLLMClient injection works (test/think-pipeline.serial.test.ts, test/think-gateway-adapter.test.ts); opts.stubResponse short-circuits before any LLM call. When neither key nor client is available, the "no LLM available" stub fires with NO_ANTHROPIC_API_KEY. Trajectory injection (default ON): runThink orchestrates classifyIntent(question) → extractCandidateEntities(question, retrievedSlugs) → findTrajectory (5s Promise.race timeout per candidate, concurrency cap 3) → formatTrajectoryBlock. buildThinkUserMessage (in src/core/think/prompt.ts) has a trajectory?: ThinkTrajectoryBlockOpts slot honoring BOTH prompt orderings (calibration mode: retrieval → calibration → trajectory → question; default mode: question → retrieval → trajectory → instruction). The MCP think op handler maps sourceScopeOpts(ctx) onto RunThinkOpts via thinkSourceScopeOpts(ctx) (operations.ts), and runThink threads the scope into runGather (src/core/think/gather.ts) — so every gather stream (hybrid retrieval, takes keyword + vector via the engines' scoped searchTakes/searchTakesVector, graph walk via traversePaths) AND trajectory resolution stay within the caller's source grant (federated sourceIds[] wins over scalar sourceId); pinned by test/e2e/think-source-isolation-pglite.test.ts. Config key think.trajectory_enabled (default true). Any error in the trajectory path degrades to "no block injected" + TRAJECTORY_INJECTION_FAILED warning — the think call never crashes from trajectory. Production path skips fallback_slugify resolutions (avoid querying invented slugs); the LongMemEval harness accepts them. Pinned by test/think-trajectory-injection.test.ts. Debug: GBRAIN_THINK_DEBUG=1 gbrain think "..." prints the spliced prompt to stderr.

• src/commands/eval-longmemeval.ts + src/eval/longmemeval/{harness,adapter,sanitize}.ts — gbrain eval longmemeval <dataset.jsonl> runs the public LongMemEval benchmark against gbrain's hybrid retrieval. One in-memory PGLite per run via createBenchmarkBrain + withBenchmarkBrain (NO EphemeralBrain class). Between questions, TRUNCATE over runtime-enumerated pg_tables (schema-migration-safe); infrastructure tables (sources, config, gbrain_cycle_locks, subagent_rate_leases) preserved. cli.ts pre-dispatch bypass so eval longmemeval skips connectEngine() — the user's ~/.gbrain brain is never opened. --expansion defaults OFF (deterministic, no per-query Haiku); pass --expansion to opt in. Default model via resolveModel() 6-tier chain with models.eval.longmemeval config key. Sanitization parity: harness.ts reuses INJECTION_PATTERNS from src/core/think/sanitize.ts so adding a pattern covers takes AND benchmarks. Retrieved chat content wrapped in <chat_session id="..." date="...">; the answer-gen system prompt declares content UNTRUSTED. LLM injection seam: runEvalLongMemEval(args, {client?: ThinkLLMClient}) lets tests stub the client without an API key. p50 25.9ms / p99 30.3ms warm reset+import+search on Apple Silicon (test/eval-longmemeval.test.ts perf gate). Hand the JSONL to LongMemEval's evaluate_qa.py to score (not bundled — needs OpenAI gpt-4o). Per-question JSONL row carries question: string (additive; evaluate_qa.py ignores unknown fields) so gbrain eval cross-modal --batch has the task text without joining; also question_type: string and recall_hit?: boolean so a --resume-from run rebuilds cumulative recallByType from the file alone. --by-type flag emits a {schema_version:1, kind:"by_type_summary", recall_by_type:{...}, aggregate:{...}} line as the FINAL line; resume-replace strips any prior summary at the tail so 5 resumed runs produce 1 summary. Empty-bucket guard: aggregate.rate is null (not NaN) when no questions had ground truth. Optional --by-type-floor F (0..1) exits non-zero with a stderr line per breached question_type (default informational). Pure buildByTypeSummary(buckets) + emitByTypeSummary(path, summary) + seedRecallByTypeFromFile(path, bucket) exported for unit tests. Inline Haiku extractor + trajectory routing (methodology change): src/eval/longmemeval/extract.ts runs extractAndInsertClaims() over each haystack session before retrieval, populating the benchmark brain's facts table inline at import. Single Haiku call per session with content-hash cache (cuts a 3-iteration run from $1.50 to $0.50 when sessions repeat). Per-question alias map (fresh per question, never leaks) collapses "Marco" + "Marco Smith" + "marco" to one canonical slug via first-mention-wins. Fail-open on every error path (malformed JSON, Haiku throw, insert collision, empty array → inserted: 0). getCacheStats() writes empirical hit rate to stderr. src/eval/longmemeval/intent.ts prefers the dataset's question_type label before falling back to the SHARED regex set from src/core/think/intent.ts — single source of truth means think and longmemeval cannot drift. runOneQuestion routes temporal/knowledge_update intents through shared extractCandidateEntities → findTrajectory → splice into the answer-gen prompt before the retrieved-sessions block. --no-trajectory bypasses BOTH extractor and intent routing (baseline default-on vs no-trajectory across 3 seeds with paired-bootstrap CI). JSON envelope adds 5 per-question fields when trajectory routing is on: intent, trajectory_points, entity_resolved, resolution_source, methodology_note. The methodology_note writes to stderr at run completion (extractor=haiku-preprocess-full-haystack-v1) — honest disclosure that the published number is "gbrain + Haiku-preprocess pipeline" vs "gbrain alone", NOT directly comparable to baseline LongMemEval scores without that note. Pinned by test/longmemeval-extract.test.ts, test/longmemeval-intent.test.ts, test/longmemeval-trajectory-routing.test.ts (end-to-end through runEvalLongMemEval with both clients stubbed).

• docs/eval-bench.md — contributor guide for using captured data to benchmark retrieval changes before merging. Linked from CONTRIBUTING.md under "Running real-world eval benchmarks (touching retrieval code)".

• src/core/eval-capture.ts — op-layer capture wrapper called from src/core/operations.ts query + search handlers (catches MCP + CLI + subagent tool-bridge from one site). Fire-and-forget; failures route to engine.logEvalCaptureFailure so gbrain doctor sees drops cross-process. Capture is off by default — isEvalCaptureEnabled resolution: explicit config.eval.capture (true/false) wins, else process.env.GBRAIN_CONTRIBUTOR_MODE === '1', else off. Contributors set export GBRAIN_CONTRIBUTOR_MODE=1. PII scrubber gate is independent and defaults to true regardless of CONTRIBUTOR_MODE.

• src/core/eval-capture-scrub.ts — zero-deps PII scrubber: emails, phones, SSN, Luhn-verified credit cards, JWT-shaped tokens, bearer tokens.

• src/core/search/hybrid.ts — Cathedral II Promise<SearchResult[]> return shape. onMeta?: (m: HybridSearchMeta) => void callback so op-layer capture records what hybridSearch actually did; existing callers leave it undefined. HybridSearchOpts.queryEmbedFn?: (text) => Float32Array | Promise<Float32Array> is the hermetic eval seam: when set, the TEXT vector arm's query embedding comes from this function instead of the gateway's query-embed path AND the no-embedding-provider keyword-only short-circuit is bypassed, so deterministic eval canaries (gbrain eval gate --embedder deterministic, scripts/run-eval-canary.ts) run the vector arm with no provider key; never set on production paths — absent, behavior is byte-for-byte unchanged, and bare hybridSearch never touches the semantic query cache so the seam can't poison query_cache. HybridSearchOpts.types?: PageType[] (on SearchOpts) threads a multi-type filter into per-engine searchKeyword + searchVector + searchKeywordChunks as AND p.type = ANY($N::text[]) (primary consumer gbrain whoknows, filters to ['person','company']); AND-applies alongside the single-value type filter. hybridSearch resolves the embedding column at the boundary via resolveColumn(loadRegistry(cfg), opts.embedding_column, cfg) from src/core/search/embedding-column.ts, threads the ResolvedColumn descriptor (not a raw string) into per-engine searchVector, and uses isCacheSafe(resolved, cfg) for the cache-skip decision so a repointed embedding builtin doesn't leak across vector spaces. cosineReScore calls engine.getEmbeddingsByChunkIds(ids, resolved.name) so rerank uses vectors from the active column, not the hardcoded OpenAI embedding, and hydrates each result's raw query↔chunk cosine onto SearchResult (the calibrated signal evidence and --explain consume). SearchOpts.onVectorPoolMeta is the engines' out-channel for searchVector's bounded pagination escalation (one dense page filling the inner candidate pool escalates the pool ×4 up to 3 times; HNSW-backed columns additionally cap at the ef_search ceiling, while exact-scan columns above the index dim ceiling are bounded by the escalation count alone); hybrid passes the collector and owns the emit, fired when the loop ends with the pre-DISTINCT pool still full — at the substrate cap or after the escalation budget. The query MCP op accepts embedding_column for per-call A/B; search (keyword-only) rejects it. Two post-fusion stages + evidence stamp: applyTitleBoost(results, query, titleBoost, floorThreshold) multiplies a result's score by the resolved title_boost when isTitlePhraseMatch fires, stamps title_match_boost, inherits the floor-ratio gate so a title match can't shove a much-stronger page below it; applyAliasHop(engine, results, query, opts) normalizes the query, calls engine.resolveAliases, and on exact normalized-alias match surfaces that page at top-of-organic + epsilon with alias_hit=true; stampEvidence(...) runs LAST (after the alias hop, before slice) on every path — keyword-only, no-embed, and full hybrid — so MCP callers and --explain read the same evidence + create_safety contract. title_boost resolved from the mode bundle and threaded in. runPostFusionStages has a 4th stage (graphSignalsEnabled, onGraphMeta, onScoreDistribution). base_score stamped at function entry idempotently (captured ONCE before any boost stage mutates score). Each post-fusion stage stamps its multiplier: applyBacklinkBoost→backlink_boost, applySalienceBoost→salience_boost, applyRecencyBoost→recency_boost. applyReranker (earlier in the pipeline) stamps reranker_delta as a rank delta (positive = improved). applyExactMatchBoost in src/core/search/intent-weights.ts stamps exact_match_boost when fired. Per-stage attribution powers gbrain search --explain — every boost surface carries its own field so formatResultsExplain reads them all without coupling to internal stage ordering. with src/core/search/sql-ranking.ts + src/core/operations.ts + src/core/types.ts: agent-warning channel. SearchResult.content_flag?: {reason, detail} (new optional field in types.ts) is stamped post-fusion by stampContentFlags (the stampEvidence precedent) in hybridSearch AND in the keyword-only search MCP op so both retrieval paths surface the marker. get_page returns a top-level content_flag parallel field via getContentFlag(page.frontmatter). buildVisibilityClause (sql-ranking.ts) ANDs in QUARANTINE_FILTER_FRAGMENT so quarantined pages are excluded from all six search call sites (alongside soft-delete + archived-source filters). Pinned by test/sql-ranking.test.ts + test/e2e/quarantine-search-exclusion.test.ts. Cross-modal routing at the embed step: effectiveModality resolves per-call opts.crossModal (literal 'auto' → undefined) → suggestions.suggestedModality → 'text'. Image route: embedQueryMultimodal + searchVector({embeddingColumn: 'embedding_image'}), skipping expansion + keyword. 'both' route: parallel text + image vector searches merged via rrfFusionWeighted with effectiveRrfK(baseRrfK, weight) from the configured cross-modal weights. Unified routing fires when search.unified_multimodal is true — bypasses dual-column branching, runs embedQueryMultimodal + searchVector({embeddingColumn: 'embedding_multimodal'}), fail-open on zero rows (non-strict falls through to dual-column). LLM modality escalation fires only when no explicit per-call opt is set AND the regex returned 'text' AND search.cross_modal.llm_intent is on AND isAmbiguousModalityQuery fires; fail-open on every error.

• docs/eval-capture.md — stable NDJSON schema reference for gbrain-evals consumers.

• test/public-exports.test.ts — runtime contract test (R2). Imports each of the 17 public subpaths via package name and pins a canary symbol per module. Paired with scripts/check-exports-count.sh.

• src/core/embedding.ts — OpenAI text-embedding-3-large, batch, retry, backoff. BATCH_SIZE=100 (per-recipe pre-split + recursive halving + adaptive shrink-on-miss live in the gateway; the outer paginator is for progress-callback granularity, not batch protection). estimateEmbeddingCostUsd(tokens) prices against the currently-configured model's rate via currentEmbeddingPricePerMTok() (resolves the per-1M-token rate via lookupEmbeddingPrice(gatewayGetModel()) from embedding-pricing.ts, falling back to the OpenAI 3-large rate 0.13 only when the gateway is unconfigured or the model is unknown to the pricing table). EMBEDDING_COST_PER_1K_TOKENS retained for back-compat with direct importers/tests. currentEmbeddingSignature(): string returns the embedding-provenance signature <provider:model>:<dims> (e.g. openai:text-embedding-3-large:1536) stamped onto pages.embedding_signature at every embed-write site; DELIBERATELY excludes the chunker version (tracked separately via pages.chunker_version) — this signature is strictly the EMBEDDING space, so a model OR dimension swap makes the stored signature differ from current and a page becomes stale. Same unconfigured-gateway fallback as the cost helpers. (See src/core/sync-delta.ts + src/core/spend-posture.ts for the #2139 cost-gate supporting modules.) willEmbedSynchronously({v2Enabled, serialFlag, noEmbed}): SyncEmbedMode is the single source of truth for whether gbrain sync --all embeds at sync time ('inline') or defers to per-source embed-backfill minion jobs ('deferred') — mirrors sync.ts's effectiveNoEmbed resolution exactly (v2Enabled && !serialFlag && !noEmbed → deferred) so cost gate and embed decision can't drift. shouldBlockSync(costUsd, floorUsd, mode, posture='gated'): boolean is the pure cost-gate decision: blocks ONLY when mode === 'inline' && costUsd > floorUsd — deferred mode never blocks (the backfill's $X/source/24h cap is the real money gate), and posture === 'tokenmax' never blocks (the operator declared cost isn't the constraint; an off/unlimited floor is Infinity and so is never exceeded). Pinned by test/sync-cost-preview.test.ts + test/embedding-signature-stale.test.ts.

• src/core/sync-delta.ts — the single "what changed since last_commit" helper (#2139), consumed by BOTH performSyncInner (sync executor) and estimateInlineNewTokens (cost estimator) so the gate's dollar figure can't drift from what the sync imports. computeSyncDelta(repoPath, fromCommit, toCommit, {detachedManifest?, detached?}) → {status:'ok', manifest} | {status:'unavailable', reason:'anchor_missing'|'diff_failed'}. Anchor reachability via git cat-file -t (#1970 discipline — a gc'd bookmark is anchor_missing, but a present-but-non-ancestor bookmark is still diffed tree-to-tree), then git diff --name-status -M from..to parsed by buildSyncManifest; merges the detached working-tree manifest when detached (buildDetachedWorkingTreeManifest, relocated here from sync.ts). NO dirty/untracked probe — attached-HEAD incremental sync imports only the commit diff, so pricing dirty files would re-introduce phantom costs on a busy brain. execFileSync array-args (shell-injection safe), 30s / 100 MiB budget. Test seam _setGitRunnerForTests. Pinned by test/sync-delta.test.ts.

• src/core/spend-posture.ts — spend-control surface (#2139). resolveSpendPosture(engine): 'gated'|'tokenmax' (DB-plane spend.posture, fail-open gated); tokenmax makes every cost gate informational across sync/reindex/enrich/onboard (spend still ledgered — removes the ceiling, not the accounting). parseUsdLimit(raw, def, {allowZero?}) accepts off/unlimited/none → Infinity; formatUsdLimit(n) renders Infinity as the string 'unlimited' (never raw — JSON.stringify(Infinity) is null); usdLimitToCap(n) maps Infinity → undefined at the BudgetTracker boundary so ledger rows never serialize null. normalizeSpendPosture/isValidSpendPosture back the config set validation. Doc: docs/operations/spend-controls.md. Pinned by test/sync-cost-preview.test.ts + test/spend-off-switch.test.ts.

• src/core/ai/dims.ts — per-provider providerOptions resolver for embed-time dimension passthrough; the single source of truth for "which provider needs which knob to produce vector(N)". Exports dimsProviderOptions(implementation, modelId, dims) (called by embed() in gateway.ts), VOYAGE_OUTPUT_DIMENSION_MODELS (private const — the 7 hosted Voyage models that accept output_dimension: voyage-4-large, voyage-4, voyage-4-lite, voyage-3-large, voyage-3.5, voyage-3.5-lite, voyage-code-3 — nano deliberately excluded), VOYAGE_VALID_OUTPUT_DIMS = [256, 512, 1024, 2048] as const, supportsVoyageOutputDimension(modelId), isValidVoyageOutputDim(dims). Voyage path uses the SDK-supported dimensions field ({ openaiCompatible: { dimensions: N } }), NOT Voyage's output_dimension wire-key — the voyageCompatFetch shim in gateway.ts:541 translates dimensions → output_dimension before the HTTP body is built (the AI SDK's openai-compatible adapter doesn't recognize the wire-key, so sending it from here would be silently dropped and Voyage would return its default 1024-dim). Runtime guard: when a Voyage flexible-dim model is configured with dims outside VOYAGE_VALID_OUTPUT_DIMS, throws AIConfigError with a paste-ready gbrain config set embedding_dimensions <256|512|1024|2048> hint at the embed boundary (most common trigger: embedding_model: voyage:voyage-4-large without embedding_dimensions, falling back to DEFAULT_EMBEDDING_DIMENSIONS=1536, an OpenAI default not a Voyage one). Every lookup in this module folds through the private modelMatchKey (trim + lowercase, #4123) so cased hub-form ids (Qwen/Qwen3-Embedding-4B) match the all-lowercase tables — the folded key is a MATCH key only, never sent to a provider (wire model ids are case-sensitive; error messages keep the original id so they stay paste-ready); the Qwen3-Embedding native-width table lives at module scope alongside the other dim tables. Consequence, deliberate: a cased Voyage/ZeroEntropy/Perplexity config that used to skip validation (and silently produce wrong-width vectors) now matches and fails loudly at init when its dims is invalid.

• src/core/ai/types.ts — provider/recipe types. EmbeddingTouchpoint has optional chars_per_token (default 4, matching OpenAI tiktoken on English) and safety_factor (default 0.8, budget-utilization ceiling), both consulted only when max_batch_tokens is also set; Voyage declares chars_per_token=1 + safety_factor=0.5 to handle dense payloads (CJK/JSON/base64). Pre-split budget = max_batch_tokens × safety_factor / chars_per_token. EmbeddingTouchpoint.multimodal_models?: string[] model-level allow-list for recipes mixing text-only + multimodal models under one touchpoint (Voyage's 12 models share supports_multimodal: true but only voyage-multimodal-3 accepts /multimodalembeddings); when omitted, recipe-level supports_multimodal is sufficient. AIGatewayConfig.embedding_multimodal_model?: string lets embedMultimodal() route to a different model than embedding_model (OpenAI text + Voyage images without flipping the primary pipeline). EmbeddingTouchpoint.trust_custom_dims?: true — passthrough tier for a user-declared --embedding-dimensions on local / bring-your-own-backend recipes (ollama, llama-server, litellm) where the model catalog can't be enumerated; consumed by isCustomDimValidForProvider in src/core/embedding-dim-check.ts AFTER Tier 1 (recipe dims_options) and Tier 2 (provider Matryoshka allowlists), so a recipe that declares fixed options (openrouter) is still governed by those and fixed-dim hosted providers (openai/voyage/zeroentropy) stay fail-closed; the provider's /embeddings response-dim validation catches a genuine mismatch pre-storage. Recipe.default_headers?: Record<string, string> (static) and Recipe.resolveDefaultHeaders?(env) (env-templated) seam for per-recipe headers riding alongside auth on every openai-compat touchpoint; mutually exclusive (declaring both throws AIConfigError at gateway-configure time); keys conflicting with the resolved auth header (Authorization, the resolver's custom header) rejected at applyResolveAuth call time so defaults can't shadow auth. Used by OpenRouter for the HTTP-Referer + X-OpenRouter-Title + X-Title attribution triple.

• src/core/ai/defaults.ts — leaf module holding the embedding/reranker default constants (no gateway import, so schema + registry helpers can read them without loading provider SDKs). Split-default: NEW_INSTALL_DEFAULT_EMBEDDING_MODEL (voyage:voyage-4) + NEW_INSTALL_DEFAULT_EMBEDDING_DIMENSIONS (1024) feed every new-install surface — init auto-pick canonical tiebreak, the interactive picker default, the no-keys hint, keyless fresh-install schema sizing (passed as an explicit init param), and all recommendation copy (playbook, banners, doctor fix-hints, advisor). NEW_INSTALL_DEFAULT_RERANKER_MODEL (voyage:rerank-2.5) is written as explicit search.reranker.model config at init whenever a Voyage key is present on either plane (env or ~/.gbrain/config.json), regardless of which embedding provider was picked (init.ts:writeNewInstallRerankerDefault, shared by the PGLite + Postgres paths); keyed non-Voyage installs get explicit search.reranker.enabled false instead (never inherit the doomed legacy bundle fallback they have no key for), keyless installs get NO reranker write (the documented keyless-recovery re-init must find virgin reranker config so its override still lands), deliberate zeroentropyai:* installs are left on the legacy bundle, and an existing explicit reranker choice is never clobbered. Quoted by the migration playbook; the runtime reranker defaults (gateway DEFAULT_RERANKER_MODEL + the mode-bundle values) stay on zerank-2 until the September removal. DEFAULT_EMBEDDING_MODEL (zeroentropyai:zembed-1) + DEFAULT_EMBEDDING_DIMENSIONS (1280) serve ONLY as the configless runtime fallback for brains with no embedding_model in file config — their stored vectors live in ZE's 1280d space, so flipping the fallback under them would break retrieval before the provider dies; the September removal release deletes the fallback and hard-errors unmigrated configless brains with the migrate command. ZEROENTROPY_SUNSET_DATE ('2026-09-04') is the single source of truth for the upgrade banners, the provider_sunset doctor check, and the ZE recipe's sunset metadata.

• src/core/ai/gateway.ts — unified seam for every AI call. embedQuery(text, opts?) and isAvailable(touchpoint, modelOverride?) accept a model override so the resolved-column path embeds via the column's provider (Voyage / ZeroEntropy / OpenAI) instead of the global default; the hybrid path passes {embeddingModel: resolved.provider, dimensions: resolved.dimensions} and the gateway resolves the matching recipe via instantiateEmbedding(). isAvailable('embedding', 'voyage:voyage-3-large') checks the override's recipe (not the default) so hybrid skips vector search only when the active column's provider is actually down. zeroEntropyCompatFetch shim (sibling to voyageCompatFetch) handles ZE's non-OpenAI-compatible wire shape — rewrites the request URL /embeddings → /models/embed, injects input_type (default 'document'; the threaded 'query'|'document' crosses the SDK boundary via the module-level __embedInputTypeStore AsyncLocalStorage populated in embedSubBatch(), because the AI SDK's openai-compatible adapter strips input_type from providerOptions before building the wire body — #1400; voyageCompatFetch injects it opt-in the same way, and openAICompatAsymmetricFetch is the fallthrough shim for every other openai-compat recipe — llama-server/litellm/ollama — a strict pass-through when nothing was threaded) and explicit encoding_format: 'float', and rewrites the response {results: [{embedding}], usage: {total_bytes, total_tokens}} → {data: [{embedding, index}], usage: {prompt_tokens, total_tokens}} so the SDK's openai-compatible Zod schema validates. Layer 1 (Content-Length) + Layer 2 (per-embedding) OOM caps via tagged ZeroEntropyResponseTooLargeError (kept separate from VoyageResponseTooLargeError because test/voyage-response-cap.test.ts does structural source-text greps pinning the Voyage name). Wired in instantiateEmbedding() via the recipe.id === 'zeroentropyai' branch. gateway.rerank() native HTTP path (no AI-SDK reranking abstraction): resolves the configured reranker via getRerankerModel(), posts to the recipe's reranker path (touchpoints.reranker.path, default /models/rerank; Voyage declares /rerank) with bearer auth — the request's top-N key is recipe-pluggable via touchpoints.reranker.top_param (default top_n; Voyage top_k) — and returns RerankResult[] sorted by relevance. warnSunsetOnce(recipe, touchpoint): once-per-(recipe,touchpoint) stderr DEPRECATED warning for recipes carrying sunset metadata, fired on actual use (embedding resolution + the rerank path) so brains still riding a dying provider hear about it on every process, not only at upgrade time; prints the sunset date plus the migrate / search.reranker.model fix, never throws, _resetSunsetWarningsForTest() is the test seam. RerankError.reason classifier: auth | rate_limit | network | timeout | payload_too_large | unknown. 5s default timeout (search hot path). Pre-flight payload guard rejects bodies over recipe.touchpoints.reranker.max_payload_bytes with reason: 'payload_too_large'. _rerankTransport test seam mirrors _embedTransport. embedQuery(text) threads inputType: 'query' through dimsProviderOptions() (4-arg). getRerankerModel() accessor + isAvailable('reranker') branch; configureGateway + reconfigureGatewayWithEngine thread reranker_model; applyResolveAuth + defaultResolveAuth widen touchpoint param to include 'reranker'. embedMultimodalOpenAICompat() routes recipes with implementation: 'openai-compatible' (LiteLLM, Anyscale, vLLM, Gemini multimodal via proxy) through the standard /embeddings endpoint with content arrays carrying image_url entries; the Voyage /multimodalembeddings path is unchanged (gateway selects by recipe implementation tag). Runtime dimension validation throws AIConfigError (with model id + observed + expected) before the vector reaches storage when the provider returns a width that doesn't match the recipe's default_dims or the brain's embedding_dimensions. Pinned by test/openai-compat-multimodal.test.ts. Module-scoped _embedTransport defaults to AI SDK embedMany, with __setEmbedTransportForTests(fn) test seam so tests drive embed() with a stubbed transport. splitByTokenBudget and isTokenLimitError exported @internal (pure functions reused by the test file). Module-level _shrinkState: Map<recipeId, {factor, consecutiveSuccesses}> halves the recipe's effective safety_factor on token-limit miss (floor 0.05) and heals back ×1.5 after SHRINK_HEAL_AFTER=10 consecutive successes. configureGateway() walks every registered recipe at construction and emits a once-per-process stderr warning for any embedding touchpoint missing max_batch_tokens (excluding the canonical OpenAI fast-path). resetGateway() clears _shrinkState, the warned-set, and restores the real transport. embedMultimodal() reads cfg.embedding_multimodal_model first (falls back to cfg.embedding_model); after the recipe-level supports_multimodal fast-fail, validates the resolved model against touchpoint.multimodal_models when declared (closes the Voyage-text-only-into-multimodal-endpoint footgun before any HTTP call). getMultimodalModel() accessor mirrors getEmbeddingModel / getChatModel. Exported VoyageResponseTooLargeError tagged class: voyageCompatFetch's two OOM-defense caps (Layer 1 Content-Length, Layer 2 per-embedding base64) throw it; the inbound response-rewriter's try/catch (which swallows parse failures so misshaped responses fall through to the SDK parser) checks instanceof VoyageResponseTooLargeError and rethrows so the cap is actually effective (regression assertion in test/voyage-response-cap.test.ts pins the instanceof ⇒ throw err line). AI SDK v6 toolLoop compat (gbrain skillopt rollouts AND production background subagent jobs both route through chat() / toolLoop): in chat(), tool defs wrap the raw JSON Schema with the SDK's jsonSchema() helper (inputSchema: jsonSchema(t.inputSchema)) — v6's asSchema() treats a bare {jsonSchema: ...} object as a thunk and throws "schema is not a function"; new exported pure toModelMessages(messages: ChatMessage[]): unknown[] converts gbrain's provider-neutral ChatMessage[] into v6 ModelMessage[] — tool results (pushed by toolLoop as role:'user' with bare-value tool-result blocks) become a dedicated role:'tool' message with structured output:{type:'json'|'text'|'error-text', value} parts; null output preserved as {type:'json', value:null} (not dropped); text/tool-call blocks pass through with v6 field names (toolCallId/toolName/input); applied at the generateText call (messages: toModelMessages(opts.messages)). The converter is the load-bearing fix for the production subagent path, not just skillopt. Pinned by test/gateway-model-messages.test.ts. Companion fix in src/core/skillopt/rollout.ts: the inline paramsToSchema dropped items on array params; it now uses the shared paramDefToSchema from src/mcp/tool-defs.ts (single source of truth, recursive on items/enum/default). Provider-agnostic plumbing: resolveNativeBaseUrl(provider, cfg) normalizes a configured ANTHROPIC_BASE_URL / OPENAI_BASE_URL to carry the /v1 suffix and is passed explicitly at every native createAnthropic / createOpenAI site (chat/expansion/embedding), so an env-injected bare host doesn't 404; returns undefined when unset so the SDK default is preserved (Google deferred until its native suffix is verified). diagnoseEmbedding fails closed with user_provided_dims_unset when a user-provided / zero-default recipe (litellm/llama-server) has no configured embedding_dimensions — this REPLACED the old user_provided_model_unset guard, which was structurally unreachable (parseModelId throws on a bare provider) and only ever false-positived for litellm:<model>, silently disabling vector search. configureGateway no longer backfills embedding_dimensions (readers default it themselves), keeping the "no dims set" signal honest for that guard and the multimodal skip. withBudgetTracker: gateway-layer enforcement via AsyncLocalStorage<BudgetTracker>. withBudgetTracker(tracker, fn) installs the tracker on the module-internal store; every gateway.chat / embed / rerank call inside the scope auto-composes (reserve before, record in try/finally). Outside-scope calls are budget no-ops. Nested scopes restore the outer tracker on exit. getCurrentBudgetTracker() is the test seam. The chat path uses the pessimistic fallback on error paths; the embed path estimates input tokens from char count × recipe's chars_per_token because the AI SDK doesn't surface per-batch embed token usage; the rerank path estimates char count of query+docs. Pinned by 6 unit cases. reconfigureGatewayWithEngine(engine) (async, called from cli.ts after engine.connect(), before every command except CLI_ONLY no-DB commands) re-resolves expansion + chat defaults through resolveModel() so models.tier.* and models.default overrides apply to both. DEFAULT_CHAT_MODEL is anthropic:claude-sonnet-4-6. __setChatTransportForTests mirrors __setEmbedTransportForTests so tests drive chat() with a stubbed transport. toolLoop per-turn permit hook (#4194/CDX-7): optional acquireTurnPermit() acquires a provider permit before EVERY round-trip and releases in finally; a lease-full throw propagates without consuming the turn (the subagent path wires it to the rate leases with provider-derived keys — Anthropic models share anthropic:messages, others get <recipeId>:chat). ToolLoopStopReason includes 'length' (#4088): a zero-tool-call turn that hit the output cap propagates 'length' instead of folding into 'end', so truncation is never reported as a clean finish. Per-part provider state (#4201): ChatBlock variants carry optional providerMetadata captured from SDK parts in chat() and re-emitted as providerOptions on the rebuilt parts in toModelMessages() (attached only when present — metadata-free blocks stay byte-identical); this is the Gemini 3.x thoughtSignature echo. isThinkingByDefaultModel(modelStr) (exported, #4087) matches Claude 5-family ids behind any provider-prefix chain with a letters-only family segment (never claude-3-5-*) and drives defaultMaxOutputTokens's 32k thinking headroom; think/index.ts shares it. expand() and generateOcrText() also record on the ambient tracker (#4121 — they call generateObject/generateText directly and never pass through chat()'s _recordBudget, so their spend was previously invisible to every cap and ledger): record-only, no reserve — a breach surfaces on the NEXT reserving call, matching chat()'s swallow of BudgetExhausted from record(). Successes record normalized SDK usage via normalizeSdkUsage (the ONE home for the v6/legacy usage shapes, used by chat's success path too; first FINITE field wins so a NaN v6 field can't shadow a real legacy value or poison the running total); failures record pessimistically under gateway.expand.failed / gateway.ocr.failed (a rejected attempt still billed provider tokens — one expand() can legitimately produce two records when the structured-output attempt fails and the text fallback runs). A recipe whose declared structured-output support is rejected at call time is remembered for the process lifetime (_structuredOutputRejectedRecipes) so the rejected attempt isn't re-paid on every call. OCR's input estimate is prompt text + a fixed per-image token constant, never base64 length (bytes are not tokens). __setGenerateObjectTransportForTests mirrors the generateText seam. + test/core/budget/expand-records-budget.test.ts + test/ai/gateway-ocr-budget.test.ts

• src/core/ai/recipes/zeroentropyai.ts — ZeroEntropy openai-compatible recipe declaring BOTH embedding (zembed-1, 7 Matryoshka dims: 2560/1280/640/320/160/80/40) AND reranker (zerank-2 flagship + zerank-1 + zerank-1-small, 5MB payload cap) touchpoints. implementation: 'openai-compatible' (pinned by regression in test/ai/zeroentropy-recipe.test.ts). base_url_default: 'https://api.zeroentropy.dev/v1' already ends with /v1, so the zeroEntropyCompatFetch URL rewrite /embeddings → /models/embed produces …/v1/models/embed (NOT …/v1/v1/… — pinned by regression). chars_per_token: 1 + safety_factor: 0.5 match Voyage's dense-content hedge. Carries sunset metadata (ZEROENTROPY_SUNSET_DATE + replacement models from ai/defaults.ts) that drives init picker/auto-pick exclusion, the gateway's once-per-process warn-on-use, and every gbrain providers rendering via the shared sunsetMarker in src/commands/providers.ts (list status cell, ⚠ explain rows, and the env deprecation block that replaces the signup funnel); the recipe itself is deleted in the September removal release.

• src/core/ai/recipes/llama-server-reranker.ts — sibling of llama-server (the embedding recipe) for llama.cpp in --reranking mode. Distinct recipe rather than dual-touchpoint extension because --reranking and --embeddings are mutually exclusive at server-launch time, so the two backends need independent base URLs (default 8081 here vs 8080 there). Declares reranker touchpoint with models: [] (user-provided id matching the --alias the user launched with), path: '/rerank' (leaf-only; consumes RerankerTouchpoint.path override; gateway concatenates with base_url_default which ends in /v1, producing …/v1/rerank), default_timeout_ms: 30_000 (consumed by src/core/search/mode.ts's reranker timeout chain — CPU-only first-call warmup headroom; the 5s mode-bundle default would fail-open as timeout), cost_per_1m_tokens_usd: 0 (recognized by FREE_LOCAL_RERANK_PROVIDERS in src/core/budget/budget-tracker.ts so --max-cost callers don't hard-fail on local rerank). Setup hint emphasizes --alias because llama-server's /v1/models defaults model id to the gguf file path without it. Covers Qwen3-Reranker via llama.cpp AND self-hosted ZE weights via llama.cpp — same recipe, different --model at launch. Pinned by test/ai/recipe-llama-server-reranker.test.ts. Voyage / Cohere / vLLM rerankers stay out of scope (different wire shapes). Same wave adds: path?: string + default_timeout_ms?: number on RerankerTouchpoint in src/core/ai/types.ts; consumed by the URL build at src/core/ai/gateway.ts:rerank() and by mode-resolution at src/core/search/mode.ts:resolveSearchMode (precedence: per-call > config-key > recipe touchpoint default > mode bundle); LLAMA_SERVER_RERANKER_BASE_URL env passthrough in src/cli.ts:buildGatewayConfig; FREE_LOCAL_RERANK_PROVIDERS set in src/core/budget/budget-tracker.ts:lookupPricing (rerank-kind-only zero-pricing for the local provider prefix); doctor-fix at src/commands/models.ts:probeRerankerConfig reads search.reranker.model via loadSearchModeConfig + resolveSearchMode (closes file-plane / DB-plane divergence where doctor said "not configured" while live search was actively reranking — the field-plane getRerankerModel() read nothing writes); probeRerankerReachability reads the recipe's default_timeout_ms so CPU-only cold-start doesn't false-fail.

• src/core/ai/recipes/openrouter.ts — OpenRouter openai-compatible recipe: single key, many providers via openrouter:<provider>/<model> strings. base_url_default: 'https://openrouter.ai/api/v1'. Embedding touchpoint: default model openai/text-embedding-3-small; per-model model_dims carries verified native widths (text-embedding-3-small 1536, text-embedding-3-large 3072, qwen/qwen3-embedding-8b 4096, bge-m3 + baai/bge-m3 1024) with default_dims: 0 so an UNLISTED proxied id has NO silent default — it errors until the user supplies explicit dims (--embedding-dimensions / embedding_dimensions), which trust_custom_dims: true accepts (#4114; gemini-embedding-2-preview is deliberately unlisted — width unverified). Matryoshka dims_options: [512, 768, 1024, 1536] still governs the default model's shrink steps; max_batch_tokens: 300_000 = OpenAI's aggregate-per-request token cap (NOT per-input). Chat touchpoint declares 8 curated entry points (gpt-5.2, gpt-5.2-chat, gpt-5.5, claude-haiku-4.5, claude-sonnet-4.6, claude-opus-4.7, gemini-3-flash-preview, deepseek-chat) but openai-compat tier accepts any model ID; deliberately no max_context_tokens because OR's catalog spans 128K to 1M+. supports_subagent_loop: false is INFORMATIONAL — the real gate is enforceSubagentCapable() in src/core/model-config.ts (capability verdicts from classifyCapabilities(): tool-less/unknown models fall back to TIER_DEFAULTS.subagent with a warn; tool-capable providers without prompt caching run with a once-per-model cost warn). Declares resolveDefaultHeaders(env) returning OR's three attribution headers: HTTP-Referer (required for OR app-attribution), X-OpenRouter-Title (preferred), X-Title (back-compat alias); defaults to https://gbrain.ai / gbrain; forks override via OPENROUTER_REFERER / OPENROUTER_TITLE env vars. Smoke-tested by test/ai/recipe-openrouter.test.ts (incl. the shape-test regression guard: every model in the chat list matches ^[a-z0-9-]+\/[a-z0-9._-]+$).

• src/core/rerank-audit.ts — failure-only JSONL audit at ~/.gbrain/audit/rerank-failures-YYYY-Www.jsonl (ISO-week rotation, mirrors src/core/audit-slug-fallback.ts). Exports logRerankFailure({reason, model, query_hash, doc_count, error_summary}) + readRecentRerankFailures(days). Deliberately no logRerankSuccess: writing once per tokenmax search is hot-path I/O churn AND success events leak query volume + timing into a local audit file. gbrain doctor's reranker_health check reads search.reranker.enabled first so "no events in window" is interpreted correctly (disabled → ok; enabled → ok). Query text SHA-256-prefix-hashed (8 hex chars) for privacy. GBRAIN_AUDIT_DIR env override honored via the shared resolveAuditDir().

• src/core/search/embedding-column.ts — single source of truth for "which content_chunks.* column does this query rank against?" Pure functions, no engine I/O: loadRegistry(cfg) walks the embedding_columns config (DB plane, JSON map keyed by column name with {provider, dimensions, type} entries), seeds the OpenAI embedding builtin when unset, validates everything before it lands (column-name regex, type ∈ vector | halfvec, dims in [1, 8192], provider format) using Object.create(null) + Object.hasOwn so a key like constructor rejects instead of resolving to Object.prototype.constructor. resolveColumn(registry, override?, cfg) is the boundary call: returns a frozen ResolvedColumn descriptor ({name, provider, dimensions, type}) honoring per-call override → search_embedding_column config → 'embedding' default; throws UnknownEmbeddingColumnError with the list of registered names on miss. isCacheSafe(resolved, cfg) compares the full embedding SPACE (provider + dimensions + name) against cfg's default so a repointed embedding builtin doesn't serve OpenAI-shaped cache rows. validateResolvedColumn(descriptor) re-validates hand-rolled descriptors that bypass the registry (internal-SDK passthrough) so the SQL-injection escape hatch through the descriptor field is closed. Consumed by hybridSearch, gateway.embedQuery(text, {embeddingModel, dimensions}), cosineReScore, and the query MCP op (per-call embedding_column param). Pinned by test/search/embedding-column.test.ts (prototype-pollution, descriptor passthrough, env-only Postgres install, empty-brain coverage gate, cache-space comparison).

• src/core/search/rerank.ts — the call-site abstraction. applyReranker(query, results, opts) slots between dedupResults() and enforceTokenBudget() in src/core/search/hybrid.ts. Slices opts.topNIn (default 30) by current RRF order, sends to gateway.rerank(), reorders by relevanceScore desc, appends the un-reranked tail unchanged (recall protection). Fail-open on every RerankError.reason: any error logs via logRerankFailure and returns the input array unchanged. Stamps rerank_score onto reordered items so downstream telemetry sees the new ordering signal. topNOut: null is the explicit "don't truncate" signal — semantically distinct from undefined ("fall through to mode bundle"). Test seam: opts.rerankerFn stubs gateway.rerank without the network.

• src/core/search/return-policy.ts (default OFF) — intent-aware adaptive return-sizing. Pure, dependency-light module that trims the final ranked candidate set to an intent-driven cap instead of returning the full top-K. entity intent gets a tight cap; temporal/event/general get a recall-preserving cap (concept is coerced to general by hybrid.ts before the call — concept queries want breadth). A minKeep failsafe (≥1) guarantees a human never gets a silent blank when candidates exist. WHY a cap, not a score-cliff detector: PrecisionMemBench instrumentation (gbrain-evals) measured the rank1→rank2 RRF gap is ~identical whether rank-1 is correct (0.602) or wrong (0.569) — mechanical decay, not a separatrix; rank-1 is right in 94% of single-answer cases, so "return a tight set" is the whole win and cliff-cutting just adds noise. Exports AdaptiveReturnConfig, DEFAULT_ADAPTIVE_RETURN (frozen: enabled=false, entityMax=2, otherMax=6, minKeep=1), AdaptiveReturnDecision ({applied, intent, cap, kept, total}), AdaptiveReturnInput (boolean | Partial<AdaptiveReturnConfig> | undefined), adaptiveReturnFromConfig(cfg), resolveAdaptiveReturn(perCall, fromConfig) (defaults → config → per-call merge), adaptiveReturnEnabled(...) (cache-skip gate check), applyAdaptiveReturn(results, intent, cfg) (the trim). Config knobs (DB or file plane): search.adaptive_return (master switch), search.adaptive_return_entity_max, search.adaptive_return_other_max, search.adaptive_return_min_keep (each clamped ≥1). Wired into hybridSearch AFTER applyReranker, BEFORE the limit slice, and ONLY on the first page (offset===0) — paginating a confidence-gated set is incoherent, so paginated calls fall through to the fixed limit. Stamps the decision onto HybridSearchMeta.adaptive_return for gbrain search --explain. hybridSearchCached SKIPS the cache when the gate is on (a trimmed set must not be served to a gate-off lookup and vice versa). SearchOpts.adaptiveReturn + HybridSearchMeta.adaptive_return declared in src/core/types.ts. Agent-facing: the query op (src/core/operations.ts) exposes an adaptive_return boolean param whose description instructs the agent WHEN to set it (single-answer → on; breadth/exploration → off; pass limit:1 for a hard single-answer cap), threaded into hybridSearchCached — end users never touch the config knob; their agent decides per query (same pattern as salience/recency). Pinned by test/search/return-policy.test.ts (mechanism) + test/search/query-op-adaptive-return.test.ts (agent surface: param exists + description teaches both directions + the never-empty contract).

• src/core/search/autocut.ts (default ON in reranked modes) — Weaviate-style autocut: score-discontinuity result-sizing on the cross-encoder rerank separatrix. applyAutocut(results, scoreOf, cfg) normalizes the reranker scores, finds the largest consecutive gap, and cuts there when it clears jumpRatio (default 0.20); robust to unsorted provider output (cuts on a sorted copy, keeps items in INPUT order via a score threshold), guards top<=0/non-finite, never returns empty, and no-ops when <2 results carry a finite rerank_score (covers the reranker fail-open path). WHY rerank_score and NOT RRF/cosine: gbrain measured (see return-policy.ts) that the RRF rank1→rank2 gap is ~flat whether rank-1 is right or wrong — not a separatrix; the cross-encoder score IS. So autocut runs ONLY where the reranker ran (the floor reaches balanced+tokenmax; conservative is a documented no-op). Weak-top floor: when the top rerank score is below minTopScore (default 0.35; config search.autocut_min_top; scale-calibrated to the current default reranker — the September reranker default flip must re-tune it), cliff trimming is skipped entirely so a low-confidence list returns the full cluster instead of collapsing to one result. Exports AutocutConfig, DEFAULT_AUTOCUT (frozen: enabled=true, jumpRatio=0.20, minKeep=1, minTopScore=0.35), AutocutDecision ({applied, signal:'rerank'|'none', cut, kept, total, gapRatio}), AutocutInput, autocutFromConfig, resolveAutocut, applyAutocut. Cache-key integration (clean path, not the adaptive-return cache-skip hack): enable+sensitivity flow through ModeBundle → ResolvedSearchKnobs → knobsHash exactly like graph_signals. mode.ts adds autocut/autocut_jump/autocut_min_keep (conservative false, balanced/tokenmax true@0.20; floor 1 in every mode — search.autocut_min_keep sets the minimum result count a cut may leave, resolved through the same bundle → config → per-call chain) AND sets reranker_top_n_in = searchLimit for reranked modes (so the reranker scores the full returned set; there is no un-scored tail for autocut to wrongly drop — closes the load-bearing recall finding). Autocut folds into knobsHash as its own parts entry (mode.ts:KNOBS_HASH_VERSION is the single source of truth for the current hash version; every bump is a one-time global cache cold-miss on upgrade). Wired into hybridSearch AFTER adaptive-return, BEFORE the limit slice, first page only; emits HybridSearchMeta.autocut. BOTH the cache-miss finalMeta and cache-HIT cachedMeta rebuilds carry autocut+adaptive_return+mode+embedding_column. Preserves alias-hop exact matches: applyAutocut takes an optional preserve predicate; hybrid passes r => r.alias_hit === true so a canonical page injected by applyAliasHop after reranking (no rerank_score) is never cut. Agent surface: query op autocut boolean (ceiling override — false forces full top-K); SearchOpts.autocut; --explain shows per-result rerank_score, formatAutocutSummary renders the decision when search meta is threaded; gbrain search modes attribution; metric glossary autocut.signal/autocut.gap_ratio. Config: search.autocut, search.autocut_jump, search.autocut_min_keep. Default-ON backed by an in-repo eval gate — test/search/autocut-eval.test.ts (also bun run eval:autocut) measures precision-lift-without-recall-regression over labeled qrels fixtures with modeled cross-encoder distributions (no API key, no sibling repo; runs in CI): mean precision 0.33→0.94, recall 1.00→0.95, ZERO recall regression on enumeration queries. Env-overridable floors. Pinned by test/search/autocut.test.ts (pure-fn), test/search/query-op-autocut.test.ts (agent surface), test/search/autocut-integration.serial.test.ts (IRON-RULE behavioral via rerankerFn DI seam: cliff trims, flat doesn't, no-reranker no-ops, autocut:false ceiling, composes with adaptive-return), test/search/autocut-eval.test.ts (the precision/recall gate), and the knobsHash assertions in test/search-mode.test.ts.

• src/core/ai/recipes/voyage.ts — Voyage AI openai-compatible recipe, home of the new-install default stack. Embedding touchpoint declares default_model: 'voyage-4' + default_dims: 1024 — the canonical pick for every "choose a model for the user" surface (models[0] stays voyage-4-large in quality order; the new-install default is voyage-4 for price/quality balance and the shared v4 embedding space — see NEW_INSTALL_DEFAULT_EMBEDDING_MODEL in ai/defaults.ts). Reranker touchpoint (the recommended zerank-2 replacement, same VOYAGE_API_KEY as embeddings): rerank-2.5 flagship ($0.05/M) + rerank-2.5-lite ($0.02/M; prices verified 2026-08-15), path: '/rerank', top_param: 'top_k' (Voyage's response wire matches ZE's {results: [{index, relevance_score}]}; only the request's top-N key differs), 5MB byte-proxy payload cap matching the ZE-era pre-flight. Declares chars_per_token=1 + safety_factor=0.5 so the gateway pre-splits Voyage batches at a 60K-character budget (50% of 120K-token cap with the dense-tokenizer ratio), avoiding the backfill loop where tiktoken-grounded budgeting undercounted Voyage's actual token usage. Declares multimodal_models: ['voyage-multimodal-3'] so the gateway rejects text-only Voyage models pointed at the multimodal endpoint with a clear AIConfigError instead of waiting for Voyage's HTTP 400. The hosted flexible-dim models that accept output_dimension live in VOYAGE_OUTPUT_DIMENSION_MODELS in src/core/ai/dims.ts (v4 trio, voyage-code-4, voyage-3-large, voyage-3.5, voyage-3.5-lite, voyage-code-3; valid widths 256/512/1024/2048); voyage-4-nano is the open-weight variant fixed at 1024-dim that does NOT accept the parameter (negative regression assertion in test/ai/gateway.test.ts: dimsProviderOptions returns undefined for voyage-4-nano). voyage-code-3 is the recommended embedding model for gstack per-worktree code brains (Topology 3 in docs/architecture/topologies.md; voyage-code-4 is the newer hosted code model, flexible dims, $0.12/M); discoverability surfaces: decision-tree branch in docs/integrations/embedding-providers.md, Topology 3 "Recommended embedding model" subsection, runtime nudge from gbrain reindex --code against non-code-tuned models. Recipe-shape regression pinned by test/ai/voyage-code-3-recipe.test.ts.

• src/core/ai/recipes/anthropic.ts — Anthropic recipe (chat + expansion touchpoints). Canonical id is claude-sonnet-4-6 (no date suffix); a reverse alias claude-sonnet-4-6-20250929 → claude-sonnet-4-6 keeps stale user configs working (rescues facts.extraction_model and models.dream.synthesize). Recipe-shape regression pinned by test/anthropic-model-ids.test.ts.

• src/core/ai/providers/claude-cli-language-model.ts (+ recipe src/core/ai/recipes/claude-cli.ts) — ai-sdk LanguageModel adapter that shells out to the locally-installed claude CLI in print mode (OAuth-subscription lane, no API key; claude-cli:<model> is config-portable with anthropic:<model>). Tool use is system-prompt-instructed JSON emission: the recipe teaches the model the <use_tools>[{name,input}]</use_tools> format and the adapter parses those blocks back into ai-sdk tool-call parts. Tool-call ids are ALWAYS gbrain-minted (toolu_claude_cli_<uuidv7>, #4155) — never model-authored: each doGenerate is a fresh subprocess replayed from an id-stripped transcript, so the model structurally cannot keep ids unique across turns (it echoed the prompt's example entropy-free and collided real dream jobs to death before migration v131 retired the job-wide unique constraint); the prompt no longer asks for an id, and a stray id field is deliberately ignored (nothing round-trips it — the loop pairs results in-memory within one turn). doStream not implemented; callers (gateway.toolLoop) use doGenerate. Pinned by test/claude-cli-recipe.test.ts.

• src/core/model-pricing.ts — single source of truth for paid-cloud CHAT/completion model pricing (USD per 1M tokens, input | output). CANONICAL_PRICING is a provider:model-keyed table (Anthropic Opus 5/4.8/4.7/4.6 $5/$25, Sonnet 4.6 $3/$15, Haiku 4.5 $1/$5 both dateless + dated, plus OpenAI / Google / Together / DeepSeek panel models). canonicalLookup(modelId) resolves bare (claude-opus-4-8), colon (anthropic:claude-opus-4-8), and slash (anthropic/...) forms — bare ids default to the anthropic: provider; nested OpenRouter ids (openrouter:anthropic/...) intentionally MISS so OpenRouter markup isn't repriced as the inner vendor; after the exact match, a case-insensitive fallback folds BOTH sides (#4123 — some canonical keys carry cased model tails verbatim), safe only while no two canonical keys collide case-insensitively (pinned by the drift guard). Every other chat-pricing table is a DERIVED view of this one (NOT a hand-copied duplicate), so cross-table price drift is structurally impossible. Embeddings live separately in embedding-pricing.ts (different unit). Pinned by test/model-pricing.test.ts whose drift guard asserts each derived view equals canonical and that the cross-modal panel models are all present.

• src/core/anthropic-pricing.ts — bare-keyed Anthropic VIEW of model-pricing.ts (the anthropic: canonical entries with the prefix stripped). Kept distinct because many callers look up by bare Claude id and because estimateMaxCostUsd(modelId, inTokens, maxOutTokens) carries the null-on-miss contract the dream-cycle budget gate depends on (non-Anthropic ids return null; BudgetMeter tries canonicalLookup first and only falls back here, so it warns BUDGET_METER_NO_PRICING and runs unbounded only when canonical has no rates either). estimateMaxCostUsd routes bare/colon/slash ids through splitProviderModelId. Do NOT hand-edit prices here — the map is derived from canonical, so it cannot drift. ANTHROPIC_PRICING is consumed by budget/budget-tracker.ts, minions/batch-projection.ts, and cycle/budget-meter.ts.

• src/core/takes-quality-eval/pricing.ts — fail-closed budget pricing for eval takes-quality run --budget-usd N. MODEL_PRICING is a curated provider:model allowlist (default panel + likely overrides) whose VALUES are derived from model-pricing.ts via canonicalLookup; an allowlisted id missing from canonical throws at module load. Schema is {input_per_1m, output_per_1m}. A model NOT on the allowlist aborts the run with an actionable error rather than guessing (distinct from cross-modal-eval/runner.ts, which silently estimates zero on unknown models — both now source numbers from canonical).

• src/core/budget/budget-tracker.ts — keystone primitive for the brainstorm cost-cathedral wave. One typed error (BudgetExhausted with reason: 'cost' | 'runtime' | 'no_pricing'), one schema-stable audit JSONL at ~/.gbrain/audit/budget-YYYY-Www.jsonl. Contracts: record() throws when cumulative spend exceeds cap (the cap is a real ceiling, not a suggestion); reserve() hard-fails with reason: 'no_pricing' when maxCostUsd is set AND the model is missing from pricing maps (warn-once preserved when cap is unset); extractUsageFromError(err, fallback) returns err.usage when the SDK provides it, else the pessimistic fallback (caller passes maxOutputTokens, not the optimistic pre-call estimate). onExhausted(cb) fires once synchronously BEFORE the throw propagates so callers can persist checkpoints. Replaces three parallel copies (inline brainstorm class, cycle/budget-meter, eval-contradictions). Adapts the old BudgetMeter (public shape preserved + schema_version: 1 stamped on every dream-budget audit line). Pinned by 18 unit cases.

• src/core/audit-week-file.ts — single source of truth for ISO-week audit JSONL filename math. Exports isoWeek(d), isoWeekFilename(prefix, now?), resolveAuditDir() (honors GBRAIN_AUDIT_DIR). Year-boundary correctness pinned by tests at 2020-W53 (the 53-week year), 2025-W01 rolling in from 2024-12-30 (Monday), 2026-W01. Four call sites migrated: src/core/minions/handlers/shell-audit.ts, src/core/facts/phantom-audit.ts, src/core/audit-slug-fallback.ts, src/core/cycle/budget-meter.ts. Each keeps its compute<X>AuditFilename thin wrapper for back-compat with existing tests.

• src/core/diarize/payload-fitter.ts — generic fit-arbitrarily-large-items-into-per-call-token-budget utility. 'batch' strategy is deterministic token-budgeted chunking with no LLM calls. 'summarize' strategy embed-clusters into ceil(items/4) groups via cheap deterministic nearest-neighbor on cosine, Haiku-summarizes each cluster via Promise.allSettled at parallelism=4. Each Haiku call composes the active BudgetTracker via the AsyncLocalStorage. Quality gate: when success_ratio < min_success_ratio (default 0.75), result is flagged degraded: true — the fitter preserves the successful subset; the caller decides whether to surface a partial result or abort.

• src/core/brainstorm/checkpoint.ts — crash-resilient checkpoint for gbrain brainstorm and gbrain lsd. Persists FULL idea bodies (~50KB/run) so resume MERGES pre-crash ideas with post-resume ideas before the judge runs (a resume that produces only second-run output is silent partial output). run_id = sha256(question + profile + sort(close_slugs) + sort(far_slugs)).slice(0,16) — NO embedding bits, stable across embedding-model swaps. Atomic write via .tmp + rename. ONE resume flag (--resume <run_id> covers both failed AND never-attempted crosses); --list-runs prints run_ids mtime-newest-first; --force-resume bypasses the 7-day staleness gate. Cycle purge phase (gbrain dream --phase purge) GCs checkpoints older than 7 days via gcStaleCheckpoints(7). Pinned by test/e2e/brainstorm-resume.test.ts (20 unit + 3 E2E cases incl. the merge contract).

• src/core/remediation-checkpoint.ts — doctor --remediate checkpoint at ~/.gbrain/remediation/<plan_hash>.json. plan_hash = sha256(JSON.stringify(sorted recommendation ids)).slice(0,16). Schema-versioned, atomic .tmp + rename. gbrain doctor --remediate --resume <plan_hash> (no arg picks newest matching) loads it and skips completed steps. Mismatched plan_hash refuses with a paste-ready message. Cleared on clean completion. Pinned by 13 unit cases.

• src/core/model-config.ts — Model-string resolution (the seam every internal LLM call walks through). Four-tier system (ModelTier = 'utility' | 'reasoning' | 'deep' | 'subagent') with TIER_DEFAULTS (utility→haiku-4-5, reasoning→sonnet-4-6, deep→opus-4-7, subagent→sonnet-4-6) and tier?: ModelTier on ResolveModelOpts. resolveModelDetailed() runs the 8-step chain and reports WHICH step won (ResolveSource): cliFlag → config key → deprecated key → models.default → models.tier.<tier> → env var (GBRAIN_MODEL) → key-aware tier default → caller fallback; resolveModel() is the thin wrapper for callers that only want the string. Step 7 is KEY-AWARE: resolveTierDefault(tier, env?) walks PROVIDER_TIER_DEFAULTS (anthropic first — zero change for keyed installs; openai second so an OPENAI_API_KEY-only install resolves servable defaults) over the merged provider env (mergedProviderEnv, config-file keys folded, env wins, empty strings dropped); injected env is used EXCLUSIVELY (no config read — hermetic for tests); no key at all → TIER_DEFAULTS unchanged. The openai entry carries NO literal model pins: it resolves per call through the latest-model discovery cache (src/core/ai/openai-latest.ts, account-discovered, priced-only) with openaiStaticTierFallback() — the openai recipe's chat list ranked by the same grammar — as the offline floor, so the recipe is the single human-updated source and the account is the runtime source. The gpt alias resolves dynamically through the same path (the map entry is a documentation floor). resolveEffectiveChatModel(fileCfg, env) / resolveEffectiveExpansionModel are the ENGINE-FREE shared effective-model resolvers (GBRAIN_MODEL > servable file pin per providerKeyReady (recipe auth_env.required) > key-aware tier default; unservable pins warn once and fall through) — used by BOTH reconfigureGatewayWithEngine's fallback layer and detectCapabilities' extraction probe so runtime routing and the capability report cannot diverge; they read RAW loadConfig() output, never gateway state (the boot fold stamps defaults, making explicit pins indistinguishable there). isAnthropicProvider(modelString) checks provider:model prefix OR claude- bare-id pattern (routes through splitProviderModelId from src/core/model-id.ts so slash-form ids like anthropic/claude-sonnet-4-6 classify correctly). enforceSubagentCapable() is the layer-2 runtime guard: tier === 'subagent' resolutions are classified via classifyCapabilities() — unusable:no_tools/unknown warn once and fall back to TIER_DEFAULTS.subagent; degraded:no_caching (e.g. OpenAI) passes with a once-per-(source, model) cost warn. _resetDeprecationWarningsForTest() clears all three warn memos (deprecation, subagent, unservable-pin). Pinned by test/model-config.serial.test.ts.

• src/core/ai/model-resolver.ts — Recipe-touchpoint validator. assertTouchpoint(recipe, touchpoint, modelId) checks the PROVIDER's capability only (anthropic has no embedding touchpoint; voyage/ollama have no chat) and never gates on the model id. Recipe models: arrays are informational — default-model selection (models[0] for --model <provider> shorthand and env-ready pickers), guard-test fixtures for the repo's own hardcoded defaults, and gbrain providers list display — NOT a runtime allowlist, so frontier models newer than a recipe work without a recipe PR. A nonexistent id surfaces as the provider's own model_not_found at call time; gbrain models doctor live-probes the configured models for a pre-flight check. Exception: gateway.rerank() keeps its own model-list check because each listed reranker id maps to a known request/response wire shape. embeddingDimsForModel matches recipe model_dims keys exactly first, then case-insensitively with BOTH sides folded (#4123 — configured ids arrive cased, and user-editable recipe tables can carry cased keys; without the fold a cased id fell through to default_dims and gbrain init built a wrong-width column), before falling back to default_dims.

• src/commands/models.ts — gbrain models [--json] read-only routing dashboard: prints tier defaults (utility/reasoning/deep/subagent), the resolved value for each (re-walking the resolution chain), every per-task override (13 PER_TASK_KEYS, now including provider-neutral models.contextual_synopsis with legacy-key/env attribution), the alias map, and a source-of-truth column (default / config: <key> / env: <VAR>). gbrain models doctor [--skip=<provider>] [--json] fires a 1-token gateway.chat() probe against each configured chat + expansion model and classifies failures into {model_not_found, auth, rate_limit, network, unknown}. The probe timeout resolves per model via resolveChatProbeTimeoutMs — the recipe touchpoint's default_timeout_ms when declared, else the flat 5000ms default (mirrors the reranker probe's recipe-default fallback; claude-cli declares 30s because its claude -p subprocess cold start routinely outruns 5s and used to false-fail every run as unknown). Wired into cli.ts dispatch + CLI_ONLY set. A zero-token embedding_config probe runs FIRST, before any chat/expansion probes spend money: probeEmbeddingConfig() reads getEmbeddingModel() + getEmbeddingDimensions() and (for Voyage flexible-dim models) checks isValidVoyageOutputDim(dims) against VOYAGE_VALID_OUTPUT_DIMS. ProbeStatus variant 'config' + optional fix?: string on ProbeResult surface a paste-ready gbrain config set ... line in human + JSON output; touchpoint label 'embedding_config' joins 'chat' and 'expansion'.

• src/core/init-embed-check.ts — embedding-key validation at gbrain init. runInitEmbedCheck(opts) runs a config-only diagnoseEmbedding (catches a missing key for ANY provider) plus a best-effort liveTestEmbed (1-token gateway.embed(['probe'], {inputType:'query', abortSignal}), 5s AbortController timeout, never throws — catches an invalid/expired key). Loud warning to stderr; init still exits 0 (--no-embedding is the deferred-setup escape; --skip-embed-check / GBRAIN_INIT_SKIP_EMBED_CHECK=1 skip the check). Builds the effective env (process.env + every file-plane provider key buildGatewayConfig folds — openai/anthropic/voyage/zeroentropy/dashscope/google, #2662 — from loadConfigFileOnly() + opts.apiKey) and configures the gateway via buildGatewayConfig before diagnose/probe, so the check sees the same keys AND provider base URLs runtime will (no false "missing key" for config.json-keyed users; the probe hits the right endpoint). Init-specific warning text names --no-embedding / --skip-embed-check, not the sync-flavored --no-embed. Wired into initPGLite + initPostgres in src/commands/init.ts, with the result added to the --json envelope as embedding_check {ok, reason?, live_ok?}. Pinned by test/init-embed-check.test.ts (hermetic via the gateway embed-transport seam + withEnv).

• src/commands/jobs.ts:refreshGatewayForJob + src/core/ai/gateway.ts:refreshGatewayEnvFromFilePlane — long-lived-worker staleness boundary, three tiers: (1) DB-plane model config re-resolves per gateway-refresh job (reconfigureGatewayWithEngine); (2) FILE-plane config (~/.gbrain/config.json, incl. provider API keys) re-folds per job via the env-ONLY refreshGatewayEnvFromFilePlane — never a full configureGateway(buildGatewayConfig(loadConfig())), which would clobber DB-plane-merged fields (base_urls, chat options) with file-plane-only values; (3) true process env vars are fixed at worker start and need a restart. gbrain config set *_api_key writes the DB plane, which loadConfigWithEngine() deliberately never merges for key fields — those writes do NOT reach workers (TODO filed to reroute them to the file plane). facts-absorb sits in GATEWAY_REFRESH_JOB_NAMES; its handler converts execution-time chat_unavailable in a KEYED worker into a typed retryable failure (factsAbsorbShouldRetry) while a keyless worker completes the job as a calm skip. Pinned by test/jobs-gateway-refresh.serial.test.ts.

• src/core/ai/openai-latest.ts — latest-model discovery: OpenAI defaults are NEVER pinned. refreshLatestOpenAIModels() (called from reconfigureGatewayWithEngine, TTL 24h, 3s-bounded, fail-open, GBRAIN_MODEL_DISCOVERY=off|0 kill switch — the test preload sets it) fetches the account's own GET /v1/models, ranks ids through a conservative grammar (parseOpenAIChatId: bare family aliases gpt-N.M + known tier suffixes sol/pro/terra/luna/nano/mini; dated snapshots, -chat Instant-class, realtime/image and UNKNOWN future suffixes are ignored — rot degrades to newest-known-shape, never a wrong pick), and maps the newest family onto the tier ladder (utility→cheap, reasoning/subagent→mid, deep→top). ONLY ids with a canonical pricing row are eligible (rankOpenAIChatModels's priced filter): BudgetTracker fails closed (no_pricing) under a cost cap, so an unpriced discovered default would brick budget-capped backfills — a newer-unpriced family warns once naming the missing model-pricing.ts row. Result lands in <configDir()>/model-cache.json (atomic tmp+rename); latestOpenAITiers() is the SYNC read (stale cache beats static fallback — TTL gates refresh, never use) consumed by resolveTierDefault's openai entry and the dynamic gpt alias. Pinned by test/openai-latest.serial.test.ts.

• src/core/ai/provider-env.ts — mergedProviderEnv(cfg, env): THE canonical provider-key/env fold. Maps file-plane config keys (openai/anthropic/zeroentropy/openrouter/voyage/dashscope/google + azure endpoint/deployment/entra) to the env names recipes read, merges env on top (env wins ONLY for keys carrying a real value — '' and undefined dropped per #1249), then applies the GEMINI_API_KEY → GOOGLE_GENERATIVE_AI_API_KEY alias (canonical env name > alias > config fallback). Three consumers: buildGatewayConfig (gateway env), detectCapabilities (capability probe), resolveTierDefault/resolveEffectiveChatModel (key-aware model resolution) — the old buildGatewayConfig/capability duplicate-and-sync pair is dead; drift is structurally impossible.

• src/core/ai/build-gateway-config.ts — buildGatewayConfig(c: GBrainConfig): AIGatewayConfig, extracted from src/cli.ts (which re-exports it for back-compat). Lets core modules (init-embed-check.ts) reuse it without importing the CLI entrypoint. Delegates the file-plane API-key fold + env merge to mergedProviderEnv (src/core/ai/provider-env.ts); keeps ownership of threading local-server *_BASE_URL env vars into base_urls. process.env wins EXCEPT empty-string / undefined values are dropped before the merge, so an injected empty ANTHROPIC_API_KEY='' (Claude Code neuters subprocess LLM calls this way) can't clobber a valid config-plane key; '0' / 'false' are preserved. Pinned by test/ai/build-gateway-config.test.ts.

• src/core/skill-trigger-index.ts — Shared loader that unions per-skill SKILL.md frontmatter triggers: with curated RESOLVER.md / AGENTS.md rows from skillsDir AND the parent dir (preserves the OpenClaw workspace-root layout). UNION semantics: explicit RESOLVER.md rows ADD to frontmatter triggers (don't replace). Dedup keyed on (skillPath, trigger.trim().toLowerCase()). Three consumers fold through this primitive — checkResolvable, runRoutingEvalCli, mounts-cache.composeResolvers — so fixing frontmatter reaches all of them. Exports loadSkillTriggerIndex(skillsDir): SkillTriggerEntry[], entriesToResolverContent(entries): string (synthesizes a markdown-table resolver string for runRoutingEval's string-content API), findPrimaryResolverPath(skillsDir): string | null, the FRONTMATTER_SECTION constant, and _resetWarnedSkillsForTests. Skip rules: non-directory entries, _*/.* prefixes, conventions/+migrations/ subdirs, skills with no SKILL.md (deprecated install/ graceful-skipped), no triggers: array, or malformed YAML (warn-once + skip). Reuses parseSkillFrontmatter from src/core/skill-frontmatter.ts, including block and wrapped flow-sequence arrays. Pinned by test/skill-trigger-index.test.ts (18 hermetic cases). CI gate bun run check:resolver (= bun src/cli.ts check-resolvable --strict --skills-dir skills/) wired into bun run verify.

• src/core/skill-catalog.ts — host-repo skill catalog backing the MCP list_skills / get_skill ops. Lets a thin MCP client (Codex desktop, Claude Code, Claude Cowork, Perplexity) DISCOVER + FOLLOW the agent repo's fat-markdown skills over gbrain serve — a skill is prose, so "using" one = fetching its body then calling the gbrain MCP tools the server already exposes. Read-scope, NOT localOnly (defensible only via the full mitigation stack): (1) publish gate — assertPublishEnabled(ctx, publishSkills); remote callers require mcp.publish_skills === true, default-OFF so an upgrade never silently grants existing read tokens host-skill read; local callers (ctx.remote === false) always pass. (2) path confinement — assertSkillNameShape rejects separators/../null/space before any FS access; the client name is a manifest LOOKUP KEY (via loadOrDeriveManifest), never a raw path segment; confineManifestPath does realpath + relative-containment + SKILL.md-regular-file check on EVERY entry (defeats poisoned manifest.json path, symlink/.. escape). (3) frontmatter allowlist — GetSkillResult.frontmatter projects a safe subset; private writes_to + sources dropped. (4) prose-only + 256KB cap (MAX_SKILL_MD_BYTES, env GBRAIN_MAX_SKILL_MD_BYTES), size-checked twice (statSync + UTF-8 byte length). (5) no install_path serve for remote — remote callers use autoDetectSkillsDir (no install-path tier) so a hosted gbrain with no agent repo returns storage_error; local callers use autoDetectSkillsDirReadOnly. (6) MCP rate-limiter caps call rate. Config reads honor BOTH planes: readMcpPublishSkills / readMcpSkillsDir prefer the DB plane (engine.getConfig) over the file plane (ctx.config.mcp). Tool-honesty: crossReferenceTools(declared, ctx) splits a skill's declared tools: into usable_tools vs unavailable_tools; buildSkillCatalog's instructions envelope (SKILL_CATALOG_INSTRUCTIONS) carries the "these are prose, follow-then-call-tools" protocol. Skills are host-filesystem repo-global — sourceScopeOpts(ctx) / ctx.brainId deliberately do NOT apply. buildSkillCatalog is resilient (one malformed/escaping skill is skipped, never throws). Config keys in src/core/config.ts: GBrainConfig.mcp?: { publish_skills?, skills_dir? } + KNOWN_CONFIG_KEYS entries mcp.publish_skills/mcp.publish_skills_prompted/mcp.skills_dir + mcp. prefix in KNOWN_CONFIG_KEY_PREFIXES. src/commands/init.ts writes config.mcp = { publish_skills: true, ... } for new installs (existing config wins on re-init). src/commands/upgrade.ts:runPostUpgrade adds a one-time consent prompt (gated by mcp.publish_skills_prompted; existing installs stay OFF until owner opts in). Three ops register in src/core/ops/skills-catalog.ts (spread into the operations.ts façade): list_skills with optional section filter + cliHints:{name:'skills'}; get_skill taking name (+ source_id for brain-resident packs) + cliHints:{name:'skill', positional:['name']}; list_brain_skillpack. They dynamically import this module to avoid the import cycle (skill-catalog statically imports the operations array). Descriptions in src/core/operations-descriptions.ts (LIST_SKILLS_DESCRIPTION, GET_SKILL_DESCRIPTION, SKILL_CATALOG_INSTRUCTIONS, SKILL_CLIENT_GUIDANCE), pinned by test/operations-descriptions.test.ts. CLI: gbrain skills / gbrain skill <name>. Pinned by test/skill-catalog.test.ts, test/skill-catalog-security.test.ts (path-confinement / poisoned-manifest / symlink-escape), test/skill-catalog-transports.test.ts (publish-gate + remote-vs-local) over test/fixtures/skill-catalog/.

• src/core/check-resolvable.ts — Resolver validation: reachability, MECE overlap, DRY checks, structured fix objects. CROSS_CUTTING_PATTERNS.conventions is an array (notability gate accepts conventions/quality.md and _brain-filing-rules.md). extractTriggers() delegates to the shared SKILL.md parser, so MECE gap detection and the trigger index agree on block lists, single-line flow sequences, wrapped flow sequences, and CRLF input. extractDelegationTargets() parses > **Convention:**, > **Filing rule:**, and inline backtick references. DRY suppression is proximity-based via DRY_PROXIMITY_LINES = 40. parseResolverEntries accepts BOTH the markdown table AND a compact list format (- **skill-name**: trigger1 | trigger2 | trigger3 or - skill-name: trigger1 | trigger2); shapes can mix in one file, folded by the multi-resolver merge. Skill name MUST be kebab-lowercase (regex [a-z][a-z0-9-]+) so prose bullets like - **Note**:/- **Convention**:/- **TODO**: don't false-match as skill rows. skillPath is ALWAYS derived as skills/<name>/SKILL.md: an optional → \skills/path`(or ASCII->) suffix is stripped from the trigger but NOT honored as the path — two consumers (routing-eval.ts:skillSlugFromPath, the manifest lookup) assume the convention; use the table format for non-conventional paths. Multi-trigger rows fan out to one entry per trigger sharing the same skillPath; checkResolvablededupes so the reachability count counts each skill once. Pinned bytest/check-resolvable.test.ts(resolver shapes plus trigger array syntax regressions) +test/check-resolvable-openclaw-compact.test.ts(8 cases overtest/fixtures/openclaw-compact-resolver/andtest/fixtures/openclaw-mixed-merge/). Tutorial: docs/guides/scaling-skills.md` (three-tier scaling: ~300-skill agent to ~4K tokens/turn from ~25K).

• src/core/repo-root.ts — Shared findRepoRoot(startDir?): walks up from startDir (default process.cwd()) looking for skills/RESOLVER.md. Zero-dependency, imported by doctor.ts and check-resolvable.ts; parameterized startDir makes tests hermetic. Read-path / write-path split: autoDetectSkillsDir (shared, read+write-safe) has tier-0 $GBRAIN_SKILLS_DIR operator override ahead of the 4-tier chain. autoDetectSkillsDirReadOnly wraps it with a tier-5 install-path fallback that walks up from fileURLToPath(import.meta.url) and gates on isGbrainRepoRoot so unrelated repos can't false-positive. Read-path callers (doctor, check-resolvable, routing-eval) use the read-only variant; write-path callers (skillpack install, skillify scaffold, post-install-advisory) stay on the shared function so install-from-~ can't retarget the bundled gbrain skills/ instead of the user's workspace. SkillsDirSource variants 'env_explicit', 'install_path'; AUTO_DETECT_HINT_READ_ONLY documents the extra tier. The --fix safety gate in doctor.ts + check-resolvable.ts refuses auto-repair when detected.source === 'install_path'.

• src/core/skills-integrity.ts — Tamper-evidence manifest for the bundled skills/ tree (#159); NOT a signature system. Pure functions over node:crypto sha256: computeSkillsManifest(dir) (recursive, sorted '/'-relative paths, excludes the manifest itself, skips symlinks), renderSkillsManifest(dir) (2-space JSON + trailing newline, deterministic), verifySkillsManifest(dir, manifest) → {modified, missing, extra}. Committed manifest lives at skills/skills.lock.json (SKILLS_MANIFEST_FILENAME); regenerate via bun run scripts/generate-skills-manifest.ts. Consumers: the warn-only skills_manifest_integrity doctor check in src/commands/doctor.ts (ok/skip when no manifest is present — user workspaces and compiled-binary installs are not drift) and the CI freshness guard scripts/check-skills-manifest-fresh.sh (bun run check:skills-manifest, in bun run verify). Pinned by test/skills-integrity.test.ts.

• src/commands/check-resolvable.ts — Standalone CLI wrapper over checkResolvable(). Exports parseFlags, resolveSkillsDir, DEFERRED, runCheckResolvable. Exit rule: 1 on any issue (warnings OR errors), stricter than doctor's ok flag. Stable JSON envelope {ok, skillsDir, report, autoFix, deferred, error, message} — same shape on success and error. --fix runs autoFixDryViolations BEFORE checkResolvable (same ordering as doctor). scripts/skillify-check.ts subprocess-calls gbrain check-resolvable --json (cached per process) and fails loud on binary-missing. AGENTS.md workspaces resolve natively (see src/core/resolver-filenames.ts). DEFERRED[] is empty. Resolver lookup is the multi-file merge in src/core/check-resolvable.ts — entries collected from every RESOLVER.md/AGENTS.md across the skills dir AND its parent, deduped by skillPath (first occurrence wins). Uses autoDetectSkillsDirReadOnly so cd ~ && gbrain check-resolvable finds bundled skills via the install-path fallback; --fix carries the same install-path safety gate (refuses to write when detected.source === 'install_path').

• src/core/resolver-filenames.ts — central list of accepted routing filenames (RESOLVER.md, AGENTS.md). Shared by findRepoRoot, check-resolvable, and skillpack install so every code path walks the same fallback chain.

• src/commands/skillify.ts + src/core/skillify/{generator,templates}.ts — gbrain skillify scaffold <name> creates all stubs for a new skill: SKILL.md, script, tests, routing-eval.jsonl, resolver entry, filing-rules pointer. gbrain skillify check <script> runs the 10-step checklist (LLM evals, routing evals, check-resolvable gate, filing audit) against a candidate skill before it lands.

• src/commands/skillify-check.ts — gbrain skillpack-check agent-readable health report. Exit 0/1/2 for CI gating; JSON for debugging. Wraps check-resolvable --json, doctor --json, and migration ledger into one payload. Required item 12 (brain_first_compliance) calls analyzeSkillBrainFirst() on the candidate SKILL.md; exits 1 when the verdict is missing_brain_first (external-lookup pattern present, no callout, no brain_first: exempt). The scaffold path in src/core/skillify/templates.ts pre-inserts the canonical Convention callout into new SKILL.md files so freshly-scaffolded skills pass item 12.

• src/commands/book-mirror.ts — gbrain book-mirror --chapters-dir <path> --slug <slug> [flags]. Submits N read-only subagent jobs (one per chapter; allowed_tools: ['get_page', 'search']), waits for all via waitForCompletion, reads each child's job.result, assembles two-column markdown CLI-side, writes a single operator-trust put_page to media/books/<slug>-personalized.md. Trust narrowing happens at the tool-allowlist layer (subagents can't call put_page) so untrusted EPUB content can't prompt-inject any people page. Cost-estimate prompt before launching; refuses to spend in non-TTY without --yes. Per-chapter idempotency keys (book-mirror:<slug>:ch-<N>) for retry-friendly re-runs. Partial-failure: assembles completed chapters + a ## Failed chapters section. Pinned by test/book-mirror.test.ts (9 cases).

• src/commands/skillpack.ts + src/core/skillpack/{bundle,scaffold,reference,migrate-fence,scrub-legacy,harvest,harvest-lint,copy,apply-hunks,diff-text,installer}.ts — managed-block install model retired; install/uninstall removed (exit non-zero with a hint to the replacement). Surface: scaffold (one-time additive copy via copyArtifacts in copy.ts; refuses to overwrite; partial-state fills missing paired sources declared in SKILL.md frontmatter sources:), reference (read-only diff lens + --apply-clean-hunks two-way auto-apply via pure-JS unified-diff parser/applier in apply-hunks.ts + diff-text.ts), migrate-fence (one-shot strip of legacy fence; cumulative-slugs receipt → row-parsing fallback; preserves rows verbatim as user-owned routing), scrub-legacy-fence-rows (opt-in row cleanup with skill-present + non-empty-triggers gate), harvest (host→gbrain inverse with symlink-reject + canonical-path containment via a validateUploadPath-style gate + default-on privacy linter in harvest-lint.ts against ~/.gbrain/harvest-private-patterns.txt plus built-in a built-in fork-name pattern + email + Slack-channel patterns; rollback on match). Paired-source declarations live in each SKILL.md's frontmatter sources: array (validated by loadSkillSources in bundle.ts). autoDetectSkillsDir (in src/core/repo-root.ts) has a cwd_walk_up tier ahead of ~/.openclaw/workspace ($OPENCLAW_WORKSPACE precedence preserved). gbrain skillpack check --strict exits non-zero on drift (CI gate); top-level gbrain skillpack-check keeps exit-1-on-issues for cron. Companion editorial skill skills/skillpack-harvest/SKILL.md drives the genericization checklist. Doc: docs/guides/skillpacks-as-scaffolding.md. Test coverage across test/skillpack-{copy,scaffold,reference,reference-apply,apply-hunks,migrate-fence,scrub-legacy,harvest,harvest-lint,frontmatter-sources}.test.ts + 9-case E2E in test/e2e/skillpack-flow.test.ts. installer.ts + test/skillpack-install.test.ts survive — gbrain skillpack diff still uses diffSkill from there.

• src/core/skillpack/{personas,bridge-state,harness-bridge}.ts + src/commands/skillpack/{shared,scaffold,reference,harness}.ts — the harness skill bridge (cathedral-7). src/commands/skillpack.ts is a peeled FAÇADE (dispatch + HELP_TOP + the v0.33 install/uninstall removal errors; module-size ratchet); per-subcommand handlers live in src/commands/skillpack/ and the flag registry scans the dir via the façade's facadeExpansion entry — spell foreign CLI flags dash-less in these modules' comments/strings (prose-bleed class, three prior incidents). scaffold --harness <claude-code|openclaw|codex|opencode> installs a persona-curated set into the harness's native skills dir: personas live in skills/plugin-lanes.json#personas (personas.ts is the SINGLE validation implementation — scripts/generate-plugin-tree.ts imports it; membership ⊆ the plugin lane set, so lane-excluded slugs are refused with their recorded reason); slugs path-resolve via bundle.ts's universe:'manifest' (the 8 lane additions are all absent from openclaw.plugin.json#skills). Safety: frontmatter fail-loud gate pre-write (a frontmatterless SKILL.md bricks Codex sessions), target-side confinement in assertTargetsConfined (deepest-existing-ancestor realpath — copy.ts confines SOURCES only), refuse-overwrite, and written-only ownership in bridge-state.ts (~/.gbrain/skillpack-bridge-state.json, schema gbrain-skillpack-bridge-v1, fail-open load, install-time sha256 per written file — never touches skillpack-state.json, whose loader drops unknown keys). --stub renders cold-pull pointers (frontmatter verbatim + <!-- gbrain-skill-stub v1 --> marker; ships the shared-dep closure AND sibling aux files — get_skill serves only the SKILL.md body) behind a three-check preflight in src/commands/skillpack/harness.ts (publish gate dual-plane, per-slug servability via verifySlugsServable, best-effort local surface warn — the module deliberately does NOT import src/mcp/surface.ts, whose comments would bleed serve flags into the allowlist; get_skill ∉ STARTER_OPS is pinned by a contract test). reference --harness is a stub-aware three-way lens (local_edit vs upstream_drift vs unknown — no install-time hash, never auto-applied — via the hash ledger; marker fallback survives state loss both directions) + --apply-clean-hunks (refuses stub files); remove --harness deletes ledger-owned files only; skillpack status renders an installed-bridges section from collectBridgesStatus. openclaw delegates to runScaffold({skillSlugs}); codex/opencode require an explicit dest until observation runs. Claude-code dirs come from host-specs.ts (claudeUserSkillsDir/claudeProjectSkillsDir, HOME-env-first). Tests: test/skillpack-{personas,bridge-state,harness-bridge,reference-harness,scaffold-harness}.test.ts. Doc: the harness-bridge section of docs/guides/skillpacks-as-scaffolding.md.

• src/core/skillpack/{manifest-v1,tarball,state,remote-source,trust-prompt,bootstrap-display,scaffold-third-party,registry-schema,registry-client,rubric,doctor,init-scaffold,pack-publish,endorse,audit}.ts + examples/skillpack-reference/ + docs/skillpack-anatomy.md + scripts/build-skillpack-anatomy.ts — third-party skillpack ecosystem. gbrain skillpack scaffold <owner/repo|https-url|./tgz|./local-dir> resolves the spec via classifySpec, fetches through SSRF-hardened git-remote.ts (git) or extracts the tarball into ~/.gbrain/skillpack-cache/<host>/<owner>/<repo>/<sha>/, validates skillpack.json (api_version gbrain-skillpack-v1), checks gbrain_min_version, surfaces a TOFU first-install identity-confirm prompt (author + source + pinned commit + tarball SHA + tier; non-TTY requires --trust), records the pin in machine-owned ~/.gbrain/skillpack-state.json (schema gbrain-skillpack-state-v1, atomic .tmp + rename, isAlreadyTrusted skips re-prompt on author+pin match), runs through enumerateScaffoldEntries → copyArtifacts (one-time additive, refuses to overwrite), then DISPLAYS runbooks/bootstrap.md WITHOUT executing (deliberately does not auto-execute). Registry catalog at garrytan/gbrain-skillpack-registry split into registry.json (PR-able, gbrain-registry-v1) + endorsements.json (maintainer-only overlay, gbrain-endorsements-v1); effectiveTier merges. registry-client.ts fetches both via If-None-Match etag with 1h soft-TTL + stale-fallback (origins fresh_fetch | cache_warm | cache_soft_stale | cache_hard_stale); hard-fail only on no-cache + no-network. CLI: gbrain skillpack {search,info,registry,doctor,init,pack,endorse}. Doctor walks SKILLPACK_RUBRIC_V1 (10 binary dimensions: 5 required CORE — manifest_valid, skills_have_skill_md, routing_evals_present ≥5 intents, skills_have_unique_triggers MECE, changelog_present_and_current — and 5 quality BADGES — unit_tests_present, e2e_tests_present, llm_eval_present ≥3 cases, bootstrap_runbook_present, license_present); tier eligibility: endorsed needs all 10, community needs core + ≥3 badges, experimental needs core only, blocked when any core fails. --quick ~5s structural sweep; --fix --yes auto-scaffolds auto_fixable: true dimensions and refuses to overwrite files whose mtime is newer than skillpack.json. gbrain skillpack init <name> lands 11 files (skillpack.json, SKILL.md, routing-eval.jsonl, test/example.test.ts, e2e/example.e2e.test.ts, evals/example.judge.json, runbooks/{bootstrap,uninstall,upgrade-template}.md, CHANGELOG, README, LICENSE); freshly-init'd scores 10/10; --minimal skips test/e2e/evals. gbrain skillpack pack packs a deterministic tarball via GNU tar (--sort=name --mtime=@0 --owner=0 --group=0 --numeric-owner + GZIP=-n + TZ=UTC); refuses on tier_eligibility === 'blocked'. Extract caps (5000 files / 100MB total / 1MB per file / 255-char paths / 100:1 compression ratio); rejects symlinks/hardlinks/devices/FIFOs. gbrain skillpack endorse <name> [--tier ...] [--push] [--dry-run] runs in a clone of the registry repo: validates the pack in registry.json, mutates endorsements.json via pure applyEndorsement, stable-key-orders the write, commits endorse: <name> -> <tier>, optionally pushes. JSONL audit at ~/.gbrain/audit/skillpack-YYYY-Www.jsonl (ISO-week rotated, honors GBRAIN_AUDIT_DIR). examples/skillpack-reference/ is a 10/10 reference pack pinned by test/e2e/skillpack-third-party.test.ts. docs/skillpack-anatomy.md auto-generated via scripts/build-skillpack-anatomy.ts (--check for CI drift). CLI dispatch in src/commands/skillpack.ts disambiguates third-party (contains /, ://, .tgz) from bundled-skill kebab; kebab routes bundled-first, registry-fallback. Tests: test/skillpack-{manifest-v1,tarball,state,remote-source,trust-prompt,registry-schema,registry-client,rubric,doctor,init-scaffold,pack-publish,endorse,audit,scaffold-third-party}.test.ts + test/e2e/skillpack-third-party.test.ts. Spec at docs/designs/SKILLPACK_REGISTRY_V1_SPEC.md.

• src/core/archive-crawler-config.ts — safety gate for the archive-crawler skill. Refuses to run unless archive-crawler.scan_paths: is explicitly set in the brain repo's gbrain.yml. Mirrors the storage-config.ts parsing pattern (sibling file, separate concern from storage tiering). loadArchiveCrawlerConfig(repoPath) throws ArchiveCrawlerConfigError(missing_section | empty_scan_paths | invalid_path | parse_error). normalizeAndValidateArchiveCrawlerConfig rejects relative paths and .. traversal; ~ is expanded; paths are stored resolved and terminated with the PLATFORM separator (path.sep) so error output reads natively on each OS. isPathAllowed(candidate, config) is the runtime per-file gate (scan_paths prefix-match with directory-boundary correctness; deny_paths overrides). Candidate, scan_paths and deny_paths all funnel through the private toComparablePrefix() before the prefix test — on Windows it folds \→/ and lowercases (NTFS is case-insensitive, so a deny_path spelled Private must still match private, else the gate fails OPEN); on POSIX it is identity apart from the trailing separator, deliberately NOT folding, since \ is a legal filename character and paths are case-sensitive. Storing a native separator while appending a hardcoded / is the mixed-separator bug that made isPathAllowed deny every real path on Windows; the two functions must stay symmetric or the prefix test is meaningless. Pinned by test/archive-crawler-config.test.ts (26 cases, platform-selected fixtures + it.if-gated win32/POSIX comparison semantics).

• test/helpers/tty-harness.ts + scripts/dx-explore.ts — the repo's single real-PTY layer, on pure Bun.spawn({terminal:}) (Bun 1.3.10+; engines.bun pin in package.json; no node-pty). launchTty spawns any CLI under a true pseudo-terminal with the hermetic env contract from test/helpers/agent-harness.ts (hermeticChildEnv; dropEnv strips pass-through auth keys), records timestamped output frames, and exposes waitFor/waitForAny/mark/sendKey/waitForQuiet/waitForExit/close. Lifecycle rule: only close() clears the wall-clock kill timer — always call it in a finally. Pure helpers (stripAnsi, computeStalls, renderStallsReport, parseDriveCommand, buildClaudeTuiSeed) are unit-tested in test/tty-harness.test.ts; that file's live-PTY smokes are describe.skipIf(!ptySupported())-gated. Transcript writes are structurally redacted: redactSecrets (secrets ≥ MIN_REDACT_SECRET_LEN → [REDACTED:<name>]) runs at every write site, coalesceSecretStraddles merges frames so a secret split across a frame boundary can't bypass redaction, and saveTranscript takes an explicit redact map (seam — dx-explore builds it, tty-harness stays import-free of it). scripts/dx-explore.ts is the DX-exploration driver built on it — a developer instrument, not a test: nothing asserts, transcripts land gitignored under .context/dx-runs/ (doc: docs/guides/bootstrap.md). The interactive gbrain init pickers are asserted for real in test/init-picker-pty.serial.test.ts (serial lane, so it runs in required CI).

• src/core/skillpack/{init-brain-pack,brain-pack-advisory,brain-pack-lint,brain-resident-locate,nag-state}.ts (#2180) — brain-resident skillpacks. manifest-v1.ts gains optional brain_resident + schema_pack (additive). runInitBrainPack scaffolds a pack beside brain content (brain_resident:true, exact gbrain_min_version, 5-section machine-parseable README); applyWritePlan is factored out of init-scaffold.ts for the shared refuse-overwrite loop. brain-pack-lint.lintBrainPackTools validates each skill's tools: against the serving op set (E6 version-skew). Topology A: src/commands/sources.ts runAdd prints brain-pack-advisory to stderr after opsAddSource, fail-open; nag-state.ts (~/.gbrain/skillpack-nag-state.json) keys declines by (source-repo brain_id, source_id, pack_name) with pure decideNagAction (first/reminder/version-bump/ceiling) — declines count ONLY on CLI-interactive displays. Topology B: brain-resident-locate.loadResidentPacksForServer (source-scoped via sourceScopeOpts) backs the list_brain_skillpack op; getResidentSkillDetail backs get_skill source_id; scaffold_spec is the git source, never a server FS path. Tests: test/skillpack-{init-brain-pack,nag-state,brain-resident-locate}.test.ts + the brain-resident cases in test/skillpack-manifest-v1.test.ts.

• src/core/advisor/{types,run,render,recommended-set,history,apply,collect-*}.ts + src/commands/advisor.ts (#2180) — gbrain advisor: read-only ranked actions from brain state. run.runAdvisor executes the hardcoded COLLECTORS array (version [cache-only], migration, schema-pack, stalled-jobs [absent-table tolerant], usage-shape, setup-smells, uninstalled-brain-pack, uninstalled-bundled, chronicle, mcp-client-fit), each in its own try/catch; collect-mcp-client-fit.ts (E3) flags full-surface MCP clients whose 30d usage fits STARTER_OPS (exact rescope-client --surface starter fix; ≥10-call threshold; automation-shaped clients excluded per D12) plus STARTER_OPS drift (top-used ops missing; starter members unused 90d) via the shared src/core/mcp-usage.ts reader — starter membership is judged against the exported ALWAYS_INCLUDED_STARTER_OPS (surface.ts) so the always-included lane never reads as unused, and the missing-from-starter arm excludes localOnly ops (never proposable for a network surface, mirroring derive-starter-ops) — REMOTE runs redact client identifiers to aggregate counts (amendment 29), and its dismiss/snooze rides the nag-state engine with its own ~/.gbrain/advisor-usage-nag-state.json (local runs only); rankFindings orders critical>warn>info then collector order, caps the info tail, and drops workspace_dependent findings when remote (A1). render.ts is the shared =-bar renderer used by the advisor AND post-install-advisory.ts (generalized to a single current-state recommended-set.RECOMMENDED, install→scaffold). history.ts appends bounded ~/.gbrain/advisor-history.jsonl (no DB migration) for since-last-run deltas; local-only. apply.resolveApplyTarget is the allowlist+injection guard for commands/advisor.ts --apply <id> (structured argv, never a shell; local-only). The advisor op (operations.ts) is read-scoped, NOT localOnly, gated by mcp.publish_advisor (config.ts; default off) and strictly read-only on remote. CLI wired in cli.ts (CLI_ONLY + dispatch). Bundled skill skills/gbrain-advisor/ + weekly cron recipe. Tests: test/advisor-{core,apply,op-gate,ranking-eval}.test.ts.

• src/core/chronicle/{eligibility,config,backstop,extract-events,ontology,narrative}.ts + src/eval/chronicle/harness.ts + src/commands/eval-chronicle.ts (#2390) — Life Chronicle: the temporal spine. eligibility.isChronicleEligible decides which pages auto-emit events (meeting/conversation/calendar-event + directory rescue; diary and event pages NEVER eligible — privacy + anti-loop). backstop.runChronicleBackstop is the put_page hook body (fires ONLY on status==='imported' + the auto-link trust gate + the default-OFF auto_chronicle flag; enqueues a chronicle_extract minion job — LLM never runs on the write path). extract-events.runChronicleExtract is the job body: deterministic when/who, injectable judge (default = chat gateway; output cap 4000 tokens by default, operator override chronicle.judge_max_tokens), an ALL-or-nothing parse barrier (isValidProposal requires a real parseable date — a malformed batch writes NOTHING), then content-addressed life/events/ pages + a timeline_entries projection via engine.upsertEventProjection (dedup (event_page_id, date); idempotent re-runs). An unusable judge response is never recorded as no_events (#2606): a stopReason: 'length' truncation or a no-JSON-array response (parseJudgeJson returns null on parse failure; [] only for a legitimate empty array) surfaces as status: 'skipped' with reason judge_truncated / judge_parse_failed. ontology.ts carries the deterministic pieces of the bi-temporal per-entity ontology that RIDES THE facts TABLE (migration v122 adds dimension/value/value_hash/dim_status): valueHash (normalized, timestamp-free → crash-retry idempotent), normalizeDimension (seed alias lexicon), isNovelDimension (novel → quarantined, excluded from resolution/context until confirmed). The engine methods (mergeOntologyFact — corroborate on same value, forward-supersede via valid_until+superseded_by on a new value, backdated conflicts kept + flagged; getOntology with --asof valid-time travel; discoverOntologyDimensions; findOntologyConflicts — currently-open rows only) live in BOTH engines; both engines are on the R8 valid_until write allow-list (engine-layer, dimension IS NOT NULL rows only). Chronicle reads (getTimelineForDate/getSince/getLastSeen/getOnThisDay) JOIN the depth page (deleted_at IS NULL), hide soft-deleted event projections at READ time, and order by event effective_date for intra-day sequence. Ops: chronicle_day/chronicle_since/chronicle_last_seen/chronicle_on_this_day/ontology_*/volunteer_chronicle (agent orientation via src/core/context/chronicle-context.ts)/chronicle_backfill (admin, localOnly). Diary privacy: diary-sourced ontology + conflict values redacted for ctx.remote !== false callers. Search: applyChronicleTypeBoost in search/hybrid.ts (bounded [1.0,1.25], fires only inside the recency !== 'off' post-fusion branch → non-temporal search bit-for-bit unchanged). Advisor collector collect-chronicle.ts (conflicts + coverage gap); doctor chronicle_projection_health (BRAIN category). Eval: gbrain eval chronicle — deterministic, own in-memory PGLite, 6 gold tasks (day order, last-seen, supersession, asof, conflict, isolation), exit 0 iff 6/6. Tests: test/chronicle-*.test.ts, test/eval-chronicle.test.ts.

• src/core/skill-manifest.ts — parser for skill-manifest.json records. Used by skillpack installer to detect drift between the shipped bundle and the user's local edits, so updates merge instead of overwriting.

• src/commands/routing-eval.ts + src/core/routing-eval.ts — gbrain routing-eval catches user phrasings that route to the wrong skill. Reads skills/<name>/routing-eval.jsonl fixtures ({intent, expected_skill, ambiguous_with?}). Structural layer runs in check-resolvable by default (zero API cost). --llm is a placeholder for a future LLM tie-break layer; today it emits a stderr notice and runs structural only. Uses autoDetectSkillsDirReadOnly and the same multi-file resolver merge as check-resolvable, so on OpenClaw layouts (skills/RESOLVER.md + ../AGENTS.md) all three commands see the same trigger index. RESOLVER.md rows carry the full frontmatter triggers: arrays so the structural matcher sees realistic phrasings; ambiguous-fixture annotations cover deliberate skill chains like enrich → article-enrichment.

• src/core/filing-audit.ts + skills/_brain-filing-rules.json — Check 6 of check-resolvable. Parses writes_pages: / writes_to: frontmatter on skills and audits their filing claims against the filing-rules JSON (error severity). Internal parseFrontmatter is a thin wrapper over the shared src/core/skill-frontmatter.ts parser so both filing-audit and skill-brain-first read the same shape (tools?, triggers?, brain_first?: 'exempt', typed brain_first_typo) from one source of truth.

• src/core/skill-frontmatter.ts — shared content-based SKILL.md frontmatter parser. Array fields (writes_to, tools, triggers) use js-yaml with the failsafe schema, accepting block lists and single-line or wrapped flow sequences while preserving the tolerant legacy regex fallback for partially malformed YAML; CRLF is normalized before fence parsing. Recognizes the brain_first: 'exempt' declarative opt-out and surfaces near-miss declarations (brain-first, BrainFirst, quoted values, unknown values) as a typed brain_first_typo field so doctor can emit a paste-ready hint rather than fail silently. Single canonical form: snake_case brain_first: exempt, lowercase, unquoted.

• src/core/skill-brain-first.ts — pure analyzer. analyzeSkillBrainFirst(skillPath, content): SkillBrainFirstResult walks the compliance ladder for every SKILL.md: (1) absent external-lookup pattern → no_external; (2) brain_first: exempt frontmatter → exempt_frontmatter; (3) canonical > **Convention:** see [conventions/brain-first.md](...) callout → compliant_callout; (4) explicit ## Phase 1: Brain heading → compliant_phase; (5) first gbrain search/query/get_page reference precedes first external pattern in the BODY (frontmatter stripped) → compliant_position; (6) else missing_brain_first warn. External pattern set: word-boundary regex over web_search, web_fetch, exa, perplexity, happenstance, crustdata, captain_api, firecrawl. Position scan is BODY-ONLY so a tools: [web_search] frontmatter declaration doesn't false-flag the skill. The 40-name FORMERLY_HARDCODED_EXEMPT list is preserved so doctor can emit a "this used to be auto-exempt, declare brain_first: exempt if still appropriate" hint. Consumed by 3 surfaces: doctor check, skillify-check item 12, dry-fix MISSING_RULE_PATTERNS.

• src/core/skill-fix-gates.ts — shared safety primitives extracted from dry-fix.ts. getWorkingTreeStatus(file) 3-state ('clean' | 'dirty' | 'not_a_repo'); isInsideCodeFence(content, offset); findAfterH1Paragraph(content) (canonical insertion offset for the auto-inserted Convention callout). Both REPLACE expanders (DRY violations) and the INSERT expander (MISSING_RULE_PATTERNS) consume from here so the install-path refusal and dirty-tree gates apply uniformly. src/core/dry-fix.ts re-exports for back-compat with existing call sites.

• src/core/audit-skill-brain-first.ts — snapshot+diff JSONL audit at ~/.gbrain/audit/skill-brain-first-YYYY-Www.jsonl (ISO-week rotated, honors GBRAIN_AUDIT_DIR via shared resolveAuditDir()). recordBrainFirstRun(results) reads the previous snapshot at ~/.gbrain/audit/skill-brain-first-snapshot.json, diffs against current results, writes transition events (detected | resolved | fixed) one line per change, then atomically overwrites the snapshot via .tmp + rename. Transition-only writes — a stable brain produces 0 audit lines per doctor run. readRecentBrainFirstEvents(days) is the readback path for the future skill_brain_first_trend doctor check. Snapshot file is last-writer-wins under concurrent doctor runs; subsequent runs reconcile.

• src/core/dry-fix.ts — gbrain doctor --fix engine. autoFixDryViolations(fixes, {dryRun}) rewrites inlined rules to > **Convention:** see [path](path). callouts via three shape-aware expanders (bullet / blockquote / paragraph). Five guards: working-tree-dirty (getWorkingTreeStatus() 3-state 'clean' | 'dirty' | 'not_a_repo'), no-git-backup, inside-code-fence, already-delegated (40-line proximity, consistent with detector), ambiguous-multi-match, block-is-callout. execFileSync array args (no shell, no injection surface). EOF newline preserved. Safety primitives are in src/core/skill-fix-gates.ts (back-compat re-exports preserved). MISSING_RULE_PATTERNS INSERT pattern type lives alongside REPLACE patterns — same auto-fix entry point + git-safety gates, but places a canonical callout at a target offset (after-h1-paragraph only). First INSERT pattern is brain_first, auto-inserting > **Convention:** see [conventions/brain-first.md](../conventions/brain-first.md) for the lookup chain (search → query → get_page → external). on any flagged SKILL.md whose verdict is missing_brain_first. Idempotent — re-runs detect the existing callout and skip.

• src/core/backoff.ts — Adaptive load-aware throttling: CPU/memory checks, exponential backoff, active hours multiplier.

• src/core/retry.ts — canonical retry primitive for transient connection errors. Exports withRetry<T>(fn, opts) execution wrapper + BULK_RETRY_OPTS constant ({maxRetries:3, delayMs:1000, delayMaxMs:10000, jitter:'decorrelated'}, tuned for Supabase Supavisor's 5-10s circuit-breaker recovery) + BATCH_AUDIT_SITES typed const (closed enum of every audit-emission site) + resolveBulkRetryOpts(env) (reads GBRAIN_BULK_MAX_RETRIES/GBRAIN_BULK_RETRY_BASE_MS/GBRAIN_BULK_RETRY_MAX_MS with >=0 validation, throws on bad input with a paste-ready hint) + abortableSleep(ms, signal?) + RetryAbortError (tagged error for clean shutdown) + computeNextDelay() (pure-fn for 3 jitter modes: 'none', 'full', 'decorrelated'). The execution wrapper is consumed by postgres-engine.ts + pglite-engine.ts batch primitives (addLinksBatch / addTimelineEntriesBatch / upsertChunks) so every caller inherits retry as part of the data-primitive's contract. CI guard scripts/check-no-double-retry.sh fails the build on withRetry(...engine.batch...) patterns (prevents 3×3=9 retry amplification); scripts/check-batch-audit-site.sh validates every string-literal auditSite: '...' against the closed BATCH_AUDIT_SITES enum. Decorrelated jitter (AWS-style: uniform(base, prevDelay*3) capped at delayMaxMs) — 'full' jitter allowed near-zero retries that re-hit the recovering breaker. WithRetryOpts has an optional reconnect?: () => Promise<void> callback awaited in the catch branch AFTER isRetryableConnError classification but BEFORE the inter-attempt sleep — lets engine-level callers rebuild a dead pool/singleton between attempts. PostgresEngine.batchRetry injects () => this.reconnect() (the race-safe _reconnecting guard kicks in). Fail-loud: a reconnect throw PROPAGATES as the new error, replacing the symptomatic "No database connection". onRetry callbacks are awaited (sync arrows work identically; async callbacks correctly delay the sleep). Pinned by test/core/retry.test.ts (37 cases), test/core/retry-stress.slow.test.ts (5 cases, 100 batches × 30% blip rate, asserts zero row loss), test/core/retry-reconnect.test.ts (5 cases), test/e2e/db-singleton-shared-recovery.test.ts (3 DB-gated cases).

• src/core/process-watchdog.ts (#1633) — out-of-band hard-deadline killer for gbrain sync. A spinning sync (synchronous catastrophic-regex / ReDoS in pack link-inference) STARVES the main event loop, so the existing SIGTERM handler (process-cleanup.ts), --timeout setTimeout, and abort-flag checks can't fire — the process becomes unkillable-by-SIGTERM and, under cron, orphans pile up for 24h+ (the reported incident). installProcessWatchdog({deadlineMs, graceMs?, label?, heartbeatMs?, onWarn?}): WatchdogHandle spawns a Bun worker_threads Worker via new Worker(code, {eval: true, workerData}) — its own OS thread + event loop fires even while main is in an unyielding sync loop. At deadlineMs it process.kill(process.pid, 'SIGTERM') (clean-shutdown chance if responsive); at deadlineMs+graceMs process.kill(process.pid, 'SIGKILL') (uncatchable — guaranteed death under starvation). Signaling SELF has NO PID-reuse footgun (current PID never reused while alive — the reason the detached-child-watches-parent design was rejected). eval: true bakes the worker body into the bun build --compile binary with no separate-file embedding. Empirically validated on Bun 1.3.13 (worker timer + SIGKILL killed a while(true){}-starved process). handle.dispose() (clean-exit finally) worker.terminate()s it; unref()'d so it never keeps the process alive. Pure watchdogDecision(elapsedMs, deadlineMs, graceMs) → 'wait'|'sigterm'|'sigkill' extracted for unit tests, and pure exported clampWatchdogTimers(deadlineMs, graceMs) + MAX_WATCHDOG_TIMER_MS clamp BOTH worker timers so the deadline AND the deadline+grace SUM stay ≤ 2^31−1 — setTimeout overflow-fires above that at ~1ms, which for the sum timer would be an instant SIGKILL of a healthy process (unit-tested as pure arithmetic only; never arm a real max-deadline worker in-suite — its firing SIGTERMs the test runner itself). Optional heartbeatMs emits periodic [<label>] parent alive Ns, hard-kill in ~Ms lines (visible in cron logs even under starvation — the diagnosis surface). Fallback: if new Worker throws, degrades to an in-process timer with a loud warning that it can't fire under starvation. Two adopters: gbrain sync (below) and the opt-in PGLite disconnect watchdog (pglite-engine.ts entry above); autopilot/cycle are follow-up candidates. Pinned by test/process-watchdog.test.ts (pure decision matrix + clamp arithmetic + handle contract) + test/process-watchdog.serial.test.ts (Bun-pinned spawn integration: a starved harness process IS killed ~deadline+grace, a no-watchdog control does NOT self-exit, clean dispose never kills). Wired into src/cli.ts sync dispatch BEFORE connectEngine (so a connect-phase hang is bounded too); deadline resolved by resolveSyncHardDeadline in sync.ts (precedence: --no-hard-deadline > --hard-deadline > --timeout(non---all) > GBRAIN_SYNC_MAX_RUNTIME_SECONDS env > non-TTY default 3600s > none).

• src/core/process-cleanup.ts — cleanup registry + abnormal-termination handlers (SIGTERM/SIGHUP/SIGPIPE, uncaughtException/unhandledRejection, EPIPE-on-stdout) that release locks before exit. registerCleanup(name, fn) returns a deregister handle; tryAcquireDbLock auto-registers. installSignalHandlers() is idempotent and called from INSIDE cli.ts's import.meta.main seam (first statement before main()), NOT at module load — installing at import time leaked a process-wide SIGTERM→process.exit(143) handler into any process that merely imports cli.ts (bun test runners died mid-suite when a test emitted a synthetic SIGTERM; the runner misread rc=143 as an external kill). Spawned/compiled CLI processes are entrypoints, so they still install. Every attached listener ref is recorded so _resetForTests() DETACHES them (clearing flags alone left the exit(143) listener live on the shared runner). Tests that must emit synthetic signals strip foreign listeners around the emit (see test/run-child-entry.test.ts).

• src/core/preferences.ts — preferences.json + the migration ledger (migrations/completed.jsonl append/read helpers; appendCompletedMigration, loadCompletedMigrations). Path resolution delegates to config.ts:gbrainPath(), so GBRAIN_HOME follows the ONE canonical convention: it is a PARENT dir and .gbrain is appended (GBRAIN_HOME=/tmp/x → /tmp/x/.gbrain/migrations/...). Its previous local resolver returned GBRAIN_HOME directly, splitting one logical home across two roots (config at $GBRAIN_HOME/.gbrain/config.json, ledger at $GBRAIN_HOME/migrations/) — while claiming in its own comment to match gbrainPath. copyForwardLegacyFile migrates the pre-unification layout once per file on first touch: atomic (temp + linkSync, EEXIST = concurrent winner), JSON-validated for prefs, chmod 0600, copy-not-move for binary rollback, once-per-process warning; a valid-but-uncopyable legacy file (read-only home) is READ IN PLACE so a transient failure can't drop a minion_mode opt-out or migration history. One-shot by design — mixed-version writers diverging post-snapshot is an accepted, documented limitation.

• src/core/audit/batch-retry-audit.ts — JSONL audit primitive for batch-retry events, built on audit-writer.ts. Schema: {ts, site, batch_size, attempt, outcome: 'success' | 'exhausted', delay_ms, error_message_summary, error_code?}. Privacy: NEVER logs slugs / page IDs / content (mirrors shell-audit.ts). logBatchRetry fires per successful retry recovery; logBatchExhausted fires when retries exhaust and rows are lost. readRecentBatchRetryEvents(hours=24) returns {events, corrupted_lines, files_scanned, files_unreadable} — corruption + permission errors surface to doctor, not silently swallowed. pruneOldBatchRetryAuditFiles(daysToKeep=30) deletes old files, called from gbrain dream --phase purge. File: ~/.gbrain/audit/batch-retry-YYYY-Www.jsonl (honors GBRAIN_AUDIT_DIR). summarizeError routes error messages through the shared redactConnectionInfo helper from src/core/audit/redact-connection-info.ts BEFORE truncation so DSNs / hostnames / credentials / IPv4 octets can't leak into operator-shared JSONL dumps. Pinned by test/audit/batch-retry-audit.test.ts (12 cases) + test/audit/batch-retry-redaction.test.ts (3 privacy regressions).

• src/core/audit/lock-renewal-audit.ts — JSONL audit primitive for per-job lock-renewal faults. Sibling of batch-retry-audit.ts, built on audit-writer.ts. Four outcomes: failure (single renewLock throw, counter incremented), success_after_failure (recovery; emits the recovery count), gave_up (time-based deadline exceeded; abort fired), executeJob_rejected (the second unhandledRejection vector — the stored executeJob(...).finally(...) promise itself rejected, e.g. failJob threw during the same DB outage). Schema: {ts, job_id, job_name, attempt?, outcome, error_message_summary?, error_code?} plus additive v0.46 (#4145) telemetry fields (cause?, lateness_ms?, overlap_skips?, load1?, cores?, via?, deadline_deferred?) threaded via an optional trailing ctx param on the sink (compactCtx copies only DEFINED fields so absent telemetry stays absent from the JSONL). Privacy: NEVER logs lock_token or job.data; error summaries route through redactConnectionInfo BEFORE truncation. Defense-in-depth: every audit call inside the lock-renewal tick's catch block is wrapped in its own inner try/catch so a misbehaving audit-writer can't re-introduce the unhandledRejection bug class. readRecentLockRenewalEvents(hours=24) walks current + previous ISO week with corrupted-line tolerance. pruneOldLockRenewalAuditFiles(daysToKeep=30) is ready for future dream-cycle purge wiring. File: ~/.gbrain/audit/lock-renewal-YYYY-Www.jsonl. Pinned by test/audit/lock-renewal-audit.test.ts (incl. ctx round-trip + pre-upgrade-line readback).

• src/core/audit/redact-connection-info.ts — Shared pure helper. redactConnectionInfo(text: string): string strips Postgres connection info before any audit JSONL write: postgres:///postgresql:// URLs, host=foo, user=foo, password=foo, pwd=foo, IPv4 octets — each match becomes <REDACTED:kind>. Negative-lookbehind/lookahead [\w.@-] on the IPv4 pattern defeats version-string false positives (v3.1.4.0, tree-sitter@0.26.3.1) while still matching real IPs in PG errors ((192.168.1.42)). Order-sensitive pattern set: URL forms first so substrings inside URLs don't get double-redacted. Idempotent, pure (no I/O), hot-path-safe (regex compiled at module load). Wired into lock-renewal-audit.ts, batch-retry-audit.ts, and cli.ts's doctor DB-fallback stderr note (layered with url-redact.ts:redactUrlsInText). Known limitations: bare-quoted hostnames (at "db.example.com") and usernames (for user "postgres.foo") are NOT caught — the highest-value leak (the IP in those shapes) IS caught. Pinned by test/audit/redact-connection-info.test.ts (15 cases: all 5 patterns + Supabase fixture + ENOTFOUND fixture + version-string false-positive defense).

• src/core/url-redact.ts — Postgres-URL + free-text credential redaction, sibling of redact-connection-info.ts. redactPgUrl(url) strips userinfo from a single postgres/postgresql URL, preserving scheme/host/port/db/query (non-URL input collapses to <redacted-url>). redactUrlsInText(text) sweeps free text (error messages, log lines) for credential shapes of any word-character scheme (the pattern is \w+://, so scheme names containing +/-/. are not matched — postgres shapes are the target): the userinfo match is greedy up to the LAST @ in the token so a raw @ inside a password can't leak its tail (over-redacts toward safety), and libpq keyword/value forms (password= / sslpassword=, including quoted values with spaces) are masked too; text without a credential shape passes through untouched. redactDeep(value) recursively redacts postgres URLs inside structured payloads about to be stringified. Consumers: the upgrade-errors + connection-events audit JSONL sites, doctor's connection_routing check output, and cli.ts's doctor DB-fallback stderr note (layered with redactConnectionInfo). CI guard: scripts/check-pg-url-redaction.sh fails the build when a new code path emits an unredacted postgres URL. Pinned by test/url-redact.test.ts.

• src/core/minions/lock-renewal-tick.ts — Pure extracted function from MinionWorker.launchJob's setInterval body; the structural fix that closes the production unhandledRejection crash class, now carrying the #4145 verify-before-evict doctrine. Exports runLockRenewalTick(deps, state) → Promise<TickResult> + resolveLockRenewalKnobs(env, lockDuration, intervalMs?) → LockRenewalKnobs + RenewalCallTimeoutError + LockRenewalTelemetryCtx. Doctrine: a thrown/timed-out renewal is NOT evidence of loss — when the NEXT tick would land past the soft deadline (lease - safetyMargin, cadence-aware: sinceLastSuccess + intervalMs >= deadline), the tick runs ONE bounded fenced VERIFY renewal. Fenced-true → starved-but-ours, lease re-extended, counter reset (audit success_after_failure with via: 'verify'); fenced-false → CERTAIN loss → lock_lost (the only certain signal); verify unreachable → defer + reconnect-once (audit failure with deadline_deferred: true), aborting only past hardEvictMs — a LOCAL decision under uncertainty bounding blind external side effects during a total outage. Four env knobs, positive-int parsed with stderr-warn-once + default fallback, then RELATIONALLY validated (margin < lease/2, callTimeout ≤ cadence, hardEvict ≥ soft deadline — warn-once clamps): GBRAIN_LOCK_RENEWAL_MAX_FAILURES (default 3, audit-labeling only), GBRAIN_LOCK_RENEWAL_CALL_TIMEOUT_MS (default min(lease/3, 15s)), GBRAIN_LOCK_RENEWAL_SAFETY_MARGIN_MS (default min(lease/6, 30s)), GBRAIN_LOCK_RENEWAL_HARD_EVICT_MS (default 2×lease, floored to the soft deadline; setting it TO the deadline approximates legacy abort-at-deadline). Telemetry: tick lateness (now - lastTickFiredAt - intervalMs, the primary local-starvation signal — interval callbacks COALESCE under a blocked loop so missed-tick counters can't measure starvation), overlapSkips (tickInFlight re-entrancy skips only), failure-cause classification via the named RenewalCallTimeoutError (call-timeout | refused | fenced-lost), optional deps.loadSnapshot (try/caught — telemetry must never throw into control flow) and deps.onRenewalSuccess (worker resets its event-loop-delay histogram). Elapsed-time arithmetic runs on the injected deps.now, which production binds to performance.now() (monotonic) — the local clock only schedules WHEN to verify, never WHETHER to evict. The race timeout also aborts the in-flight call via AbortSignal threaded to renewLock (best-effort — the fence is the correctness authority). The tick checks state.cancelled() at every await boundary (entry, post-resolve, post-throw, post-verify). Result is a tagged union: should_abort carries {cause, latenessMs, sinceLastSuccessMs, overlapSkips, load1?, cores?} and lock_lost carries {cause: 'fenced-lost', via: 'renewal'|'verify'}; the worker stashes the result as per-launch abortMeta so the grace-evict log (30s later) reports the classified cause. The in-tick verify is reconciled in-code with queue.ts's no-background-retry rationale: it is synchronous, cancelled()-guarded, and callTimeoutMs-bounded — both UPDATEs are same-token idempotent lease extensions, so a fenced row cannot gain two holders. Pinned by test/worker-lock-renewal.test.ts (hermetic state-machine suite incl. the fake-time #4145 incident replay, CDX-4 cadence-quantization pin, hard-backstop timelines, relational-clamp cases) + test/e2e/worker-lock-renewal-starvation.test.ts (real-PG foundations). LockRenewalDeps.renewLock carries an optional per-call {signal}; the timeout race aborts it so the losing UPDATE releases its slot (issue #6 abandoned-racer class).

• src/core/minions/worker-exit-codes.ts — single source of truth for reserved worker process exit codes, shared by the worker (sets them) and supervisor/CLI (classify them). Exports WORKER_EXIT_RSS_WATCHDOG = 12. The RSS watchdog drain must be self-identifying: a code-0 exit is indistinguishable from a healthy queue-drain, so the supervisor's code===0 → clean_exit classifier never counted it and a respawn loop stayed invisible. A distinct code makes the drain likely_cause=rss_watchdog. Code 12 is deliberately outside {0 clean, 1 runtime_error} and the 128+N signal range. Also reserves the jobs run-child codes: 13 usage/PGLite, 14 not-claimed/token-mismatch, 15 result-write-failed (result-file presence, not the exit code, classifies the normal path).

• src/core/minions/rss-default.ts — cgroup-aware auto-sized default for the worker RSS watchdog cap. resolveDefaultMaxRssMb(opts?) / describeDefaultMaxRss(opts?) (provenance for the startup log) / readCgroupMemLimitBytes(readFile?). Replaces a flat 2048MB default at every spawn site (jobs work, jobs supervisor, autopilot, MinionSupervisor). Formula clamp(round(0.5 × basisMB), 4096, 16384) where basis = min(cgroupLimit, totalmem). LOAD-BEARING NUANCE: plain os.totalmem() reports HOST RAM, so in a 4GB cgroup on a 126GB host it would pick 16GB, the watchdog would never fire, and the kernel OOM-killer would SIGKILL at 4GB. The cap MUST sit below the real ceiling so the graceful drain (distinct exit code, loud log) beats the kernel's silent kill; the 4096 floor applies only when it stays below the basis. Reads cgroup v2 /sys/fs/cgroup/memory.max (literal max = unlimited) then v1 /sys/fs/cgroup/memory/memory.limit_in_bytes. Explicit --max-rss (including 0 to disable) always wins. Pinned by test/rss-default.test.ts.

• src/core/cycle/extract-atoms-drain.ts — pure single-hold bounded drain for the silent lens-phase backlog. runExtractAtomsDrain(deps, opts) over injected deps (withLock, runBatch, countRemaining, now, optional onBatch) loops bounded batches under ONE continuous lock hold, rediscovering eligibility each batch (idempotent NOT-EXISTS-on-source_hash, so content mutated by a concurrent process simply doesn't match — no cross-window stale cursor), until the backlog is empty OR the time window elapses. Returns {phase, status, extracted, skipped, remaining, batches, stopped}. Backs gbrain dream --phase extract_atoms --drain. Takes the SAME cycleLockIdFor(sourceId) the routine cycle takes (a concurrent autopilot tick genuinely defers with cycle_already_running); NO release/reacquire-between-windows primitive. The shared wiring helper runExtractAtomsDrainForSource(engine, {sourceId, windowSeconds, brainDir?, maxBatches?, onBatch?}) owns the lock+batch+count+defer wiring (dynamic imports of db-lock/cycle/extract-atoms keep the pure loop cheap to unit-test) and is the ONE drain path for three callers — gbrain dream --drain (which calls it), the extract-atoms-drain Minion handler, and autopilot auto-drain — so lock id / window / defer-on-busy can't drift. sourceId: undefined → legacy gbrain-cycle lock + 'default' extraction; a real id → gbrain-cycle:<id>. LockUnavailableError propagates to the caller (each reports the busy case its own way). Pinned by test/extract-atoms-drain.test.ts.

• scripts/check-worker-lock-renewal-shape.sh — CI guard wired into bun run verify. Two invariants on src/core/minions/worker.ts: (1) the bug pattern lockTimer = setInterval(async ...) must NOT appear (narrowed via lockTimer = prefix so unrelated setInterval(async) calls — like the stall detector — don't false-fire), (2) runLockRenewalTick must remain referenced so the pure-function test seam survives refactors. Bug-pattern-specific by design — a future refactor to setTimeout-recursion or AbortController-based scheduling passes as long as the bug pattern stays absent. POSIX ERE + [[:space:]] for BSD-grep portability. Honors GBRAIN_LOCK_RENEWAL_SHAPE_TARGET env override for fixture-based meta-tests. Pinned by test/scripts/check-worker-lock-renewal-shape.test.ts (5 cases).

• src/core/doctor-cause-rank.ts — pure cause-ranking for gbrain doctor. rankIssues(checks) returns non-ok checks ordered fail-before-warn then root-before-symptom then name (deterministic). ROOT_CAUSE_CHECKS / SYMPTOM_CHECKS are ORDERING ONLY — tier membership asserts no causality. downstream_of is set ONLY from a small map of KNOWN grounded edges (queue_health / supervisor → worker_oom_loop, since they read the same aborted: watchdog / rss_watchdog source) AND only when the named root is itself failing — never a root×symptom cartesian (co-occurrence never implies causality). fix prefers details.fix_hint else the message. CAUSE_GRAPH_NAMES + allKnownCheckNames() back a drift guard asserting every graphed name is a real check. Consumed by computeDoctorReport (top_issues field, additive, schema_version stays 2) + the "Top issues (ranked by cause)" header in outputResults. Pinned by test/doctor-cause-rank.test.ts.

• src/core/audit/pool-recovery-audit.ts — reap/reconnect audit on the shared audit-writer cathedral. Events: reap_detected (CONNECTION_ENDED), reconnect_other (network/auth/health-check), reconnect_succeeded, reconnect_failed. readRecentPoolRecoveries(hours=1) returns {reaps, recoveries, failures, others, events}. Error summaries route through redactConnectionInfo before truncation (DSN/host/IP safe). Emitted ONLY from PostgresEngine.reconnect(ctx?) (the rare reap-retry path, near-zero hot-path cost); reconnect() classifies the threaded error via isConnectionEndedError (in retry-matcher.ts) so only true pooler reaps are labeled reap_detected. The retry callback in retry.ts threads the triggering error as (ctx?: {error?}) => Promise<void>. Pinned by test/audit/pool-recovery-audit.test.ts.

• src/core/audit/db-disconnect-audit.ts — JSONL audit for every call to db.disconnect() and PostgresEngine.disconnect(). Built on audit-writer.ts. Schema: {ts, engine_kind: 'postgres'|'pglite'|'unknown', connection_style: 'module'|'instance'|'unknown', caller_stack, command, pid}. caller_stack captured via new Error().stack truncated to ~20 frames so operators identify the offending caller without inflating JSONL. Privacy: stack frames carry file paths but NO SQL content / row data / user strings. File: ~/.gbrain/audit/db-disconnect-YYYY-Www.jsonl (honors GBRAIN_AUDIT_DIR). readRecentDbDisconnects(hours=24) walks current + previous ISO week and returns {count, most_recent_caller, files_scanned}. Wired into src/core/db.ts:disconnect and src/core/postgres-engine.ts:disconnect, logging BEFORE the early-return branches so even no-op disconnects on never-connected engines are recorded (that case may itself be a caller-side bug). Pinned by test/db-disconnect-audit.test.ts (6 cases: round-trip, stack truncation, sort order, empty-dir nulls, stable feature name, EROFS best-effort).

• src/core/facts/queue.ts:FactsQueue.drainPending — method drainPending({timeout?: number}): Promise<{drained, unfinished}>. Semantically distinct from shutdown() (which calls this.internalAbort.abort() and would abort the very facts:absorb worker trying to log its post-completion event). Drain lets in-flight finish; only the wait is bounded. Default timeout 1000ms so commands that don't enqueue facts pay one fast 0ms check before exit. src/cli.ts op-dispatch finally block awaits getFactsQueue().drainPending({timeout: 1000}) BEFORE engine.disconnect(). Lazy-import keeps the facts-queue module off the hot path for ops that never touch it. Closes the trailing 'No database connection' line after gbrain capture (post-page-write facts:absorb outlived the CLI process). Pinned by test/facts-queue-drain-pending.test.ts (4 cases: empty fast-path, in-flight settled without abort, unfinished count on timeout, default timeout = 1000ms).

• scripts/check-no-double-retry.sh + scripts/check-batch-audit-site.sh — CI lint guards wired into bun run verify. The former greps src/ for withRetry(...engine.{addLinksBatch|addTimelineEntriesBatch|upsertChunks}) patterns and fails the build on hit (prevents 3×3=9 retry amplification on incomplete reverts); its single-line pattern crosses arrow-callback parens (the canonical banned shape is withRetry(() => engine.addLinksBatch(...)) — a paren-stopping regex cannot see it), and its multi-line fallback runs under perl (always present locally and in CI). Both are proven fail-able by the guard self-test fixtures under test/fixtures/guards/. The latter extracts every string-literal auditSite: '...' from src/ and validates each appears in the BATCH_AUDIT_SITES const in src/core/retry.ts (typo guard — prevents fragmented doctor output).

• src/core/fail-improve.ts — Deterministic-first, LLM-fallback loop with JSONL failure logging and auto-test generation.

• src/core/transcription.ts — Audio transcription: Groq Whisper (default), OpenAI fallback, ffmpeg segmentation for >25MB.

• src/core/enrichment-service.ts — Global enrichment service: entity slug generation, tier auto-escalation, batch throttling. Write path is trust-gated (issue #160): enrichEntity / enrichEntities / extractAndEnrich take EnrichmentTrustOptions { trusted?, sourceId? }; only an explicit trusted: true writes authoritative people/ / companies/ stubs. Anything else (undefined/false — fail-closed, mirroring OperationContext.remote) creates the stub with the extraction quarantine markers from src/core/extraction-review.ts and reports quarantined: true in EnrichmentResult. The ONLY sanctioned op surface is extract_entities (operations.ts), which grants trusted solely for ctx.remote === false callers passing --trusted-extraction.

• src/core/extraction-review.ts — Extraction quarantine lane markers (issue #160), sibling of src/core/quarantine.ts / embed-skip.ts (frontmatter-key pattern, no schema migration). Auto-extracted stubs from untrusted input carry the PAIR provenance: 'auto-extracted' + status: 'unverified' (both required — user pages with their own status/provenance never match). Exports quarantineMarkers(), isUnverifiedExtraction() (JS predicate) and unverifiedExtractionFragment(alias) — the single SQL source of truth consumed by buildSourceFactorCase (namespace source-boost guard), both engines' getUnverifiedExtractionPageIds, the extraction_pending op, and the unverified_extractions doctor check, so filter and marker keys can never drift. Consequences: unverified stubs are excluded from the compiled-truth fusion boost + the people//companies/ source-boost (rank as ordinary content), stamped unverified: true in search results (stampUnverifiedExtractions, hybrid.ts), listed by extraction_pending, promoted (status → verified, provenance kept for audit) or rejected (soft-delete) by the owner-only extraction_review op. Pinned by test/extraction-review.test.ts (PGLite) + test/e2e/extraction-review-postgres.test.ts (live Postgres parity).

• src/commands/enrich.ts + src/core/enrich/thin.ts + src/core/cycle/enrich-thin.ts — gbrain enrich --thin: batch-develops stub (thin) pages via brain-internal grounded synthesis. gbrain's model tooling sees only brain-internal context (search / get_page / facts / backlinks), not the web, so enrich consolidates what the brain ALREADY knows about an entity (scattered across meetings, other pages, deals, facts) into one cited page via ONE gateway.chat call per page; web research stays the agent-driven enrich SKILL's job. runEnrichCore(engine, opts, signal) (strict per-source; multi-source iteration is the caller's job) drives enrichOne per candidate: withRefreshingLock('enrich:<src>:<slug>') → getPage → deterministic retrieve (hybridSearch + getBacklinks + facts + raw_data, source-scoped, sanitized via INJECTION_PATTERNS) → assessGrounding gate (skip < MIN_CONTEXT_CHARS, no LLM) → buildEnrichPrompt (grounded dossier, [Source: slug] citations, SKIP sentinel) → synth → put_page handler (remote:false, auto-link + write-through) stamping enriched_at + enriched_by:'cli:enrich'. Candidate selection is the SQL-native engine.listEnrichCandidates(opts) (src/core/engine.ts interface + EnrichCandidate/EnrichCandidatesOpts/ENRICH_ORDER_SQL in src/core/types.ts + pg/pglite impls): thin-filter + per-page source-correct inbound count (to_page_id = p.id, mentions excluded) + enriched_at recency guard + whitelisted ORDER BY + LIMIT, lightweight projection (NO bodies). Resume via src/core/op-checkpoint.ts (local enrichFingerprint); budget via BudgetTracker + withBudgetTracker (best-effort under --workers > 1 — runSlidingPool aborts new claims on BUDGET_EXHAUSTED but does NOT cancel in-flight gateway.chat; pin --workers 1 for a hard ceiling). sanitizeContext (thin.ts) neutralizes the <context>…</context> data-envelope delimiters (injection escape, mirrors the </trajectory> convention); the --background multi-source fan-out idempotency key carries the run fingerprint via exported backgroundIdempotencyKey(sid, args) (a bare enrich:${sid} would return stale completed jobs); runEnrichCore flags budget_exhausted post-hoc when tracker.totalSpent > tracker.cap even when the gateway swallowed the final-call throw (via read-only BudgetTracker.cap getter); body() flushes the checkpoint on BudgetExhausted before it propagates so resume doesn't re-charge. The opt-in enrich_thin cycle phase (default OFF via cycle.enrich_thin.enabled) trickles max_pages_per_tick (default 3) per source with per-source cost cap enforced as min(per_source_cap, brain_wide_remaining) + brain-wide total + walltime caps. Wired into cycle.ts (CyclePhase/ALL_PHASES between conversation_facts_backfill and skillopt/embed; PHASE_SCOPE='source'; NEEDS_LOCK; dispatch), cli.ts (CLI_ONLY + CLI_ONLY_SELF_HELP + THIN_CLIENT_REFUSED_COMMANDS + dispatch), jobs.ts (Minion enrich handler, strict per-source, NOT in PROTECTED_JOB_NAMES). DI seam opts.synthesizeFn keeps tests hermetic (no API key, no mock.module). Pinned by test/enrich/thin.test.ts, test/enrich/idempotency.test.ts, test/enrich-cycle-phase.test.ts, test/e2e/enrich-pglite.test.ts (grew-cited, skip, ordering, multi-source, recency, resume, budget abort + checkpoint flush, final-call overage, lock-skip, provenance), test/e2e/engine-parity.test.ts (listEnrichCandidates pg↔pglite parity).

• src/core/data-research.ts — Recipe validation, field extraction (MRR/ARR regex), dedup, tracker parsing, HTML stripping.

• src/commands/embed.ts — gbrain embed [--stale|--all] [--slugs ...]. --stale first calls engine.countChunklessPagesWithContent() (chunkless-page safety net: a page written directly via putPage — e.g. an enrichment-generated stub — that never went through chunking has ZERO content_chunks rows, so it has no row to go stale and is otherwise invisible to this command forever; the predicate excludes quarantined/embed_skip pages, both intentionally chunkless). When found, healChunklessPages chunks them locally (mirrors embedPage's chunkless branch: same chunkText calls over compiled_truth/timeline) with embedding = NULL, folding the new rows into the SAME pass; immediately before writing it re-fetches the LIVE page via getPage (chunks CURRENT content, not the batch-list snapshot) and re-checks getChunks, narrowing (NOT fully closing — accepted residual risk, see the function's docstring) the check-then-write window: a concurrent writer landing chunks in the gap between that re-check and the upsertChunks call can still have them overwritten with this sweep's stale-content chunks, the same unmitigated-until-now window embedPage's single-page chunkless branch already ships with. Each page's work is try/caught (a bad chunkless page records a failure via the same EmbedResult.failures/recordFailure path as every other embed failure and the sweep moves on — it never aborts the whole --stale run before the normal stale-chunk pass even starts). listChunklessPagesWithContent's default batch is 50 (not the 2000-row default elsewhere in this file) because each row carries a full page body. It honors the caller's pacer, mirrors --catch-up (removes its cap entirely, matching the main loop below), and otherwise shares ONE GBRAIN_EMBED_TIME_BUDGET_MS wall-clock budget with the main stale loop (both measure from the same overallStartedAt, not two independent 30-minute windows) so a large damaged brain can't run the combined --stale pass unbounded; an abort during healing stops the whole function before falling through to invalidateStaleSignatureEmbeddings. Pinned by test/embed-stale-chunkless-pages.serial.test.ts + test/e2e/engine-parity.test.ts. Then --stale calls engine.countStaleChunks() (single SELECT count(*) WHERE embedding IS NULL, ~50 bytes wire) so a fully-embedded brain short-circuits with no further reads beyond those two counts. When stale chunks exist, engine.listStaleChunks() returns just the chunks needing embeddings (slug + chunk_index + chunk_text + metadata, no vector(1536) payload); caller groups by slug, embeds, re-upserts via upsertChunks. Every re-embed merge carries per-chunk metadata through the ONE shared carryChunkMetadata(chunk, loaded) field list in src/core/embed-stale.ts — modality plus the code fields (language, symbol_name, symbol_type, start_line). This list is load-bearing: upsertChunks overwrites from EXCLUDED (not COALESCE), so any re-embed path that omits a field resets it — omitting modality flips every image chunk to modality='text' and silently zeroes the image search arm (its filter is cc.modality = 'image'). Never hand-roll a per-path field list. Pinned by test/embed-modality-preserved.test.ts. All console.log/console.error call sites use slog/serr from src/core/console-prefix.ts so when runEmbedCore runs inside a per-source withSourcePrefix scope (installed by the gbrain sync --all worker pool) every line carries the [<source-id>] prefix; standalone callers see identical output because slog/serr fall through to bare console fns outside the wrap. Every embed-write path stamps pages.embedding_signature via engine.setPageEmbeddingSignature(slug, {sourceId, signature: currentEmbeddingSignature()}) so a later model/dims swap is detectable as stale. The per-slug path (embedPage, used by gbrain embed <slug> AND sync's post-import embed step) and the full-re-embed path (embedAll) stamp per page when every chunk embedded cleanly. The stale path (embedAllStale) first calls invalidateStaleSignatureEmbeddings on a live run so signature-drifted pages flow through the NULL cursor, then stamps each page — but ONLY when EVERY chunk was stale this pass (a partially-stale page keeps preserved chunks of unknown provenance, so it stays unstamped rather than falsely marked current; embed --all fully re-embeds + stamps those). dry-run never mutates: it counts signature-drift via the widened countStaleChunks({signature}) predicate without NULLing anything. --include-null-signature (#3391) lifts the NULL-signature grandfather clause: threads includeNullSignature: true into the invalidation + counts so pages that predate the v108 stamp re-embed too after a model swap (both engines' countStaleChunks/sumStaleChunkChars/invalidateStaleSignatureEmbeddings accept the flag; predicate becomes sig IS NULL OR sig <> current). Without the flag, a live stale run that just invalidated drifted rows probes for left-behind NULL-signature chunks and emits a loud stderr warning naming the count + the fix — mixed embedding spaces in one index are never silent. Pinned by test/embedding-migration.test.ts + test/e2e/migrate-embeddings-postgres.test.ts. Embed failures are never silent (#3037): all three page paths embed via embedPageTexts, which tries the page's chunks in one batch and, on a PERMANENT request-shaped failure (non-429, non-AITransientError, non-auth), retries once per chunk so one bad chunk costs one chunk instead of darkening the whole page (failed chunks stay embedding IS NULL for the next --stale pass; a partially-failed page is never signature-stamped). Rate-limit/outage/auth failures do NOT fan out (cost bounding — embedBatchWithBackoff already owns 429 backoff). Failed chunk counts land on EmbedResult.failures + capped failure_samples, and src/cli.ts's embed case sets a non-zero exit verdict on failures > 0 (mirror of the import errors>0 guard). Pinned by test/embed-partial-failure-3037.serial.test.ts + test/embed-exit-code-3037.serial.test.ts (real spawned CLI). applies the embed-skip filter at all 5 stale-chunk sites: runEmbedCore --stale, runEmbedCore --all, the embed-stale Minion helper, plus both engines' listStaleChunks + countStaleChunks via EMBED_SKIP_SQL_FRAGMENT. A soft-blocked page is queryable by title/slug but its chunks never enter the embed sweep. The shared helper from src/core/embed-skip.ts is the regression guard — no per-site ad-hoc filter allowed. Pinned by test/embed-skip.test.ts. both inline sliding-pool sites (embedAll simple at :458-467 and embedAllStale paginated + AbortSignal at :586-632) call runSlidingPool from the shared worker-pool helper. Invariant-level contract preserved (counts + cost + AbortSignal propagation + per-batch rate-limit retry via embedBatchWithBackoff); byte-equality on progress-event ORDERING is NOT promised. The GBRAIN_EMBED_CONCURRENCY || 20 default is preserved and embed bypasses resolveWorkersWithClamp because the 20-worker default would otherwise silently change every brain's embed hot path. Pinned by test/embed-helper-migration.test.ts (asserts the helper is wired in AND the pre-migration let nextIdx = 0 + Promise.all(Array.from({length: numWorkers}, ...)) shapes are gone). wires --background as the reference integration for the maybeBackground() helper. gbrain embed --stale --background submits as a Minion job, prints job_id=N to stdout, exits 0. Composable: JOB=$(gbrain embed --stale --background | grep -oE 'job_id=[0-9]+' | cut -d= -f2); gbrain jobs follow $JOB. The other six commands (extract, lint, backlinks, reindex, integrity, pages) adopt the same pattern in a follow-up wave. #1737: runEmbedCore accepts an optional signal threaded down both the --stale and --all paths (embedAllStale/embedAll/embedPage); each composes it with the internal wall-clock budget via anySignal and checks isAborted/effectiveSignal.aborted in every per-slug loop, page-claim pool, and embedBatch call, so a worker abort (wall-clock timeout / lock loss / SIGTERM) stops embedding within a batch. Pinned by test/embed.serial.test.ts. Keyless brains (embedding_disabled: true): the exported pure predicate isKeylessStaleRefusal(args, embeddingDisabled) gates a CLEAN refusal at the top of runEmbed — a bare stale run prints a stderr hint and returns a zero-failure result (exit 0), because the documented agent-scheduler chain gbrain sync ... && gbrain embed --stale must stay green on a keyless install; explicit asks (a slug, a slugs list, the all flag) and dry-run keep exiting 1 via EmbeddingDisabledError, mirroring the dispatch precedence where a slugs list wins over stale. Pinned by test/embed-keyless-guard.test.ts + test/agent-scheduler-contract.serial.test.ts.

• src/core/retrieval-upgrade-planner.ts — legacy ze-switch planner, scheduled for wholesale deletion in the v0.47 ZE-removal wave; CLI-unreachable (the ze-switch shim refuses every operation) and kept ONLY as a test vehicle: applyRetrievalUpgrade/resumeRetrievalUpgrade carry the multimodal-column preservation pins and env-override gate cases in test/retrieval-upgrade-planner.test.ts + test/ze-switch-env-override.test.ts. The shared primitives it used to own (runSchemaTransition, transitionDimPinnedColumn, TEXT_EMBEDDING_DIM_PINNED_TABLES, detectEnvOverride, EnvOverrideWarning, formatEnvOverrideWarning) LIVE in embedding-migration.ts (the survivor module); this file re-imports/re-exports them for back-compat until the deletion. Its resume/undo paths probe readContentChunksEmbeddingDim first and skip the schema transition when the column is already at the target width — a same-width DROP+ADD still deletes every stored vector. Note the plane caveat: apply/undo write DB-plane config (engine.setConfig) that the post-v0.37 file-plane-canonical embed pipeline does not read — one reason the CLI actions were retired.

• src/core/embedding-migration.ts — provider-agnostic embedding migration core (#3390) and the v0.47 survivor module; owns the schema-transition + env-gate primitives (moved from the planner). runSchemaTransition(engine, targetDim): ONE transaction rebuilds all three dim-pinned text-embedding-space columns (content_chunks.embedding, query_cache.embedding, facts.embedding) preserving each column's vector/halfvec type, HNSW gated on hnswIndexExpected (dims > 2000 skip the index; exact scans stay correct — 2048d targets work); image/multimodal columns deliberately untouched; AFTER commit it clears embedded_at in yielding 50k batches (belt-and-braces hygiene — read surfaces key on the vector itself). planEmbeddingMigration: workload via widened stale predicates (absent-column fallback counts every chunk), cost, signature_census (top-5 page signatures — DB-reality corroboration of From), synopsis_tier_pages (context-tier downgrade consent), bundle-aware reranker_warning, dim_change via the shared schemaRebuildNeeded (null ⇒ rebuild, same computation apply uses). applyEmbeddingMigration: env≠target refusal (detectEnvOverride; detectEnvPresence drives the ==target notice) → marker v2 write (same-target re-apply preserves started_at; retarget records superseded history + force_sunset_target) → full rebuild when the chunks column is off-width, else INDEPENDENT repair of stale dim-pinned columns (readDimPinnedWidths) → NULL-signature-inclusive invalidation BEFORE config writes (same-dim-swap crash safety) → DB plane → file-plane callback → cache purge. verifyMigrationComplete: the ONLY basis for "nothing to migrate" — column + pinned widths, wide stale census, missing_embeddings residue, chunkless-pages census, marker state, un-merged file plane (or env-canonical), env-contradiction blocker; never trusts from_model. completeEmbeddingMigration: marker delete + completion stamp in ONE transaction (no lost-receipt crash window); accepts content-free extra (smoke-check outcome). readMigrationState (corrupt-safe), readMigrationStatus (read-only, spend-free, everything-degrades-to-null), verifySearchRoundTrip (completion smoke check: query-side embedQuery + searchVector, hit identity by page_id, NEVER throws, warn-don't-block, content-free samples), resolveRerankerExposure/resolveRerankerPlan/applyRerankerAction (D8 companion switch: bundle-resolved exposure; auto→target-provider default reranker, never a silent third provider; config write + cache purge in one tx), reconcilePageSignatures (batch-boundary stamp repair). Engine-pure; every step idempotent under crash + re-run — the NULL-embedding column is the checkpoint. Pinned by test/embedding-migration.test.ts, test/migrate-embeddings-hardening.serial.test.ts, test/e2e/migrate-embeddings-postgres.test.ts.

• src/core/ze-exposure.ts — ZeroEntropy sunset exposure detection: the one shared answer to "is this brain still depending on ZeroEntropy?", consumed by the v0.46.3 version migration (src/commands/migrations/v0_46_3.ts) and the stage-2 upgrade banner. Standalone module by design — it must survive the September deletion of the ze-switch/retrieval-upgrade subsystem. detectZeExposure(engine, fileCfg?, env?) resolves exposure from the EFFECTIVE embedding model (env GBRAIN_EMBEDDING_MODEL → file embedding_model → the legacy configless runtime fallback — resolution-based, NOT vector evidence, so a configless brain is exposed even with zero vectors), the resolved reranker (through resolveSearchMode, the same plane search actually reranks with), and ZE-backed custom embedding_columns (file + DB planes). Tri-state status: a failed DB probe downgrades to 'unknown', never to 'clear' — callers nag on 'unknown' (fail-safe). Blast-radius counts (ZE-stamped pages, embedded chunks, est. re-embed cost at the recommended target) are LIMIT-capped at BLAST_RADIUS_CAP (100K) so a million-chunk brain can't stall apply-migrations on a full-table COUNT; blast-radius probe failures are informational and never flip status. renderZeActionRequired(exposure) renders the shared ACTION REQUIRED body both consumers wrap (migrate command with --dim 1024 + the 1280-not-a-valid-Voyage-width note, the voyage:rerank-2.5 reranker fix, the no-automated-custom-column-off-ramp honesty, and the env-override callout when GBRAIN_EMBEDDING_MODEL itself forces ZE).

• src/commands/migrate-embeddings.ts — gbrain migrate embeddings --to <provider:model> [--dim N] [--dry-run] [--yes] [--json] [--no-embed] [--status] [--reranker auto|off|keep|<model>] [--retarget] [--batch-size N] [--pace[=mode]] [--ignore-env-override] [--force-sunset-target] (alias: gbrain retrieval-upgrade, dies v0.47). ONE shared orchestrator for CLI and the migrate_embeddings op: planMigrationFlow (plan + verifyMigrationComplete + env presence + un-merged file plane + brain/DB identity via redactPgUrl + concurrent-writer census + reranker plan + in-flight-other marker) and executeMigrationFlow (global gbrain-embedding-migration DbLock → retarget gate under it → all-source embed locks sorted with includeArchived → live embed probe → apply → reranker probe + switch → drain via runEmbedCore({heldLocks, …}) so the migration never lock_skips itself, with a 5-min heartbeat whose refresh-false/3-errors ABORTS as lock_lost → reconcile → completion smoke check stamped into the marker → transactional complete; locks released in finally). The skip path exits 0 ONLY on verify.complete with no pending retarget decision and no pending reranker action (a resolved switch/disable runs as a config-only completion). --status is read-only/spend-free and never refuses on env (it REPORTS planes, key PRESENCE booleans only, censuses, markers verbatim incl. corrupt, the exact resume command, and the last completion + smoke-check outcome). persistEmbeddingFileConfig writes through loadConfigFileOnly (never persists env-sourced keys) and supports env-canonical no-file deployments (env pins target ⇒ proceed with notice). Exit codes: 0 completed/verified-no-work, 1 locked/refused/failed/incomplete (message names which; lock_skipped and lock_lost get their own copy), 2 non-TTY without --yes. Pinned by test/migrate-embeddings-flow.serial.test.ts, test/migrate-embeddings-boundary.serial.test.ts, test/migrate-embeddings-hardening.serial.test.ts. Discovery surfaces all render the canonical command from renderCanonicalMigrationCommands (src/core/ai/defaults.ts): gateway deprecation line, init warnings, upgrade ACTION REQUIRED banner, doctor provider_sunset, ze-switch refusal, advisor — drift-guarded by test/canonical-migration-command.test.ts; the shutdown date lives once as ZEROENTROPY_SUNSET_DATE in defaults.ts.

• src/commands/ze-switch.ts — pure refusal/redirect shim for the retired ZeroEntropy switch. Every invocation refuses or redirects with exit 1 and reason: 'provider_sunset', printing the off-ramp (gbrain migrate embeddings --to voyage:voyage-4 --dim 1024 --dry-run); the --json refusal envelope is {status:'refused', reason:'provider_sunset', migrate, migrate_preview, message} (live command + cost preview, each carrying an explicit --brain suffix); --undo REDIRECTS (reads the ze_switch_previous_snapshot config row and prints the exact migrate command that returns the brain to its pre-switch provider — {status:'redirected', reason:'provider_sunset', undo_command, undo_preview, message} in --json; missing/corrupt snapshot degrades to the refusal); --help answers engine-free via CLI_ONLY_SELF_HELP + the SELF_HELP_WITHOUT_ENGINE wrapper in cli.ts (exit 0, truthful sunset copy). Retired flags stay REGISTERED (quoted literals feed the generated registry row) so old scripts reach the refusal instead of a pre-dispatch unknown-flag error — the shim never consults them. Nothing here mutates the brain; the retired undo ACTION wrote DB-plane config the file-plane-canonical runtime never read. The whole command is deleted in the September removal release. Pinned by test/ze-switch-cli.test.ts + test/cli-help-without-brain.serial.test.ts.

• src/commands/providers.ts — gbrain providers list | test [--touchpoint T] [--model ID] | env <id> | explain [--json]: provider-recipe discovery + smoke-testing over the recipe registry. list renders formatRecipeTable against the SAME env the gateway actually sees (buildGatewayConfig(cfg).env, file-plane keys folded in) so the STATUS column matches what providers test and init would report. Home of the ONE shared sunset-marker primitive (sunsetMarkerText/sunsetMarker, generic on recipe.sunset — any future provider sunset inherits it; the v0.47 ZE-removal wave keeps it) consumed by all three human-facing renderings so they can't drift: the list status cell, explain rows (lead marker is ⚠ regardless of key readiness — never a green ready-check on a sunsetting provider), and the env block, where the pure formatEnvOutput(recipe, env) (testable without spawning the CLI) replaces the signup funnel (setup_url/setup_hint) with the deprecation notice, replacement models, and the canonical migration command from renderCanonicalMigrationCommands — key STATUS still renders for existing users. Pinned by test/providers.test.ts.

• src/core/conversation-parser/ — 17-pattern built-in chat-format registry + opt-in LLM polish/fallback. Modules: types.ts (PatternEntry + ParseResult + DateContext + CaptureMap + TimezonePolicy), builtins.ts (17 hand-vetted patterns sourced from public format docs — iMessage/Slack, Telegram bracket + text-export, bold-paren-time, bold-time-dash, bold-name-no-time, Discord classic + export, WhatsApp ISO + US, Signal, Matrix/Element, IRC classic + weechat, Teams export; module-load validation runs every test_positive[] + test_negative[] sample at startup so a typo in any built-in regex makes gbrain refuse to start; DEFAULT_SPEAKER_CLEAN exported as a module-level default), parse.ts (orchestrator with pattern-priority scoring across the first 10 lines + date derivation chain explicit > frontmatter.date > effective_date > '1970-01-01' + multi-line continuation + timezone warning; also populates ParseResult.unrecognized_headings (#4136) — when the WINNING pattern is heading-anchored, heading-shaped lines whose label is outside the pattern's speaker set FOLD into the previous turn's body (or drop before the first anchor) while the parse still returns regex_match, silently crediting one speaker with another's words; detection is diagnostic-only and unconditional (not behind opts.diagnostic — the extractor's decline gate depends on it), fence-aware (a fence closes only on ITS OWN marker; an unclosed fence suppresses detection below it), labels deduped/capped at 10 entries ≤48 chars, undefined when empty so healthy-page JSON stays byte-identical; gbrain conversation-parser scan surfaces the field in both human and JSON output), llm-base.ts (shared runLlmCall<T> with content-hash cache in-process + DB-persistent via migration v97 + 4-strategy JSON repair + Anthropic-key probe; polish and fallback are thin wrappers), llm-polish.ts (opt-IN; headroom guard skips when tracker within $0.10 of cap; pure applyPolish for merge/drop/edit ops), llm-fallback.ts (opt-IN; NO regex inference + NO persistence), eval.ts (scoreFixture + aggregateScores + parseFixtureJsonl for the fixture-corpus CI gate), nightly-probe.ts (DI-stubbed; mode-gated default tokenmax=ON, conservative/balanced opt-in; adversarial false-positive detection). Pattern bold-name-no-time (regex /^\*\*(?!\[)(.+?):\*\*\s*(.*)$/, ordered after the time-bearing bold patterns) parses **Speaker:** text with NO per-line timestamp (Circleback/Granola/Zoom), anchoring every message at T00:00:00Z of the frontmatter date (line order preserves sequence, same no-time convention as irc-classic); the (?!\[) lookahead rejects telegram-bracket **[18:37] Name:**; non-shadow is the colon-INSIDE-bold regex (NOT declaration order — parse.ts scores every candidate independently, order is only the tie-break). Because **Label:** text is a common prose idiom, the pattern sets optional PatternEntry.score_full_body: true so parse.ts recomputes the winner's acceptance score over the FULL body before the SCORING_MIN_ACCEPTANCE floor, keeping a bold-label notes page at no_match. Pattern bold-paren-time parses **Speaker** (HH:MM): text and (HH:MM:SS) (date_source: frontmatter). Fallback gates: SCORING_HEAD_TRIGGER_THRESHOLD = 0.3 triggers a full-body re-score when the head pass scores below that; SCORING_MIN_ACCEPTANCE = 0.05 blocks essay false-positives. Exported scorePatternFull(body, entry); private getNonBlankLines(body, headCap?) + scoreFromLines(lines, entry) DRY the quick_reject+regex loop. CLI surfaces at src/commands/eval-conversation-parser.ts (gbrain eval conversation-parser <fixture.jsonl> exit 0/1/2, wired into bun run verify via check:conversation-parser) and src/commands/conversation-parser.ts (scan <slug> debug, list-builtins, validate <file>). Doctor checks: conversation_format_coverage, progressive_batch_audit_health, conversation_parser_probe_health. Pinned by test/conversation-parser/{parse,llm-base,llm-fallback,llm-polish,nightly-probe}.test.ts + the 27-case baseline at test/extract-conversation-facts.test.ts (back-compat invariant). Migration v97 (conversation_parser_llm_cache_table). Fixtures at test/fixtures/conversation-formats/{imessage,imessage-time-only-12h,telegram-bracket,whatsapp-iso,whatsapp-us,signal-export,irc-classic,irc-weechat,matrix-element,teams-export,all,adversarial,bold-name-no-time,bold-time-dash}.jsonl with scripts/check-fixture-privacy.sh banning real-name leaks. Maintainer guidance: conversation parser patterns.

• src/core/progressive-batch/ — shared ramp-up + cost-cap + verification primitive (trial 10 → ramp 100 → ramp 500 → full, with verification at each stage), with verifier+policy injection (callers describe HOW TO MEASURE SUCCESS, not WHEN TO WAIT FOR CTRL-C). Modules: types.ts (Stage, StageVerdict, AbortReason, discriminated Verifier union OutputCountVerifier | IdempotentMutationVerifier | NoopVerifier, Policy, StageReport), orchestrator.ts (runProgressiveBatch(items, verifier, policy, runner) — reads getCurrentBudgetTracker() ahead of Policy.maxCostUsd fail-closed; null both ways triggers abort_cost_cap reason='no_budget_safety_net'), audit.ts (ISO-week JSONL at ~/.gbrain/audit/progressive-batch-YYYY-Www.jsonl via the shared audit-writer primitive), stage-report.ts (ASCII formatter for the default Policy.onStageReport). Env knobs: GBRAIN_PROGRESSIVE_BATCH_DISABLED=1, GBRAIN_PROGRESSIVE_BATCH_AUTO=1 (skip Ctrl-C grace), GBRAIN_PROGRESSIVE_BATCH_STAGES=10,100,500. Sites that "jump straight to full" stay that way by default; ramp is opt-in per-site via Policy.interactiveAbortMs > 0. Pinned by test/progressive-batch/orchestrator.test.ts (35 cases, every verdict path).

• src/commands/extract-conversation-facts.ts + src/core/cycle/conversation-facts-backfill.ts — bulk fact extraction for long-form conversation pages. Walks conversation/meeting/slack/email/imessage/imessage-daily pages, splits them into time-windowed segments (30-min gap or 30-msg cap), prepends a topical/temporal header, and uses the strict extractFactsFromTurnWithOutcome() path so provider and output failures remain retryable instead of becoming successful empty pages. Invariants: strict per-source core (runExtractConversationFactsCore({sourceId, ...}) always takes one sourceId; CLI + cycle phase each do their own multi-source iteration because PHASE_SCOPE='source' is taxonomy-only); bounded two-phase enumeration (paginated listPages({type, sourceId, limit:10}); per-page body cap MAX_PAGE_BODY_BYTES=25MB); page-global row_num accumulator (the facts unique index is (source_id, source_markdown_slug, row_num)); versioned snapshot-bound outcomes (cli:extract-conversation-facts:terminal:v2 for complete pages and a separate non-extractable:v2 source for recognized pages with no eligible segment); operation checkpoints are scheduling hints only and never suppress a replay without a matching v2 outcome; optional opts.budgetTracker? is used as-is, while an absent tracker is created with maxCostUsd; body reads cover compiled truth, timeline, and configured raw-transcript sidecars; facts.extraction_enabled kill-switch with --override-disabled; --types LIST allowlist (conversation,meeting,slack,email,imessage,imessage-daily); --background via maybeBackground; and speaker-shaped-fold decline (#4136) — when the parse reports unrecognized_headings containing a speaker-shaped label (1-2 title-cased words, not in the doc-heading stoplist — the stoplist gates the DECLINE only, so a miss is warn-noise, never data loss) AND the parse produced fewer than two distinct speakers, the page is declined instead of extracted under wrong attribution: counted in pages_skipped_unrecognized_speaker (Result/CLI/cycle surfaces), warned to stderr with the folding pattern id, and deliberately NON-terminal (no durable audit row and no orphan cleanup, so a future parser/pattern fix retries the page); multi-speaker pages with folds proceed warn-only. The companion conversation_facts_backfill cycle phase is default-off, iterates every source, and enforces per-source plus brain-wide cost and wall-time caps. Migration v94 provides the partial facts index used by outcome lookups. computeConversationFactsBacklogCheck reports fresh completed, scanned-not-extractable, and unfinished counts separately, warning when more than 10 eligible pages lack a fresh v2 outcome. sources audit exposes facts_backfill_estimate: {pages, est_segments, est_cost_usd, types}. Pinned by test/extract-conversation-facts.test.ts and test/doctor-conversation-facts-backlog.test.ts. --workers N for LLM-bound fact extraction over conversation pages, with a per-page advisory lock via src/core/db-lock.ts:withRefreshingLock (lock id extract-conversation-facts:<source>:<slug>, TTL PER_PAGE_LOCK_TTL_MINUTES=2 with 20s refresh via Math.max(15s, 120s/6); LockUnavailableError triggers skip-and-continue with rate-limited log per (source, minute) + pages_lock_skipped counter + CLI exits 3 when non-zero AND no hard failures). deleteOrphanFactsForPage(engine, sourceId, slug) provides delete-orphans-first replay safety — wipes facts from a prior crashed run for this (sourceId, slug) before re-extracting, closing the "terminal audit row written after partial insertFacts failure" class. assertFactsEmbeddingDimMatchesConfig(engine) is the startup preflight (throws FactsEmbeddingDimMismatchError with paste-ready ALTER hint BEFORE the first insert; cached per engine via WeakMap). Result type carries pages_lock_skipped + orphan_facts_cleaned. Checkpoint state is a shared cpMap: Map<slug, endIso> (NOT a per-page-mutated cpEntries: string[]) so atomic Map.set survives parallel workers. Minion handler extract-conversation-facts in src/commands/jobs.ts round-trips workers via job.data.workers for --background --workers 20. Cycle config key cycle.conversation_facts_backfill.workers (default 1; opt-in concurrency under brain-wide cost + walltime caps). Pinned by test/extract-conversation-facts-workers.test.ts + the existing extract-conversation-facts behavioral tests. with src/commands/doctor.ts durable outcome authority: page completion survives operation-checkpoint GC through versioned terminal audit rows (cli:extract-conversation-facts:terminal:v2), while recognized pages with no eligible segment use the separate cli:extract-conversation-facts:non-extractable:v2 source. Each outcome is bound to the exact parsed snapshot: regular pages use content_hash plus the UTC effective date; raw-conversation sidecars and legacy null-hash pages use a canonical SHA-256 over every parser-relevant input. Selection checks the token before locking, refetches under the lock, and verifies it again before writing the outcome, so an edit cannot be certified by stale work. The strict extraction path treats provider, refusal, truncation, malformed/schema-invalid output, segment-write, cleanup, and terminal-write failures as unfinished work; bulk failures increment pages_failed, affect CLI/cycle receipts and exit status, and never advance the legacy checkpoint. Checkpoints are only a scheduling hint: a slug without a matching v2 outcome is replayed delete-first. no_match, errors, cancellation, and dry runs never become durable negatives. Result, CLI, cycle, and doctor surfaces keep completed, scanned-not-extractable, unfinished, failed, and lock-skipped counts separate. See Conversation backfill durable outcomes for the operator and maintainer contract. Pinned by test/extract-conversation-facts.test.ts and test/doctor-conversation-facts-backlog.test.ts.

• src/core/facts/conversation-types.ts — single-source conversation-type allowlist (ALLOWED_TYPES: conversation, meeting, slack, email, imessage, imessage-daily + AllowedType). Every consumer derives from this frozen leaf module — extract-conversation-facts.ts (which re-exports both names verbatim for its existing importers), the cycle backfill phase, doctor.ts + doctor/checks/search-eval.ts, sources.ts, jobs.ts — replacing five hand-copied lists that could drift. It lives under src/core/facts/ (not src/commands/) because scripts/generate-flag-registry.ts scans option-shaped literals one relative-import level deep — importing the constant straight from extract-conversation-facts.ts transitively attributed that command's whole option surface to doctor/jobs/sources in the generated CLI_ONLY registry (#4135). Drift-guarded by test/conversation-facts-type-allowlist-drift.test.ts.

• src/core/link-extraction.ts — shared library for the graph layer. extractEntityRefs (canonical) matches [Name](people/slug) markdown links and Obsidian [[people/slug|Name]] wikilinks; extractPageLinks, inferLinkType heuristics (attended/works_at/invested_in/founded/advises/source/mentions), parseTimelineEntries, isAutoLinkEnabled. #2576: markdown links, bare-slug prose refs, and slash-shaped wikilinks match ANY dir-shaped path (ANY_DIR_SEGMENT), not a directory whitelist — nonexistent targets are dropped by the persist paths' page-existence checks (resolveCandidateSources, put_page's allSlugs filter, addLinksBatch INNER JOINs) and counted as skippedMissingTarget in the extract summaries; the DIR_PATTERN whitelist survives only as the typed fast-path for pass-2b wikilinks (non-whitelisted [[dir/...]] get an equivalent direct typed candidate in pass 2c, plus the flag-gated suffix rescue for non-exact matches). Used by extract.ts, operations.ts auto-link post-hook, and backlinks.ts. Opt-in global-basename wikilink resolution (issue #972, default off): WIKILINK_GENERIC_RE catches bare [[name]] wikilinks outside DIR_PATTERN (third pass 2c in extractEntityRefs); EntityRef.needsResolution: true tags refs from this pass (the ref's slug is the wikilink TARGET, name the optional display alias). SlugResolver gains optional resolveBasenameMatches(name): Promise<string[]> (multi-match by design — emits one edge per matching page). The single shared basename matcher is buildBasenameIndex(slugs) + queryBasenameIndex(index, name) + normalizeBasename (keys raw/lower/slugified tail, stable-sorted shorter-first then lexical), used by makeResolver, the FS resolveBasenameMatchesFromSlugs, AND the doctor check so they cannot drift. makeResolver(engine, {mode, sourceId}) builds the index lazily via engine.getAllSlugs({sourceId}) — source-scoped so a bare [[name]] never resolves to a same-tail page in a different source. extractPageLinks gains opts.globalBasename (routes needsResolution refs through resolveBasenameMatches keyed on ref.slug, emits candidates tagged linkType: 'wikilink_basename' + linkSource: 'wikilink-resolved', skips self-loops) and opts.skipFrontmatter (replaces the old nullResolver ternary). All three surfaces (FS extract, DB extract, put_page auto-link) tag provenance with link_source='wikilink-resolved'; put_page includes it in its reconcilable-edge set so stale basename edges are removed when the wikilink or the flag goes away. Exports WIKILINK_BASENAME_LINK_TYPE + isGlobalBasenameEnabled(engine) (resolution order: env GBRAIN_LINK_RESOLUTION_GLOBAL_BASENAME → DB config link_resolution.global_basename → default false). gbrain doctor's link_resolution_opportunity check surfaces a paste-ready enable hint when ≥5 bare wikilinks would resolve AND ≥20% match. Migration v113 widens links_link_source_check to admit 'wikilink-resolved'; v114 (#1941) then opens it to any kebab-case provenance (^[a-z][a-z0-9]*(-[a-z0-9]+)*$, ≤64 chars) so external derivers register their own tag (e.g. citation-graph) without a migration. LINK_EXTRACTOR_VERSION_TS also lives here (bump like CHUNKER_VERSION to invalidate prior extract-stale stamps). Pinned by test/link-extraction.test.ts, test/extract-fs.test.ts, test/doctor.test.ts, test/e2e/global-basename-pglite.test.ts.

• src/commands/extract.ts — gbrain extract links|timeline|all [--source fs|db] [--source-id <id>]: batch link/timeline extraction. fs walks markdown files, db walks pages from the engine (mutation-immune snapshot iteration; use for live brains with no local checkout). No in-memory dedup pre-load — candidates buffered 100 at a time and flushed via addLinksBatch / addTimelineEntriesBatch; ON CONFLICT DO NOTHING enforces uniqueness at the DB layer, created counter returns real rows inserted. ExtractOpts.slugs?: string[] enables incremental extract via extractForSlugs() (single combined links+timeline pass); the cycle path threads sync's pagesAffected through. walkMarkdownFiles(brainDir) still runs to build allSlugs for link resolution. --source-id <id> scopes extraction to one source on federated brains (resolved via resolveSourceWithTier() before any SQL; failures hint gbrain sources list). gbrain extract --stale [--source-id <id>] [--catch-up] [--dry-run] [--json] branch (extractStaleFromDB) — incremental DB-source link+timeline sweep over pages whose pages.links_extracted_at watermark is stale. Stale predicate (shared by both engines + the doctor check): links_extracted_at IS NULL OR links_extracted_at < LINK_EXTRACTOR_VERSION_TS::timestamptz OR updated_at > links_extracted_at (the updated_at arm catches MCP put_page / sync --no-extract edited-since-extract). Three new BrainEngine methods (parity in postgres-engine.ts + pglite-engine.ts + bootstrap probes): countStalePagesForExtraction(opts?), listStalePagesForExtraction({batchSize, afterPageId?, sourceId?, versionTs?}) (returns page CONTENT to avoid N+1 getPage; rowToStalePage in utils.ts maps the row, StalePageRow in types.ts), markPagesExtractedBatch(refs, defaultExtractedAt) (3-array unnest slug[],source_id[],ts[]; each ref may carry its own extractedAt). STALE_BATCH_SIZE default 25 (GBRAIN_EXTRACT_STALE_BATCH; small because page bodies are unbounded — the LIMIT is the only fetch-time memory bound); STALE_TIME_BUDGET_MS 30min wall-clock (--catch-up removes the cap). Non-swallowing flush: link/timeline flush throws propagate and abort the batch; stamp LAST so a crash leaves pages unstamped and they re-extract idempotently (addLinksBatch ON CONFLICT DO NOTHING + timeline dedup). Race fix: extractStaleFromDB stamps with each row's READ updated_at (not now()), so a concurrent edit during the sweep keeps the page stale and it re-extracts next run rather than marked fresh-with-old-content. Source-correct stamping at DB-extract sites via stampExtracted (best-effort, never throws); extractLinksFromDB only stamps the combined watermark when subcommand === 'all' (a links-only run must not hide timeline staleness). LINK_EXTRACTOR_VERSION_TS lives in src/core/link-extraction.ts (bump like CHUNKER_VERSION to invalidate all prior stamps). Migration v112 (pages_links_extracted_at) adds nullable TIMESTAMPTZ + composite (source_id, links_extracted_at) index (CONCURRENTLY + invalid-remnant pre-drop on Postgres, plain on PGLite), NO backfill so the real backlog surfaces on first gbrain doctor. Schema parity in schema.sql + pglite-schema.ts + schema-embedded.ts + REQUIRED_BOOTSTRAP_COVERAGE. src/commands/doctor.ts:checkLinksExtractionLag (the links_extraction_lag check, also in doctorReportRemote) warn-only by default (>GBRAIN_EXTRACTION_LAG_WARN_PCT, default 20%; shared EXTRACTION_LAG_WARN_PCT_DEFAULT + EXTRACTION_LAG_MIN_PAGES=100 + exported _resolveEnvNumber), hard-fails only when GBRAIN_EXTRACTION_LAG_FAIL_PCT is set; vacuous-skips <100 pages (no --source); pre-v112 brains graceful-skip via isUndefinedColumnError; strictly a SQL COUNT (safe on remote/thin-client). src/commands/sync.ts gains --no-extract (threaded through single-source + --all + syncOneSource), stamps links_extracted_at for pagesAffected at the inline-extract call site, and maybeExtractionNudge prints a one-line stderr nudge after a synced | first_sync | up_to_date sync that leaves a backlog (shouldNudgeAfterSync pure predicate; GBRAIN_SYNC_NO_EXTRACT_NUDGE suppresses). src/core/retry.ts adds 'extract.stale' to BATCH_AUDIT_SITES; src/core/doctor-categories.ts adds links_extraction_lag to BRAIN_CHECK_NAMES. Pinned by test/extract-stale.test.ts (incl. edited-after-stamp regression + crash-contract), test/sync-inline-extract-stamps.serial.test.ts, test/sync-nudge-status-gate.test.ts, test/doctor-links-extraction-lag.test.ts, engine-parity (Postgres↔PGLite) for the 3 methods + v112 round-trip. The stale SELECT in both engines projects a deterministic full-µs UTC string to_char(updated_at AT TIME ZONE 'UTC', 'YYYY-MM-DD"T"HH24:MI:SS.US"Z"') AS updated_at_iso (carried on StalePageRow.updated_at_iso, populated by rowToStalePage in utils.ts with an ISO-only fallback — never String(Date), which ::timestamptz misparses); extractStaleFromDB stamps that exact-precision value, not a JS Date (which truncates to milliseconds), so on Postgres links_extracted_at equals the row's updated_at to the microsecond and links_extraction_lag clears — a ms-truncated stamp stays strictly below the µs updated_at and leaves every page perpetually stale, which extract --stale could never satisfy. to_char (not raw ::text, which is DateStyle-fragile) keeps the projection deterministic. The markPagesExtractedBatch SQL is unchanged, so callers passing an explicit (e.g. backdated) extractedAt still control the stamp and the edited-since arm is exact. A deterministic PGLite regression in test/extract-stale.test.ts injects a µs updated_at, runs --stale, and asserts the lag is 0 and stays 0.

• Extract CLI help — EXTRACT_HELP in src/commands/extract.ts is the canonical detailed usage shared by --help and invalid-subcommand errors. src/cli.ts routes extract --help before engine connection so help works on unconfigured installs; the top-level TOOLS block advertises every mode-specific flag. Pinned by test/cli-help-discoverability.test.ts.

• src/core/extract/receipt-writer.ts + src/core/extract/rollup-writer.ts + src/commands/extract-status.ts + src/commands/extract-explain.ts + src/commands/extract-benchmark.ts + src/core/schema-pack/scaffold-extractable.ts — unified extract operator surface. Every shipped extractor (deterministic facts.conversation in src/commands/extract-conversation-facts.ts + three LLM-backed cycle phases at src/core/cycle/{extract-atoms,synthesize-concepts,propose-takes,extract-facts}.ts) writes ONE receipt page per run (writeReceipt) + UPSERTs a row to extract_rollup_7d (upsertExtractRollup). Receipt slug extracts/{date}/{kind}/{source_id}/{run_id_short}/round-{N}.md; frontmatter stamps BOTH type: extract_receipt AND dream_generated: true (belt+suspenders against extraction-loop guard drift). extract_receipt joins ALL_PAGE_TYPES in src/core/types.ts; extracts/ prefix gets a 0.3x source-boost demote in src/core/search/source-boost.ts. Migration v104 adds extract_rollup_7d (kind, source_id, day, cost_usd, halt_count, eval_pass_count, eval_fail_count, round_completed_count, rollup_write_failures, updated_at) with PK (kind, source_id, day) + idx_extract_rollup_7d_day. Rollup writes best-effort with process-scoped error-dedup so transient DB failures bump rollup_write_failures instead of crashing the cycle. extract_health doctor check reads last 7 days, warns at halt-rate > 10% AND when rollup_write_failures > 0; pre-v104 brains report ok. CLI: gbrain extract status [--source-id ID] [--kind X] [--verbose] [--json] (7-day rollup, sorted halt_rate desc + cost desc, top-5 + "more rows" hint, stable schema_version: 1); gbrain extract --explain <kind> (resolution chain pack-declared vs built-in cycle phase, prompt_template + fixture_corpus paths with ✓/(missing), last 7d rollup); gbrain extract benchmark --pack X --kind Y (loads pack fixture corpus through strict path validation — rejects absolute paths, .. traversal, null bytes, AND symlinks resolving outside pack root; ships as a stub-reporter). src/core/schema-pack/manifest-v1.ts widens extractable from z.boolean() to z.union([z.boolean(), ExtractableSpecSchema]) (carries prompt_template, fixture_corpus, eval_dimensions, benchmark_min_recall, plus reserved verifier_path — parses but refuses at runtime); extractableSpecsFromPack + getExtractableSpec + refuseVerifierPathInV042 in src/core/schema-pack/extractable.ts; gbrain schema scaffold-extractable <type> --pack <pack> declares the type extractable, generates 5 placeholder fixtures + a prompt template stub under packs/<pack>/{fixtures,prompts}/extract/, refuses to overwrite without --force. Pinned by test/extractable-spec-widening.test.ts (22), test/extract/receipt-writer.test.ts (12, canonical PGLite block R3+R4), test/extract/benchmark.test.ts (17), test/extract/status.test.ts (15), test/schema-pack/scaffold-extractable.test.ts (15, privacy guards), test/doctor-extract-health.test.ts (8).

• src/commands/import.ts — gbrain import <path> [--source-id <id>]: page import with the path-set checkpoint. runImport contains NO process.exit: all five preflight/argv failure sites (deferred-setup embedding sentinel, missing embedding credentials, invalid --workers, missing dir arg, unreadable target) throw the exported typed ImportAbortError (carries exitCode; the user-facing message is printed at the throw site), so in-process callers — the sync_brain MCP op, autopilot, the Minions import handler — survive a failed preflight as a normal tool/job error instead of the whole serving process dying mid-call. The CLI's import case catches it and exits e.exitCode, byte-identical to the old behavior. Pinned by test/import-abort-error.test.ts. --source-id <id> routes pages to the named source (resolved via resolveSourceWithTier() at the boundary; consistent across import, extract, graph-query, sources current). Pinned by test/import-source-id.test.ts. gbrain import CLI + runImport library entrypoint. Uses a path-set checkpoint via src/core/import-checkpoint.ts (the walk still applies sortNewestFirst() for embed-cost ordering, but checkpoint correctness no longer depends on sort order). A file enters completed: Set<relativePath> only when its processFile returns success (including content-hash short-circuit no-ops); failed files never enter the set so the next run retries them automatically with no manual ~/.gbrain/import-checkpoint.json delete. This closes three classes: parallel-import-with-slow-worker dropping the slow file on crash-resume (the slow file isn't in completed until its own processFile resolves), failed-file-bumps-counter-past-itself (failures don't add to completed), and sort-flip-drops-newest-N-on-cross-version-resume (order is no longer part of the checkpoint). Old positional checkpoints are detected and discarded with a stderr line on first resume (re-walking is cheap because content_hash short-circuits unchanged files). Checkpoint persists every 100 successful adds, not every 100 processed files. The managedBookmark opt (set by performFullSync when runImport is the full-sync engine) suppresses runImport's own sync.last_commit advance so the shared applySyncFailureGate (src/core/sync-failure-ledger.ts) owns the bookmark + failure-ledger gating on that path — one gate decides advance/block/auto-skip across both sync paths. Pinned by test/import-checkpoint.test.ts + test/import-resume.test.ts (incl. the SLUG_MISMATCH retry regression). collectSyncableFiles' shared emit filter isCollectibleForWalker applies the SAME segment-level pruneDir gate as incremental sync's classifySync — load-bearing for the git ls-files fast path, which enumerates tracked files under dot-dirs/vendored trees that the FS walk never descends into; without it sync --full imported (and resurrected soft-deleted) pages incremental sync excludes (#2607). Pinned by test/import-git-fastpath-prune.test.ts. runImport opts also carry exclude (glob filter over dir-relative paths, threaded by performFullSync for sync --exclude; warns when every file is excluded — NAV-4) and slugRoot (slug/source_path base for monorepo subdir syncs, #753/#774; the resume checkpoint stays dir-relative per resumeFilter's contract).- src/core/import-checkpoint.ts — loadCheckpoint(brainDir), saveCheckpoint(brainDir, completed), resumeFilter(files, completed, brainDir), clearCheckpoint(), plus the ImportCheckpoint type. Path-set format {schema_version, brainDir, completed: string[]}. Atomic write via .tmp + rename() so a mid-write crash never leaves a partial JSON. loadCheckpoint returns null on: missing file, malformed JSON, brainDir mismatch (ran against a different brain), and the old positional format (logged to stderr before discard). resumeFilter returns {toProcess, skippedCount} — pure, no I/O, deterministic. clearCheckpoint is no-op-on-missing for clean-exit cleanup. Honors GBRAIN_HOME via gbrainPath() so withEnv({GBRAIN_HOME: tmpdir}) test isolation works without monkey-patching fs. Best-effort persistence — saveCheckpoint logs warnings on write errors but never throws.

• src/commands/graph-query.ts — gbrain graph-query <slug> [--type T] [--depth N] [--direction in|out|both] [--include-foreign]: typed-edge relationship traversal (renders indented tree). Foreign-edge footer always present (X foreign edges (use --include-foreign to traverse)) so cross-source edges never disappear silently; --include-foreign widens the SQL filter to walk them. Pinned by test/graph-query.test.ts.

• src/commands/sources.ts — gbrain sources {list,add,remove,archive,restore,archived,purge,current,status,audit}. current [--json] calls resolveSourceWithTier() and prints source_id, tier (flag | env | dotfile | local_path | brain_default | seed_default), and optional detail (decision table in skills/conventions/brain-routing.md). status [--json] — read-only per-source dashboard (last sync, staleness, page count, embedding coverage, unacked failures); thin wrapper around buildSyncStatusReport + printSyncStatusReport from src/commands/sync.ts; --json emits stable {schema_version: 1, sources, ...} on stdout; filters input to local_path IS NOT NULL AND archived IS NOT TRUE. audit <id> [--json] — read-only dry-run disk scan for size distribution + would-blocks + junk-pattern hits WITHOUT touching the DB; walks sources.local_path, reads each markdown file, runs assessContent() from src/core/content-sanity.ts, aggregates by verdict (ok | warn_oversize | hard_block_junk_pattern). The live runStatus health table gains a BACKFILL column between EMBED and FAILS (active(N) beats queued(N) beats idle, from SourceMetrics.backfill_active / backfill_queued in src/core/source-health.ts) so operators see deferred embed-backfill minion work after sync --all exits 0; jobCountsBySource in source-health.ts widens its minion_jobs SQL with two COUNT(*) FILTER (WHERE name = 'embed-backfill' AND ...) aggregates (best-effort, all-0 on pre-minions brains). remove pre-checks OAuth-client referents (guided refusal via formatClientReferentsBlock — the raw FK violation never reaches the operator), then commits the row DELETE atomically with an in-tx referents re-check (a registration racing the pre-check maps to the same guided refusal); durability-scaffolding teardown (unhardenBrainRepo: hook/cron/credential) runs only AFTER the commit, so a refused delete leaves the scaffolding intact. purge runs the same referents pre-check before its hard DELETE. Pinned by test/content-sanity.test.ts, test/import-file-content-sanity.test.ts, test/source-health.test.ts.

• src/commands/reindex-frontmatter.ts — gbrain reindex-frontmatter. reindexFrontmatterCli(engine, args) takes the ALREADY-CONNECTED engine from cli.ts's dispatch (#1963); it must never build/connect its own engine — a second connect on the same PGLite data dir self-deadlocks on the data-dir lock (this process already holds it) and timed out 100% of the time on PGLite. Same rule applies to runBackfillCommand(engine, args) in src/commands/backfill.ts and any future command dispatched from cli.ts's engine-connected switch. Pinned by test/reindex-frontmatter-connect.test.ts (library path) and test/reindex-frontmatter-pglite-spawn.serial.test.ts (CLI dispatch seam, both commands).

• src/core/source-config-sql.ts + src/core/sources-load.ts — canonical recovery for historical non-object sources.config values. The application reader unwraps nested JSON strings and merges recoverable array fragments left-to-right; the shared SQL expression mirrors that policy atomically for both engines, source config updates, archive/restore, and the paste-ready source_config_shape doctor repair. localFederatedSourceIds reads config through the same parser so stdio/CLI federation cannot silently disagree with sources list. sourceConfigHasRemoteUrl uses that parser for autopilot pull policy, including PGLite's JSON-string config shape. Invalid fragments degrade to {} rather than throwing. Pinned by test/sources-load.test.ts, test/job-pull-policy.test.ts, test/list-all-sources.test.ts, test/local-federated-search-scope.test.ts, test/destructive-guard.test.ts, and test/doctor-source-config-shape.test.ts.

• src/core/source-resolver.ts — 6-tier source resolution. resolveSourceWithTier(engine, explicit, cwd) returns { source_id, tier: SourceTier, detail? } alongside resolveSourceId() (unchanged). SOURCE_TIER_NAMES = ['flag', 'env', 'dotfile', 'local_path', 'sole_non_default', 'brain_default', 'seed_default'] (7 entries; order matches priority). Tier sole_non_default slots between local_path and brain_default: when NO sources.default config is set AND exactly one registered source has local_path AND isn't 'default', auto-route to it; archived sources excluded (try/catch for pre-v34 brains); private pickSoleNonDefaultSource(engine) shared by both resolver entry points so they cannot drift. Exported formatSoleNonDefaultNudge(sourceId): string | null builds the user-facing stderr nudge (null when GBRAIN_NO_SOLE_NON_DEFAULT_NUDGE=1). src/commands/sync.ts:1497-1519 calls resolveSourceWithTier unconditionally so the tier fires; src/commands/import.ts:96-128 mirrors with the tier-gated nudge. Consumed by gbrain sources current, import --source-id, extract --source-id, and the source_routing_health doctor check. Pinned by test/source-resolver-with-tier.test.ts (withEnv() per test-isolation lint), test/source-resolver-sole-non-default.test.ts (14 cases), test/sync-sole-non-default-routing.test.ts (3 PGLite cases driving real runSync). Also exports noGrantFederatedScope(engine, hasSourceGrant, sourceId), the #3242 widening decision transports share: returns localFederatedSourceIds(..., 'seed_default') ONLY when hasSourceGrant === false (the legacy-bearer no-grant floor), undefined for a granted token, for an OAuth client (flag undefined — a falsy gate here would widen every OAuth client), and when the resolver throws (best-effort; the scalar scope stands rather than failing the request). Called by src/commands/serve-http.ts; pinned by test/no-grant-federated-scope.test.ts (6 cases).

• src/core/migrate.ts — schema-migration runner. Owns the MIGRATIONS array (source of truth for schema DDL). Migration interface carries sqlFor?: { postgres?, pglite? } (engine-specific SQL overrides sql) and transaction?: boolean (false for CREATE INDEX CONCURRENTLY, which Postgres refuses in a transaction; ignored on PGLite). Key migrations: v14 (handler branches on engine.kind for CONCURRENTLY-on-Postgres with invalid-remnant pre-drop via pg_index.indisvalid, plain CREATE INDEX on PGLite); v15 (minion_jobs.max_stalled default 1→5 + backfill non-terminal rows); v24 rls_backfill_missing_tables (sqlFor: { pglite: '' } no-op — PGLite has no RLS engine, targets subagent tables absent from pglite-schema.ts); v30 dream_verdicts (file_path TEXT, content_hash TEXT, worth_processing BOOL, reasons JSONB, judged_at TIMESTAMPTZ, PK(file_path, content_hash)) (RLS-enabled under BYPASSRLS; synthesize reads/writes to avoid re-judging); v35 auto-RLS event trigger auto_rls_on_create_table fires on ddl_command_end for WHEN TAG IN ('CREATE TABLE','CREATE TABLE AS','SELECT INTO') running ALTER TABLE … ENABLE ROW LEVEL SECURITY on new public.* tables (no FORCE) + one-time backfill on every existing public.* base table whose comment doesn't match ^GBRAIN:RLS_EXEMPT\s+reason=\S.{3,} (per-table failure aborts the offending CREATE TABLE; no EXCEPTION wrap; PGLite no-op via sqlFor.pglite: ''; breaking change: intentionally-RLS-off public tables need the GBRAIN:RLS_EXEMPT comment before upgrade); v40 pages_emotional_weight (pages.emotional_weight REAL NOT NULL DEFAULT 0.0, column-only metadata-only); v46 mcp_request_log_params_jsonb_normalize (UPDATE ... SET params = params::text::jsonb WHERE jsonb_typeof(params) = 'string', idempotent); v60-v65 six-migration chain wiring source-scoping into oauth_clients — v60 (oauth_clients_source_id_fk: source_id TEXT NULL→'default' backfill + FK to sources(id) ON DELETE SET NULL), v61 (federated_read TEXT[] NOT NULL DEFAULT '{}'), v62 (explicit-CASE backfill so source_id IS NULL → '{}'), v63 (fail-loud check every row's source_id is in its federated_read array), v64 (FK flipped to ON DELETE RESTRICT), v65 (GIN index for array-containment); v68 eval_candidates_embedding_column (eval_candidates.embedding_column TEXT NULL per-row provenance for gbrain eval replay to reproduce the same retrieval space; NULL-tolerant); v108 pages_embedding_signature (pages.embedding_signature TEXT NULL = <provider:model>:<dims> stamped via setPageEmbeddingSignature; GRANDFATHER — stale predicate is embedding_signature IS NOT NULL AND embedding_signature <> $current so NULL is NEVER stale and upgrade never re-embeds the whole corpus; no index; metadata-only); v109 sources_newest_content_at (sources.newest_content_at TIMESTAMPTZ durable newest-COMMIT HEAD committer time written by writeSyncAnchor, read by the REMOTE staleness path instead of shelling to git; mirror in pglite-schema.ts + schema.sql + bootstrap probe); v110 page_aliases ((id, source_id, alias_norm, slug, ...) with UNIQUE (source_id, alias_norm, slug) + lookup indexes on (source_id, alias_norm) and (source_id, slug); alias_norm is normalizeAlias() output so WRITE/READ key on the same form; also in src/core/pglite-schema.ts); v111 search_telemetry_rank1_columns (ADD COLUMN IF NOT EXISTS on both engines: sum_rank1_score, count_rank1, three buckets rank1_lt_solid/rank1_solid/rank1_high on search_telemetry — aggregate not per-query rows so rank-1 median drift is bounded-growth; ALTERs right after v57 which created the table); v114 links_link_source_check_kebab_regex (#1941, opens link_source from the closed allowlist to a kebab-case format gate ^[a-z][a-z0-9]*(-[a-z0-9]+)*$ + char_length<=64; Postgres branch uses NOT VALID + VALIDATE CONSTRAINT with transaction:false, PGLite plain DROP+ADD; existing built-ins all satisfy the regex so VALIDATE never fails on existing data); v116 code_edges_source_backfill_and_callee_index (#2073, idempotent: backfills NULL code_edges_symbol/code_edges_chunk source_id from each edge's from_chunk page — NULL never matched a scoped AND source_id = … filter so scoped code-callers/code-callees returned 0 rows on multi-source brains — plus plain CREATE INDEX on from_symbol_qualified for both edge tables, which had no index and seq-scanned per BFS node); v129 dream_verdicts_triage_v1_columns (#4152, additive ADD COLUMN IF NOT EXISTS widening dream_verdicts into a scored triage record — score, content_type, segments, entities, model, triage_version; legacy rows keep score NULL and read as cache misses, re-judged once; no backfill, no index; same SQL on both engines since dream_verdicts is migration-created on PGLite too, so the columns take the COLUMN_EXEMPTIONS route in test/schema-bootstrap-coverage.test.ts rather than bootstrap probes). The dedup-index self-heal (timeline_dedup_index, see timeline-dedup-repair.ts) is NOT version-gated: runMigrations invokes repairTimelineDedupIndex on every pass (including the no-pending early-return path) because a merge-renumbered migration can leave the version counter past the index change while the index stays the old shape. retry-matcher.ts and timeline-dedup-repair.ts are static dependencies because runMigrations() executes from live engine initialization; the engine dynamic-import guard scans this file with both engine implementations. v95: pages_dedup_partial_index adds CREATE INDEX pages_dedup_idx ON pages (source_id, content_hash) WHERE deleted_at IS NULL. Postgres uses CREATE INDEX CONCURRENTLY with transaction: false + pre-drops any invalid remnant; PGLite uses plain CREATE INDEX. Powers findDuplicatePage hot path (O(log n) instead of O(n)). v74 mcp_spend_log uses BTREE on (client_id, created_at) + (token_name, created_at) — date_trunc('day', TIMESTAMPTZ) is NOT IMMUTABLE so can't appear in index expressions; a created_at range scan covers the per-day rollup. v75 embedding_multimodal_column is column-only (no HNSW index — deferred to post-reindex per pgvector best practice).

• src/cli.ts — no-DB fallbacks announce themselves on stderr instead of degrading silently. dream dispatch binds the caught engine-connect error and emits [dream] WARNING: could not connect to DB (...) before falling through to filesystem-only phases; the runDream(null, ...) no-DB fallback is preserved (pinned by test/cli-dream-engine-warn.test.ts, 2 subprocess cases against good + bad DATABASE_URL). doctor dispatch does the same: when connectEngine OR the DB-backed runDoctor run throws, it emits [doctor] DB-backed doctor run failed (...) — falling back to filesystem-only checks, scrubbing the error message through BOTH url-redact.ts:redactUrlsInText and redact-connection-info.ts:redactConnectionInfo first, because doctor output is exactly what users paste into issues and CI logs (pinned by the fallback case in test/doctor-minions-check.test.ts: stderr note present, credentials absent, stdout stays parseable --json).

• skills/conventions/brain-routing.md — agent-facing convention skill documenting the canonical 6-tier source resolution chain (flag → env → dotfile → local_path → brain_default → seed_default) with paste-ready decision tables. Linked from CLAUDE.md's "Two organizational axes" section and from gbrain sources current's hint output.

• test/operations-trust-boundary.test.ts + scripts/check-operations-filter-bypass.sh — operations trust-boundary contract coverage. Pure assertions over all 74 ops (every op has a scope annotation; every mutating op has a non-read scope; localOnly: true ops are excluded from operations.filter(op => !op.localOnly); the seven historically-sensitive localOnly ops snapshot-pinned by name) plus targeted handler-invocation regressions for the two historically-broken HTTP-callable classes: submit_job with name='shell' + ctx.remote=true MUST reject (the HTTP MCP shell-job RCE class), and search_by_image with image_path + ctx.remote=true MUST reject (the P0 image-leak class). file_upload and sync_brain omitted from handler-invocation tests because they're localOnly: true (that path would test an impossible production scenario). The shell guard greps src/ for any module importing the operations value outside the canonical filter site at src/commands/serve-http.ts (three import shapes: destructured, aliased, namespace), with an explicit 10-entry allow-list + a literal-string check that serve-http.ts still contains operations.filter(op => !op.localOnly). Wired into bun run verify.

• src/core/content-sanity.ts — pure assessor for the content-sanity defense. assessContent(content, opts): SanityVerdict returns one of ok | warn_oversize | hard_block_junk_pattern | soft_block_oversize with {reason, bytes, matched_pattern_name?}. Six built-in junk patterns (Cloudflare challenge dumps, CAPTCHAs, 403 dumps, bare error-page titles) compiled at module load; operator literal substrings via loadOperatorLiterals() from src/core/content-sanity-literals.ts. ContentSanityBlockError tagged class is the typed throw shape every wrapper site (gbrain import, put_page MCP op, gbrain sync, /ingest webhook) catches via the existing exception flow. The bytes-parity contract pins Buffer.byteLength(content, 'utf8') against the embedder's actual byte count so a 499K-byte page can't be soft-blocked on assessment then overflow on embed. Knob resolution chain env > file (~/.gbrain/config.json) > DB > defaults. Four knobs: content_sanity.bytes_warn (50_000), content_sanity.bytes_block (500_000), content_sanity.junk_patterns_enabled (true), content_sanity.disabled (false; GBRAIN_NO_SANITY=1 is the loud-stderr kill-switch). New assessContentSanity(opts): SanityAssessment returns the three-tier disposition (shouldQuarantine / shouldFlag + reason/detail) consumed by importFromContent and gbrain quarantine scan; adds the fuzzy prose-vs-markup ratio pass (markup chars / total above max_markup_ratio; code pages exempt; gated by prose_check_enabled) on top of the byte + junk-pattern passes. Three more knobs: content_sanity.junk_disposition (quarantine default | reject; no env override — a destructive flip belongs in explicit config), content_sanity.max_markup_ratio (0.85, env GBRAIN_MAX_MARKUP_RATIO, clamped (0,1]), content_sanity.prose_check_enabled (true). Pinned by test/content-sanity.test.ts. new assessContentSanity(opts): SanityAssessment returns the three-tier disposition (shouldQuarantine / shouldFlag + reason/detail) consumed by importFromContent and gbrain quarantine scan. Adds the fuzzy prose-vs-markup ratio pass (markup chars / total chars above max_markup_ratio, default 0.85; code pages exempt; gated by prose_check_enabled, default true) on top of the byte + junk-pattern passes. Three config knobs: content_sanity.junk_disposition (quarantine default | reject; no env override), content_sanity.max_markup_ratio (0.85, env GBRAIN_MAX_MARKUP_RATIO, clamped (0,1]), content_sanity.prose_check_enabled (true). Same env > file > DB > defaults resolution chain. Pinned by test/content-sanity.test.ts.

• src/core/content-sanity-literals.ts — operator literal-substring loader. Reads ~/.gbrain/junk-substrings.txt, one literal per non-comment non-blank line; optional # name=<id> header pairs an identifier with the following literal so audit JSONL groups by site (linkedin_auth_wall, reddit_blocked, etc.). Fail-soft on ENOENT (missing file = empty array). Loaded on every ingest. Deliberately literal substrings (NOT regex) to defeat ReDoS. Pinned by test/content-sanity-literals.test.ts.

• src/core/embed-skip.ts — 5-site shared predicate for the soft-block embed-skip filter. Exports shouldSkipEmbedding(frontmatter): boolean (JS predicate for callers holding the page in memory), EMBED_SKIP_SQL_FRAGMENT (parameterized SQL clause shared by Postgres + PGLite via executeRaw), and buildEmbedSkipMarker(reason: string) (writes frontmatter.embed_skip = {at: ISO_TIMESTAMP, reason} so the JSONB shape stays uniform). The 5 sites: embed.ts --stale, embed.ts --all, the embed-stale Minion helper, plus both engines' listStaleChunks + countStaleChunks. Single source of truth so the filter cannot drift. Pinned by test/embed-skip.test.ts (cross-site invariant + JSONB shape).

• src/core/audit/content-sanity-audit.ts — ISO-week JSONL audit at ~/.gbrain/audit/content-sanity-YYYY-Www.jsonl built on the audit-writer.ts primitive. Records every hard-block, soft-block, warn-trip, and quarantine/flag event with {kind, source_id, slug, bytes, matched_pattern_name?, reason, ts}. Doctor reads the last 7 days, aggregates by (matched_pattern_name, source_id) so operators see which scraper is the problem. Honors GBRAIN_AUDIT_DIR for shared-filesystem multi-host setups. Pinned by test/audit/content-sanity-audit.test.ts.

• src/core/quarantine.ts — the two frontmatter markers the content-quality gate writes, sibling of src/core/embed-skip.ts (same marker-as-JSONB-object pattern, same JSONB ? existence check that works on Postgres AND PGLite; no schema migration — both are frontmatter JSONB keys). quarantine (key QUARANTINE_KEY) HIDES: set ONLY for high-confidence junk, writes zero chunks, excluded from search via quarantineFilterFragment(pageAlias) / QUARANTINE_FILTER_FRAGMENT (the p-aliased constant), the single source of truth buildVisibilityClause calls so the search filter and marker key can't drift. content_flag (key CONTENT_FLAG_KEY) WARNS, does NOT hide: set for fuzzy markup-heavy / oversize, page stays searchable, marker is READ INTO search/get_page output — deliberately NO SQL filter fragment. Three distinct markers, three reasons (never overloaded): embed_skip = oversized-but-clean, quarantine = junk hidden, content_flag = odd-examine-still-here; a page can carry more than one (oversize → embed_skip + content_flag:oversized) and each clears independently. Exports buildQuarantineMarker / isQuarantined / filterOutQuarantined, buildContentFlagMarker / getContentFlag / hasContentFlag, plus the two key constants. Pinned by test/quarantine.test.ts.

• src/commands/quarantine.ts — gbrain quarantine <list|clear|scan> operator surface for the content-quality gate. list [--json] [--include-flagged] paginates listPages and reports quarantined (HIDDEN) pages, optionally also content_flag (FLAGGED, searchable) pages. clear <slug> [--force] [--no-embed] [--json] drops both markers and re-imports through the normal pipeline so the page re-chunks + re-embeds and becomes searchable; the gate re-runs on import so genuinely-junk pages re-quarantine (exit 1) unless --force sets GBRAIN_NO_SANITY=1 for that one import. scan [--limit N] [--apply] [--no-embed] [--json] re-assesses already-ingested pages so junk predating the gate gets marked (unchanged content short-circuits normal sync, so it never re-assesses otherwise); dry-run uses the SAME effective content_sanity config thresholds --apply will use, idempotent (skips already-marked pages), --apply re-imports with forceRechunk to set markers + (for quarantine) drop chunks. Dispatched in cli.ts. Pinned by test/quarantine-cli.test.ts.

• src/core/zombie-reap.ts — idempotent installSigchldHandler() so JS-spawned children get reaped via Bun's internal waitpid(). Bun (like Node) only auto-reaps when a SIGCHLD listener is registered; without it, every child the worker spawns (shell jobs, embed batches, sub-agents) becomes a zombie on exit and holds connection slots. Called once at module load from src/cli.ts (Windows platform guard — SIGCHLD doesn't exist on Windows). Cross-file leak guard via _uninstallSigchldHandlerForTests(). Layer 1 of the three-layer zombie defense; Layer 2 is tini-as-PID-1 wrapping the worker subtree (via src/core/minions/spawn-helpers.ts); Layer 3 is the container's own tini for hard Bun crashes.

• src/core/minions/ — Minions job queue: BullMQ-inspired, Postgres-native (queue, worker, backoff, types, protected-names, quiet-hours, stagger, handlers/shell).

• src/core/minions/queue.ts — MinionQueue class (submit, claim, complete, fail, stall detection, parent-child, depth/child-cap, per-job timeouts, cascade-kill, attachments, idempotency keys, child_done inbox, removeOnComplete/Fail). add() takes a 4th trusted arg (separate from opts to prevent spread leakage); protected names in PROTECTED_JOB_NAMES require {allowProtectedSubmit: true} and the check runs trim-normalized (whitespace-bypass safe). add() plumbs max_stalled through with a [1, 100] clamp; omitted values let the schema DEFAULT (5) kick in. handleWallClockTimeouts(lockDurationMs) is Layer 3 kill shot for jobs where FOR UPDATE SKIP LOCKED stall detection and the timeout sweep both fail to evict (wedged worker holding a row lock via a pending transaction). The submission backpressure guard covers two options sharing one pg_advisory_xact_lock namespace keyed on (name, queue, source): maxWaiting (rate cap, counts waiting only, NULL-source-as-wildcard scope) and maxPending (single-flight, counts waiting + live-lock active rows where lock_until > now(), EXACT source scope via COALESCE(data->>'sourceId', data->>'source_id') — an expired-lock active never suppresses, keeping the waitingClaimable wedge detectors fed). All three coalesce return paths (idempotency fast-path, cap-hit, ON CONFLICT race fallback) stamp non-persisted coalesced: true metadata on the returned job. Both filter on queue in addition to name so cross-queue same-name jobs don't suppress each other. claim and renewLock issue their UPDATE via engine.executeRawDirect (not executeRaw) so the lock heartbeat runs on the direct session-mode pool that the transaction pooler won't recycle mid-hold; on PGLite this is identical to executeRaw. The two terminal dead-letter paths (handleWallClockTimeouts wall-clock kill and the stall dead-letter CTE in the stall sweep) BOTH increment attempts_made so a long job killed there reads as an honest attempt instead of attempts 0 / started N; the stall path also bumps stalled_counter, surfaced by gbrain jobs get as Attempts: M/N (started: X, stalled: S/MaxS). At submit, add() stamps a default timeout_ms via defaultTimeoutMsFor(jobName) (from handler-timeouts.ts) when the caller passed none, and claim() COALESCEs a still-NULL timeout_ms from HANDLER_DEFAULT_TIMEOUT_MS (raw-object jsonb bind) deriving timeout_at from the coalesced value — the durable invariant covering rows that predate submit-time stamping; an explicit opts.timeout_ms always wins. The #4145 lock lease follows the identical three-layer shape: add() stamps opts.lock_duration_ms (clamped [5s,1h] via the shared clampLockDurationMs; INSERT-only — an idempotency-key re-submit never mutates the first submitter's lease) else defaultLockDurationMsFor(jobName); claim() derives lock_until from COALESCE(lock_duration_ms, map, worker default) and stamps the resolved lease, SQL-clamping the row/map-resolved value to [5s,1h] (the worker-default fallback passes through unclamped — operator-configured, and tests legitimately use sub-5s leases) so a bypass-written out-of-range row can't produce a pathological lease; handleWallClockTimeouts' null-timeout fallback uses COALESCE(lock_duration_ms, worker default). handleStalled(graceMsOverride?) applies the stall-sweep reclaim grace (GBRAIN_MINION_STALL_RECLAIM_GRACE_MS, default 15s, 0 = legacy predicate, capped at 600s with a warn-once clamp so an oversized value can't disable stalled-job recovery) to all three sweep predicates — a lease that lapsed within the grace is a starved owner's head start, not a steal candidate. Guarded by test/queue-lock-retry.test.ts (claim never falls back to executeRaw), test/postgres-execute-raw-direct.test.ts (routing decision matrix), and test/minions.test.ts (attempt accounting + default-timeout stamping). MinionQueue.add() gates subagent jobs on capability, not provider: data.model is classified via classifyCapabilities() (lazy-imported from src/core/ai/capabilities.ts to keep queue's eager-load surface small) and rejected only when the model cannot run a tool loop (unusable:no_tools) or names an unknown provider; degraded verdicts pass through with a gateway cost warning. Layer 1 of the three-layer subagent capability enforcement (layers 2+3: model-config.ts:enforceSubagentCapable runtime fallback + src/commands/doctor.ts subagent_provider check). Pinned by test/agent-cli.test.ts. All three terminal reaper paths (stall dead-letter, wall-clock kill, cascade) route through the ONE private killJobs(tx, rows, cause, message) tail: it emits child_done(outcome) to each non-terminal parent's inbox and flips any waiting-children parent whose last open child just died back to waiting — so a dead-lettered child can never strand its aggregator parent. Callers lock parents FIRST via lockParentsOrdered (ascending-id row locks, matching failJob's parent-before-child order) so the reapers and failJob can never deadlock on parent/child lock acquisition. An idempotent stranded-parent sweep runs once per stall tick (~30s): any waiting-children parent with zero non-terminal children flips back to waiting (single UPDATE, NOT EXISTS on an indexed FK) — self-heals every stranding class, including parents stranded before the sweep existed. Every automatic re-run path clears started_at (failJob's delayed retry branch, the stall requeue, lease release, promoteDelayed, and the parent-unblock flips) so the per-attempt wall clock measures execution, not backoff/queue wait — a retried job can't be dead-lettered by the wall-clock sweep before executing a line. Pinned by test/queue-stall-parent-unblock.test.ts + test/queue-started-at-retry.test.ts. renewLock accepts optional {signal} forwarded to executeRawDirect so the renewal tick's timeout race CANCELS a hung UPDATE instead of orphaning a checked-out pool slot (best-effort — the token fence is the correctness authority; a late-landing renewal can only extend a lease nobody else claimed).

• src/core/minions/worker.ts — MinionWorker class (handler registry, lock renewal, graceful shutdown, timeout safety net). Aborted jobs call failJob with reason (timeout/cancel/lock-lost/shutdown); shutdownAbort (instance field) fires on SIGTERM/SIGINT and propagates to ctx.shutdownSignal (shell handler listens; non-shell handlers don't). Per-job timeout fires abort.abort(new Error('timeout')) then a 30s grace-then-evict safety net force-evicts the job from inFlight and marks it dead if the handler ignores the abort signal (the moved-out generic abort listener now fires for ANY abort reason). The launchJob lock-renewal block is a thin sync wrapper around the pure runLockRenewalTick from src/core/minions/lock-renewal-tick.ts (NEVER setInterval(async () => await renewLock(...)) — that shape was the unhandledRejection crash class during PgBouncer rotation). Gaps closed: (1) cancelled flag captured in the timer closure stops in-flight IIFEs writing misleading audit events after the job ended; (2) re-entrancy guard tickInFlight (skips now counted as overlapSkips telemetry) + per-call Promise.race timeout with best-effort AbortSignal cancellation; (3) #4145 verify-before-evict: eviction requires a fenced-false (certain loss) or the hardEvictMs backstop — never bare local arithmetic; the per-job lease (job.lock_duration_ms ?? opts.lockDuration) drives the renewal state, and the cadence clamps to min(lease/2, 60s); (4) explicit .catch() on the stored executeJob(...).finally(...) promise closes the second unhandledRejection vector; (5) exported INFRASTRUCTURE_ABORT_REASONS = new Set(['lock-renewal-failed', 'lock-lost']) so executeJob's catch skips failJob for these (PgBouncer blips don't dead-letter healthy jobs; the stall detector reclaims); (6) inFlight generation-safety — force-evict and the handler's finally delete the inFlight entry ONLY when it still carries their own lockToken (the token is the generation; an evicted execution's late delete can no longer remove a same-worker re-claim's entry); (7) eviction observability — the worker keeps a perf_hooks.monitorEventLoopDelay histogram (reset on every successful renewal, sampled ns→ms at eviction) plus raw loadavg, and both the abort and grace-evict log lines carry cause / since-last-success / tick-lateness / overlap-skips / load / event-loop-delay from the stashed abortMeta. CI guard scripts/check-worker-lock-renewal-shape.sh (in bun run verify) asserts the bug pattern stays absent AND launchJob keeps calling runLockRenewalTick. Engine-ownership invariant: start() does NOT call engine.disconnect() on shutdown — the CLI handler in src/commands/jobs.ts case 'work' owns engine lifecycle via try/finally with loud error logging. RSS watchdog uses non-file-backed pages on Linux: exported parseRssFromProcStatus(status) (pure parser; field-presence regex so RssAnon: 0 + RssShmem: 512 parses correctly) and getAccurateRss(readStatus?) (reads /proc/self/status for RssAnon + RssShmem, falls back to process.memoryUsage().rss on macOS / restricted containers / kernel <4.5); the default getRss in WorkerOpts is getAccurateRss. checkMemoryLimit tracks peak RSS, fires an 80%-of-cap soft-warn (once per crossing, carrying peak + in-flight job kinds), and on exceed sets _rssWatchdogTriggered=true (exposed via get rssWatchdogTriggered()) so jobs work's finally can process.exit(WORKER_EXIT_RSS_WATCHDOG) after disconnect (drain self-identifying instead of an opaque code-0 exit). The poll loop wraps claim in try/catch: on a retryable conn error it reconnects ONCE and continues to the next tick rather than blind-retrying (a retry after UPDATE...RETURNING committed but the socket died would double-claim). LockRenewalDeps is wired with reconnect when the engine supports it. The self-health DB-liveness probe now runs EVEN under a supervisor (GBRAIN_SUPERVISED=1): the outer guard is if (this.opts.healthCheckInterval > 0) and only the STALL-detection block is wrapped in if (!isSupervisedChild) — so a supervised worker whose own pool dies self-exits unhealthy(db_dead) after dbFailExitAfter probes (the supervisor watches a different connection and can't see this worker's dead pool), while the supervisor's progress watchdog owns forward-progress (#1801). Pinned by the test/worker-lock-renewal.test.ts hermetic suite, test/audit/lock-renewal-audit.test.ts, test/scripts/check-worker-lock-renewal-shape.test.ts, test/worker-shutdown-disconnect.test.ts (asserts disconnectSpy).not.toHaveBeenCalled()), test/worker-rss.test.ts (11), test/worker-supervised-db-probe.test.ts (3). Per-job process isolation: MinionWorkerOpts.jobIsolation (inline|process) + childCliInvocation/childTiniPath swap handler(context) for runJobInChild(...) in executeJob — every reporting branch (completeJob, failJob, lease release, infra no-burn) is reused on the child outcome; when isolated the parent-side context is not built at all. Three extra no-burn child classes in the catch: ChildSpawnInfraError + ChildWorkerShutdownError (released, no attempt burned) and ChildNotClaimedError (the child proved the claim was already gone — reclaimed/cancelled before the handler ran — so nothing is recorded against it). The health probe delegates to runDbProbe (db-probe.ts) with a cancellation signal on every probe and emits a verdict (pool_starved/server_unreachable/unknown) on the db_dead unhealthy payload. getHandler(name) is the read-only registry accessor run-child uses.

• src/core/minions/supervisor.ts — MinionSupervisor process manager. Spawns gbrain jobs work as a child, restarts on crash with exponential backoff, periodic health check. consecutiveHealthFailures counter; on 3 consecutive failures emits health_warn with reason: 'db_connection_degraded' and calls engine.reconnect() to swap in a fresh pool, then resets. Worker exit classifier emits likely_cause on worker_exited events: oom_or_external_kill (SIGKILL), graceful_shutdown (SIGTERM), runtime_error (code 1), clean_exit (code 0), unknown. Consumes detectTini() + buildSpawnInvocation() from src/core/minions/spawn-helpers.ts to wrap the worker subtree in tini-as-PID-1 when tini is on PATH (handles native-addon zombie reaping the in-process SIGCHLD reaper can't reach); exposes isTiniDetected read-only accessor. The spawn-and-respawn loop is the shared ChildWorkerSupervisor core: MinionSupervisor composes it via runSuperviseLoop() → new ChildWorkerSupervisor({...}) and maps ChildSupervisorEvent back through emit() SupervisorEvent (JSONL audit consumers see byte-compatible output). PID lock, signal handlers, health check, and process.exit on the HARD crash ceiling stay in MinionSupervisor. Crossing the SOFT budget (maxCrashes) no longer permanently gives up (#1994/#2227): the core drops into degraded retry (capped backoff + a crash_budget_degraded health_warn) and self-heals when a respawn runs stably; permanent process.exit(MAX_CRASHES) fires only at the hard ceiling resolveHardStopMaxCrashes(maxCrashes) (default maxCrashes × 10, env GBRAIN_SUPERVISOR_HARD_STOP_CRASHES, 0 = never). Separately, gbrain jobs supervisor status + gbrain doctor detect a live supervisor through this queue lock (inspectLock + isLockHolderLive, freshness-keyed so PID reuse can't false-positive) when the $HOME-derived pidfile is absent, so a split-$HOME deployment no longer reads a healthy supervisor as "not running" (#2227). code=0 leaves crashCount untouched (so a worker alternating real crashes + watchdog drains still trips max_crashes); cleanRestartBudget (default 10 restarts per 60s) caps the macOS/non-Linux-fallback tight-loop via health_warn { reason: 'clean_restart_budget_exceeded' } + backoff. shutdown() drains via childSupervisor.killChild('SIGTERM') + awaitChildExit(35_000). Progress watchdog (#1801): healthCheck() restarts an alive-but-wedged child via childSupervisor.restartCurrentChild(35_000) when a queue has claimable work, 0 live-lock active jobs, and stale completions across wedgeRestartChecks (default 3) consecutive checks past wedgeRestartMinutes (default 15, 0 disables) + a startupGraceMs window; bounded by wedgeRestartLoopBudget (default 3 / wedgeRestartLoopWindowMs) which switches to a one-shot wedge_restart_loop alert. The wedge query is the exported queryWedgeSignals(engine, queue, handlerNames) — name+queue-scoped, active_healthy = live-lock only (an expired-lock active row does NOT mask the wedge), due-delayed counted. Claimable names are derived at start via a throwaway registerBuiltinHandlers worker (its new quiet opt). Flags --wedge-restart-minutes / --wedge-restart-checks + env GBRAIN_WEDGE_RESTART_MINUTES / GBRAIN_WEDGE_RESTART_CHECKS. The worker argv is built by the exported pure buildWorkerArgs(opts) (appends --nice N when opts.nice_requested is set, alongside --concurrency/--queue/--max-rss); the niceness apply RESULT (nice_requested/nice_effective/nice_error, computed by the CLI in jobs.ts — the supervisor doesn't call setPriority) rides on the started/worker_spawned audit emissions (#1815). Queue-scoped singleton (#1849): the real authority is a DB lock (tryAcquireDbLock from src/core/db-lock.ts) keyed on supervisorLockId(queue) = gbrain-supervisor:<queue> — keyed on the QUEUE ALONE because the lock row lives inside the target database, so the (database) half of the mutex is physical, not part of the key (an earlier revision mixed in a config-derived DB identity, which let two supervisors on the same physical DB via different-but-equivalent URLs compute different ids and both acquire — fixed). Two supervisors with different $HOME/--pid-file against the same (database, queue) no longer both run with conflicting --max-rss; the second exits LOCK_HELD. The pidfile-cleanup process.on('exit') listener is installed BEFORE the DB-lock acquisition so the LOCK_HELD early-exit can't strand the pidfile this process just created. The default pidfile is now brain-scoped (supervisor-<brainId>.pid) so different brains under one HOME don't false-block. The lock refreshes on its own setInterval (TTL 5min, refresh 60s, max 3 failures = 180s < TTL); a refresh that THROWS past the threshold exits LOCK_LOST (code 4) rather than risk a split-brain, while a fenced refresh returning false (0 rows matched — the lock was stolen or force-cleared) is treated as CERTAIN loss, not a blip: the supervisor emits health_error { reason: 'supervisor_lock_lost' } and exits LOCK_LOST immediately (counting it toward the failure threshold would let two supervisors drain the same queue for up to two more refresh windows). shutdown() releases the lock so a clean restart re-acquires immediately. The started audit now records max_rss_mb so gbrain doctor's supervisor_singleton check can surface the effective cap. Exports supervisorLockId() and the pure classifySupervisorSingleton({lockLive, lockHolderHost, lockHolderPid, localHost, localPid}) → 'no_lock'|'single'|'mismatch' (host+pid compare, bare pid meaningless cross-host) that doctor consumes. Pinned by test/supervisor.test.ts (16 cases), test/supervisor-tini.test.ts, test/supervisor-wedge.test.ts, test/supervisor-build-worker-args.test.ts, and test/supervisor-db-lock.test.ts. SupervisorOpts.jobIsolation passes --job-isolation process to the spawned worker via a CONDITIONAL buildWorkerArgs push (inline argv stays byte-identical). queryWedgeSignals/probeQueueState thread a per-probe AbortSignal; the probe timeout cancels the losing query (pool-slot release under exhaustion).

• src/core/minions/child-worker-supervisor.ts — shared spawn-and-respawn core reused by both MinionSupervisor (standalone gbrain jobs supervisor daemon) and src/commands/autopilot.ts (autopilot daemon), so the two consumers can't drift into parallel-loop bugs. Pure class: NO PID file, NO signal handlers, NO process.exit, NO health check. Lifecycle events fire via injected onEvent: (ChildSupervisorEvent) => void. Exit classifier: code === 0 leaves crashCount UNCHANGED (preserves flap detection across mixed exit sequences); code != 0 follows runDuration > stableRunResetMs ? 1 : ++crashCount. Clean-restart budget: sliding window of code=0 exits; when count exceeds cleanRestartBudget (default 10) inside cleanRestartWindowMs (default 60s), emits health_warn { reason: 'clean_restart_budget_exceeded' } and applies cleanRestartBudgetBackoffMs (default 1s). The exit classifier special-cases WORKER_EXIT_RSS_WATCHDOG — likely_cause='rss_watchdog', and that exit does NOT bump crashCount (routes to its own breaker); a dedicated _watchdogExitTimestamps sliding window trips a loud rss_watchdog_loop health_warn naming the cap when N watchdog exits land inside the window, INDEPENDENT of the stable-run reset (which would otherwise hide a >5-min-run watchdog drain loop). New opts watchdogLoopBudget (3), watchdogLoopWindowMs (600000), watchdogBackoffMs (30000); ChildSupervisorEvent extended. Public read-only accessors childAlive, inBackoff, crashCount; killChild(signal) gates on liveness (exitCode === null && signalCode === null), NOT .killed — .killed flips true once a signal is sent, so the old !this._child.killed guard made a follow-up SIGKILL after an ignored SIGTERM a silent no-op (#1801; the bug also lived in the shutdown() drain). restartCurrentChild(graceMs) (#1801 wedge self-heal) captures the CURRENT child ref, SIGTERM→grace→SIGKILLs THAT ref (never the respawn — closes the timer-kills-fresh-worker race), and flags _intentionalRestart so the exit is likelyCause='wedge_restart', leaves crashCount UNTOUCHED (never trips max_crashes; like rss_watchdog), and respawns immediately (backoff ms:0 reason='wedge_restart'). awaitChildExit(timeoutMs) short-circuits when child.exitCode !== null || child.signalCode !== null so fast-SIGTERM responders don't cause a 35s shutdown hang. Degraded-retry (#1994/#2227): the run() loop no longer fires onMaxCrashesExceeded at the soft maxCrashes; it announces health_warn { reason: 'crash_budget_degraded' } once per episode and keeps respawning with capped backoff (the 60s cap makes it a paced retry, not a hot loop), re-arming after a stable-run reset drops the count. Permanent give-up fires only at hardStopMaxCrashes (default maxCrashes × HARD_STOP_CRASH_MULTIPLIER = 10×; 0 disables). Test hooks _backoffFloorMs, _now. supervisor-audit.ts adds rss_watchdog as a non-clean cause + its own CrashSummary.by_cause bucket, and wedge_restart to CLEAN_EXIT_CAUSES (a self-heal, not a crash; denylist preserved so future causes route to legacy). Pinned by test/child-worker-supervisor.test.ts (12 cases).

• src/core/minions/spawn-helpers.ts — pure detectTini() + buildSpawnInvocation() consumed by both supervisor.ts and autopilot.ts (resolves the DRY violation between the two spawn sites and makes tini wrapping testable without mock.module(), rule R2 of scripts/check-test-isolation.sh). detectTini() calls execFileSync('which', ['tini']) with explicit env: process.env so Bun sees runtime PATH mutations. buildSpawnInvocation(tiniPath, cmd, args) returns {cmd, args} with tini prepended when present, or the bare invocation otherwise. Pinned by test/spawn-helpers.test.ts (5) and test/supervisor-tini.test.ts (4).

• src/core/minions/job-isolation.ts — per-job process-isolation protocol (issue #5): atomic outcome-file codec (writeChildOutcomeFile tmp+rename, decodeChildOutcomeFile with a 32MiB cap that throws UnrecoverableError — oversize results die loudly on attempt 1, decode errors report byte counts never content), encodeHandlerError/reconstructHandlerError preserving the two instanceof classes executeJob branches on (UnrecoverableError, RateLeaseUnavailableError), the child argv/env contract (CHILD_ENV, buildChildArgs), resolveChildCliInvocation (env override → compiled binary → bun-dev fallback → null for fail-fast), and killProcessGroup(pid, sig) — children are spawned detached (own group) because SIGKILL on a tini pid alone orphans the handler grandchild, and Bun rejects negative pids in process.kill (oven-sh/bun#15791) so group signaling falls back to POSIX /bin/kill. Pinned by test/job-isolation-protocol.test.ts (incl. real-process grandchild-death).

• src/core/minions/child-job-runner.ts — parent-side runner: runJobInChild(opts) spawns the child (detached + tini when available, stdio inherit for handler logs, per-job lifecycle log lines), maps per-job abort → group SIGTERM now + group SIGKILL at +25s (CHILD_KILL_GRACE_MS, inside the 30s force-evict backstop), gives worker-shutdown children the drain window to finish AND report (a non-reporting shutdown kill throws ChildWorkerShutdownError → released, no attempt burned), classifies pre-exec spawn failure as ChildSpawnInfraError (released, no attempt burned), and bounds child pools via env (GBRAIN_POOL_SIZE default 3, GBRAIN_DIRECT_POOL_SIZE=1). Pinned by test/child-job-runner.test.ts (real children) + test/worker-job-isolation.test.ts (full parent path on PGLite).

• src/core/minions/run-child.ts — runChildJobEntry(engine, opts, injectables): the jobs run-child core. Re-reads the job row and validates status+token (exit 14 on mismatch, handler never runs), builds the shared token-fenced context against the CHILD's engine, runs the handler, writes ONE atomic outcome file (handler failure = reported outcome = exit 0; only write-failure exits 15). Installs a SIGTERM→shutdownSignal-ONLY handler (inline signal-separation parity: ctx.signal stays live so cooperative handlers finish + report inside the drain window; the parent's group SIGKILL at drain end is the backstop) and a parent-liveness watchdog polling process.kill(parentPid, 0) (ppid checks are dead code under tini) that aborts BOTH signals on parent death with a hard exit after grace. No worker machinery (parent owns liveness). Pinned by test/run-child-entry.test.ts.

• src/core/minions/job-context.ts — shared buildJobContext(engine, queue, job, lockToken, signal, shutdownSignal) (extracted verbatim from executeJob) so inline mode and the run-child child wire identical token-fenced DB callbacks.

• src/core/minions/db-probe.ts — hermetic DB-liveness probe with pool-starvation disambiguation (issue #6): runDbProbe(deps) probes the read pool (signal-cancelled at timeoutMs), on failure probes the DIRECT lane (DIRECT_PROBE_TIMEOUT_MS, only when dual-pool is genuinely active) and returns a verdict — pool_starved ("server IS reachable; fault is in the transaction-pooler path — client pool exhaustion or a pooler-layer fault", deliberately an honest disjunction), server_unreachable, or unknown. Gauge counts render as a labeled tracked SUBSET; no waiter/available arithmetic. Pinned by test/db-probe.test.ts.

• src/core/minions/niceness.ts — OS scheduling-priority (niceness) primitives for the --nice flag. parseNiceValue(raw) whole-string parses + range-validates to POSIX [-20, 19] (rejects "3.5"/"10abc" that parseInt would silently truncate). applyNiceness(nice, setPriority?, getPriority?) calls os.setPriority(0, n) and ALWAYS re-reads os.getPriority(0) afterwards — in both the success and the catch paths — so a denied renice (EPERM) or an RLIMIT_NICE clamp records the real effective value (e.g. 0), not null; returns {applied, requested, effective, error?}. getEffectiveNiceness(pid, getPriority?) reads an arbitrary pid's niceness (null on dead/unreadable). formatNice(n) → +10/0/-5. Applied only at the CLI layer (jobs.ts) so worker.ts/supervisor.ts stay embeddable. Pinned by test/niceness.test.ts.

• src/core/minions/worker-registry.ts — live worker registry backing niceness observability. Each running gbrain jobs work self-registers worker-<pid>.json under gbrainPath('workers') (brain-isolated via GBRAIN_HOME; entries tagged with currentBrainId() so multiple DBs under one home don't cross-report). registerWorker(info) is best-effort (never blocks the worker) and returns a cleanup fn the caller wires to BOTH the shutdown finally AND process.on('exit') (the unhealthy process.exit(1) bypasses the awaited finally). readWorkers(getNice?) enumerates the dir, drops confirmed-dead pids (classifyLiveness: ESRCH = dead/prune, EPERM = alive/keep), applies a pid-reuse start-time guard (ps -o lstart, rejects a pid whose process started >5s after the entry was written), and re-measures each live worker's niceness now. Reports the worker's REAL pid, sidestepping the tini-wrapper-pid problem. Pinned by test/worker-registry.test.ts.

• src/core/minions/supervisor-pid.ts — readSupervisorPid(pidFile) → {pid, running}: the shared existsSync → readFileSync → parseInt → process.kill(pid,0) PID-file + liveness reader extracted from the three copies in jobs.ts (supervisor status), jobs.ts (stats), and doctor.ts. EPERM from the liveness probe counts as running. Pinned by test/supervisor-pid.test.ts.

• src/core/minions/handler-timeouts.ts (#1737, #4145) — per-handler-type defaults for BOTH per-job time knobs, co-located so they can't drift apart unseen (they are different quantities: the budget bounds total runtime, the lease bounds dead-worker reclaim — never derive one from the other). HANDLER_DEFAULT_TIMEOUT_MS: 30 min for subagent, subagent_aggregator, embed-backfill, autopilot-cycle, autopilot-global-maintenance; 10 min for chronicle_extract + facts-absorb; 60 min for contextual_reindex_per_chunk. HANDLER_DEFAULT_LOCK_DURATION_MS: 300 s for the long LLM/loop handlers, 120 s for the single-LLM-call handlers, shell deliberately absent (fast dead-worker reclaim; verify-before-evict protects it anyway). defaultTimeoutMsFor / defaultLockDurationMsFor return the mapped default or null (short handlers keep the tight null-default wall-clock / the 30 s worker lease). clampLockDurationMs + LOCK_DURATION_MS_MIN/MAX ([5s, 1h]) is the ONE clamp shared by queue.add, the CLI --lock-duration-ms flag (--dry-run echoes the clamped value), and the MCP submit_job param; the same bound is mirrored in SQL at claim time and by the minion_jobs.lock_duration_ms range CHECK, so every layer agrees. Layers (explicit value always wins): MinionQueue.add() stamps at submit; MinionQueue.claim() COALESCEs NULL columns from the maps (durable invariant); migration v128 one-shot backfilled timeout_ms with authoring-time snapshot values — do NOT sync v128 when editing the maps (lock_duration_ms has no backfill: NULL = worker default = pre-#4145 behavior). Pinned by test/minions.test.ts + test/migrations-v128.test.ts + test/migrations-v130.test.ts.

• src/core/minions/admission.ts — submit-side queue admission control (the drain-side pool-starvation half is v0.46.1.0's isolation work; claim fairness is a filed TODO, deliberately out of scope). Three primitives resolved per name via resolveAdmissionPolicy (config minions.* > per-name defaults tables, 60s in-process cache, fail-open with a once-per-process stderr warn; env kill-switch GBRAIN_MINIONS_ADMISSION=0 disables all three): PARAM-COALESCING (PARAM_COALESCE_DEFAULT — on for subagent; computeParamHash = sha256 of stable-stringified payload excluding only __param_hash itself — __owner_client_id is deliberately INCLUDED so owner lanes never cross; parentless + waiting-only + age-bounded to ttl/2), WAITING-TTL (WAITING_TTL_DEFAULT_HOURS — 48h for subagent; swept by MinionQueue.handleWaitingTTL through cancelJobs(ids, {reason, rootStatuses:['waiting']}) so descendants cancel, child_done lands, aggregator parents resolve, and the reason stamps ROOT ids only; ≤500/tick oldest-first; warn-before-act is runWaitingTtlTick — first tick counts affected + stamps TTL_NOTICE_SHOWN_KEY with an ISO timestamp, sweeping starts only after ttlNoticeGraceMs() (1h default, env GBRAIN_MINIONS_TTL_NOTICE_GRACE_MS) elapses; gbrain upgrade prints the same one-shot notice and starts the same clock; legacy 'true' flag values sweep immediately), and NAME-GLOBAL QUOTA (QUOTA_MAX_WAITING_DEFAULT EMPTY by operator decision — activates only via minions.quota_max_waiting.<name>; counts the name across ALL queues so per-run dream-inline-* fanout queues can't dodge it, EXACT under concurrency via a minion_quota:<name> advisory xact lock taken only when a quota is configured; throws typed QueueQuotaExceededError, checked everywhere via isQueueQuotaExceededError — dream submitters record a phase skip, synthesize rolls back the current transcript's fresh chunks, agent fanout cancels the whole tree, submit_agent maps to a structured rate_limited OperationError). TTL_REASON_PREFIX is the single source for the sweep's error_text prefix and the stats/doctor LIKE patterns; safeConfigSegment gates untrusted job names out of copy-pasteable config hints. Alerting rides getStats (drained_completed/failed/dead/cancelled keyed on finished_at + waiting_now + oldest_waiting_minutes), the jobs stats DIVERGENT-QUEUE / waiting-TTL screams (GBRAIN_QUEUE_DIVERGENCE_RATIO=2, GBRAIN_QUEUE_DIVERGENCE_MIN_WAITING=50; divergence compares intake vs COMPLETED so TTL-cancel storms can't masquerade as throughput) + --json, and doctor checkQueueHealth. Pinned by test/minions-admission.test.ts + test/jobs-stats-divergence.serial.test.ts.

• src/core/minions/types.ts — MinionJobInput + MinionJobStatus + handler context types. MinionJobInput.max_stalled is optional; omitted values let the schema DEFAULT (5) kick in, provided values are clamped to [1, 100].

• src/core/minions/protected-names.ts — side-effect-free constant module exporting PROTECTED_JOB_NAMES + isProtectedJobName(). Kept pure so queue core can import without loading handler modules. PROTECTED_JOB_NAMES includes synthesize, patterns, consolidate. These phases internally submit subagent children with allowProtectedSubmit=true and can spend Anthropic credits. Only trusted local callers (CLI, autopilot, doctor --remediate) can submit them; MCP requests are rejected by submit_job's protected-name guard.

• src/core/minions/handlers/shell.ts — shell job handler. Spawns /bin/sh -c cmd (absolute path, PATH-override-safe) or argv[0] argv[1..] (no shell). Env allowlist PATH, HOME, USER, LANG, TZ, NODE_ENV + caller env: overrides + inherit:-resolved keys. UTF-8-safe stdout/stderr tail via string_decoder.StringDecoder. Abort (either ctx.signal or ctx.shutdownSignal) fires SIGTERM → 5s grace → SIGKILL on child. Requires GBRAIN_ALLOW_SHELL_JOBS=1 on worker (gated by registerBuiltinHandlers). ShellJobParams.inherit?: string[] is a free-form list of snake_case config-key names; the worker resolves each via loadConfig() and injects the value under the derived env key (database_url → GBRAIN_DATABASE_URL; else uppercased). Names persist in minion_jobs.data (and the shell-audit JSONL); values never do. The canonical validator validateShellJobParams (sibling shell-validate.ts) runs PRE-ENQUEUE in both submit surfaces — gbrain jobs submit shell (jobs.ts:271) AND the submit_job op for name='shell' (operations.ts:2085); the handler-entry re-validation here is defense-in-depth (closes the bug class where validation ran AFTER queue.add() persisted the row). The validator does NOT police which config keys the agent inherits — same-uid trust model treats the agent as a peer of the worker.

• src/core/minions/handlers/shell-inherit.ts — three helpers. INHERIT_NAME_RE (/^[a-z][a-z0-9_]*$/) is the snake_case shape guard used by the validator; rejects __proto__, leading-underscore, uppercase, and path-traversal shapes so audit logs stay readable and prototype-pollution lookups can't smuggle through. deriveEnvKey(name) maps config-key → child-env-key (name.toUpperCase() with one override: database_url → GBRAIN_DATABASE_URL because plain DATABASE_URL is ambiguous). resolveInheritValue(cfg, name) is the value lookup; uses Object.hasOwn to defeat prototype-pollution lookups, returns undefined for missing / non-string / empty-string values. No closed enum — agent and worker share a uid, so refusing arbitrary config keys defends nothing in that trust model.

• src/core/minions/handlers/shell-validate.ts — validateShellJobParams(data, opts?) shared pre-enqueue validator. Throws UnrecoverableError with paste-ready operator hints on every failure. Three rules: (1) cmd/argv/cwd/env shape, (2) inherit array shape + snake_case regex per element (prototype-pollution defense), (3) fail-fast on missing config value with gbrain config set <key> hint. Optional redact_secrets?: boolean for output-side scrubbing. Deliberately does NOT police WHICH secrets the agent passes — single-uid trust model. Test seam: opts.config drives the validator hermetically without mocking. Re-called at shell.ts handler entry for defense-in-depth (catches rows submitted before the pre-enqueue validator existed).

• src/core/minions/handlers/shell-redact.ts — opt-in output-side scrubbing for shell-job stdout/stderr. Pure redactSecretsInText(text, secrets): string-mode replaceAll so regex metacharacters in values stay literal. When the caller passes redact_secrets: true (or --redact-secrets), the handler builds a Map of inherit-name → resolved-value and post-processes both tails before throw/return so persisted result.stdout_tail / result.stderr_tail / error_text carry <REDACTED:name>. Only inherit:-resolved values are scrubbed; caller-supplied env: values pass through. Heuristic — defeats echo "$GBRAIN_DATABASE_URL", not adversarial encode-then-print. Default false.

• src/core/config.ts:ensureGitignore — idempotent retroactive writer of ~/.gbrain/.gitignore (single line *). Called from saveConfig() so every config-writing path lays it down, AND from runPostUpgrade() so existing users pick it up on gbrain upgrade. Never clobbers a user-customized .gitignore (checks file exists + content non-empty before writing). Scope: blocks casual git add ~/.gbrain from inside an enclosing worktree, but does NOT cover already-tracked files, screenshots, backups (Time Machine / iCloud / Dropbox), or git add -f. The doctor check home_dir_in_worktree surfaces what .gitignore can't.

• src/core/minions/handlers/shell-audit.ts — per-submission JSONL audit trail at ~/.gbrain/audit/shell-jobs-YYYY-Www.jsonl (ISO-week rotation; override via GBRAIN_AUDIT_DIR). Best-effort: mkdirSync(recursive) + appendFileSync; failures logged to stderr, submission not blocked. Logs cmd (first 80 chars) or argv (JSON array). Never logs env values.

• src/core/minions/handlers/supervisor-audit.ts — supervisor lifecycle JSONL audit at ~/.gbrain/audit/supervisor-YYYY-Www.jsonl (ISO-week rotation; shares computeIsoWeekName() with shell-audit.ts). writeSupervisorEvent(emission, supervisorPid) appends one line per event (started, worker_spawned, worker_exited, backoff, health_warn, health_error, max_crashes_exceeded, shutting_down, stopped, worker_spawn_failed). readSupervisorEvents({sinceMs}) is the readback for gbrain doctor. Exports isCrashExit(event), summarizeCrashes(events), CrashSummary type, and CLEAN_EXIT_CAUSES denylist ('clean_exit' | 'graceful_shutdown'). Single regression point — both gbrain doctor (supervisor check) and gbrain jobs supervisor status import from here so the two surfaces can't drift. isCrashExit classifies a single worker_exited against the denylist: clean/graceful are NON-crashes; everything else (incl. any future likely_cause from child-worker-supervisor.ts) is a crash; audit lines lacking likely_cause fall back to code !== 0. summarizeCrashes returns {total, by_cause: {runtime_error, oom_or_external_kill, unknown, legacy}, clean_exits} — the legacy bucket catches both old fallback entries AND unrecognized future causes (fail-loud, not silent underreport); denylist-over-allowlist is deliberate. Pinned by test/supervisor-audit.test.ts (14 cases) and 4 source-grep wiring assertions in test/doctor.test.ts.

• src/core/minions/backpressure-audit.ts — sibling of shell-audit.ts for maxWaiting AND maxPending coalesce events. JSONL at ~/.gbrain/audit/backpressure-YYYY-Www.jsonl. One line per coalesce with (queue, name, waiting_count/max_waiting OR pending_count/max_pending, returned_job_id, ts). readRecentCoalesceCounts feeds the jobs stats Backpressure line (reads current + previous ISO-week files so a 24h window survives week boundaries, filtered per queue). Closes the silent-drop vector the backpressure guards introduced. Pinned by test/backpressure-audit-read.test.ts.

• src/core/minions/handlers/subagent.ts — LLM-loop handler. Two-phase tool persistence (pending → complete/failed), replay reconciliation for mid-dispatch crashes, dual-signal abort (ctx.signal + ctx.shutdownSignal), Anthropic prompt caching on system + tool defs. makeSubagentHandler({engine, client?, ...}) factory; MessagesClient is an injectable interface the real SDK implements structurally. Per-turn output cap resolves via resolveMaxOutputTokens (data.max_tokens → agent.max_output_tokens config → 8192 default); a stop_reason: 'max_tokens' final turn surfaces as SubagentStopReason 'max_tokens' (not a silent end_turn), and a max_tokens stop mid-tool-round injects a truncation note into the tool-result turn so the model re-issues the dropped call. Throws RateLeaseUnavailableError (renewable) when rate-lease capacity is full. Both loop paths (the direct Anthropic SDK turn loop and the gateway toolLoop's acquireTurnPermit) heartbeat the held lease at ttl/3 for the duration of each provider call — single-flight renewals so a stalled renewal never stacks behind a starved pool; a FALSE renewal means the lease row was pruned/stolen (the slot is already re-admitted), so the in-flight call aborts and converts to a lease-full requeue instead of running above maxConcurrent. Anthropic 400 prompt is too long responses (status 400 + body matches /prompt is too long|prompt_too_long|context.*length/i) classify as UnrecoverableError so the job goes straight to dead on first attempt instead of stalling three times. Catches both initial-prompt overflow and turn-N tool-loop accumulation that synthesize.ts's chunker can't bound ahead of time. terminal-state short-circuit on resume. When a stored message thread already ends in stop_reason: 'end_turn', the handler returns { ok: true } immediately instead of issuing another messages.create call (re-prompting past end_turn would get a 400 and dead-letter an already-successful job). Pinned by test/subagent-handler.test.ts. Oneshot dispatch (#4216): data.mode === 'oneshot' on a FRESH job (zero persisted messages) routes to runSubagentOneshot (subagent-oneshot.ts) before either loop; a validation fallback re-enters the loops in the SAME job, stamped synth_mode_used: 'agentic_fallback' + fallback_reason. Write accounting (#4217, finalizeWriteAccounting in subagent-persistence.ts): every job's result carries pages_attempted/written/failed derived from the tool-execution ledger (settled rows only); data.require_writes jobs (dream synthesize + patterns fan-outs) throw UnrecoverableError → dead when attempted>0 with zero successes. resolveMaxOutputTokens takes the model: thinking-by-default Claude 5 defaults to 32000 when neither per-job nor config caps are set. Gateway-path onToolCallStart has a uniq_subagent_tools_use_id backstop (#4155): a provider repeating a tool id across turns persists under a #m<idx>o<ordinal>-suffixed debug id (second violation reconciles to the existing row's gbrain_tool_use_id) instead of dead-lettering the job. Persistence helpers live in subagent-persistence.ts (pure peel; __testing unchanged). Tool-execution rows carry NO job-wide unique on the raw provider tool_use_id (migration v131 drops uniq_subagent_tools_use_id — providers like claude-cli legitimately re-mint the same short id every turn, and the collision dead-lettered the job); row identity is the stable (job_id, message_idx, ordinal) unique, and readers/settlement resolve an execution by (message_idx, tool_use_id). Settle writes (complete/failed) target exactly ONE row — the call's own ordinal first, then a legacy ordinal=NULL row, never a row that already settled complete (a broader status disjunct could only capture a same-id sibling's row); pending inserts guard legacy NULL-ordinal rows via NOT EXISTS and use the stable-id ON CONFLICT as the zombie-worker backstop. Replay/reconcile resolve an execution by persisted ordinal first (validated against the raw id), then by (message_idx, tool_use_id) only when the id is unique within the turn, then the same-tool legacy positional fallback. Mixed-version window: a still-running pre-v131 gbrain jobs work daemon errors on tool persistence after the migration until it restarts (its two-phase writes targeted the dropped constraint)

• src/core/minions/handlers/subagent-oneshot.ts — #4216 oneshot synthesis runner. ONE rate-leased tool-less gateway.chat call (static ONESHOT_SYSTEM JSON contract rides the prompt-cache prefix; sub-budget min(5 min, timeout/4) → fallback_reason: 'oneshot_timeout'), then all-or-nothing validation BEFORE any write: JSON contract (parseOneshotResponse, ≤12 pages), slug grammar + allowed_slug_prefixes + reflections/originals task shape + the exact oneshot_slug_suffix (the idempotency boundary, enforced structurally), exact-match wikilink rule against existing ∪ in-batch slugs (extractWikilinkTargets; cold-brain relaxation: <5 pages AND no manifest accepts syntactic presence). Writes go through the SAME brain_put_page ToolDef the loop uses (fences/side-effects/provenance identical) with deferEmbeds, bracketed by standard ledger rows under invocation-scoped ids oneshot-<inv8>-p<i>; a post-batch autoLinkWrittenPage pass materializes in-batch forward wikilink edges. Ledger-first crash recovery: any prior oneshot rows → finalize from the ledger, never re-call the nondeterministic model. Transcript rows persist ONLY after success (a failed attempt is never replayable as a completed result). Every failure shape returns {kind:'fallback', reason} and the same job falls through to the agentic loop. Pinned by test/minions/subagent-oneshot.test.ts + the oneshot describes in test/subagent-handler.test.ts and test/e2e/dream-synthesize-pglite.test.ts.

• src/core/minions/handlers/subagent-persistence.ts — subagent transcript + tool-execution persistence (pure peel from subagent.ts): loadPriorMessages/Tools/ToolsV2, persistMessage, persistToolExecPending/Complete/Failed (all $N::text::jsonb discipline), plus finalizeWriteAccounting (#4217): derives pages_attempted/written/failed from the job's put_page ledger rows (settled only — pending counts toward neither), merges them into every SubagentResult, and throws UnrecoverableError on require_writes jobs whose every attempted write failed; scopeToolUseIdPrefix narrows the scan to the oneshot invocation family.

• src/core/minions/handlers/subagent-aggregator.ts — subagent_aggregator handler. Claims AFTER all children resolve (queue guarantees every terminal child posts a child_done inbox message with outcome). Reads inbox via ctx.readInbox(), builds a deterministic mixed-outcome markdown summary. No LLM call.

• src/core/minions/handlers/subagent-audit.ts — JSONL audit + heartbeat writer at ~/.gbrain/audit/subagent-jobs-YYYY-Www.jsonl. Events: submission (one per submit) + heartbeat (per turn boundary: llm_call_started | llm_call_completed | tool_called | tool_result | tool_failed, plus the oneshot markers oneshot_fallback | oneshot_timeout; oneshot-path events carry mode: 'oneshot' and fallback events a reason — both rendered by gbrain agent logs). Never logs prompts or tool inputs. readSubagentAuditForJob(jobId, {sinceIso}) is the readback for gbrain agent logs.

• src/core/minions/rate-leases.ts — lease-based concurrency cap for outbound providers (default key anthropic:messages, max via GBRAIN_ANTHROPIC_MAX_INFLIGHT). Owner-tagged rows with expires_at auto-prune on acquire; pg_advisory_xact_lock guards check-then-insert; CASCADE on owning job deletion. renewLeaseWithBackoff retries 3x (250/500/1000ms). Canonical home of RateLeaseUnavailableError (thrown when acquire finds no slot; the worker and the inline dream drain both recognize it and requeue WITHOUT burning an attempt — lease-full is a scheduling condition, not a failure; subagent.ts re-exports it for compatibility) and leaseFullBackoffMs() (the shared 1–3s jittered lease-full requeue backoff worker.ts and inline-drain.ts both use, so the two curves cannot silently desync).

• src/core/minions/handlers/contextual-reindex-per-chunk.ts — per-page contextual re-embed handler. Resolves models.contextual_synopsis once and isolates cross-worker leases by the full resolved model id. GBRAIN_CONTEXTUAL_SYNOPSIS_RPM controls the cap; GBRAIN_CONTEXTUAL_HAIKU_RPM is the compatibility alias.

• src/core/minions/wait-for-completion.ts — poll-until-terminal helper for CLI callers. TimeoutError does NOT cancel the job; AbortSignal exits without throwing. Default pollMs: 1000 on Postgres, 250 on PGLite inline.

• src/core/minions/transcript.ts — renders subagent_messages + subagent_tool_executions to markdown. Tool rows splice under their owning assistant tool_use by (message_idx, tool_use_id) — raw provider tool ids may repeat across turns, so tool_use_id alone is not an identity; echoed tool_result blocks check ownership against the nearest preceding assistant turn's key. UTF-8-safe truncation; unknown block types fall through to fenced JSON.

• src/core/minions/plugin-loader.ts — GBRAIN_PLUGIN_PATH discovery. Absolute paths only, left-wins collision, gbrain.plugin.json with plugin_version: "gbrain-plugin-v1", plugins ship DEFS only (no new tools), allowed_tools: validated at load time against the derived registry.

• src/core/minions/tools/brain-allowlist.ts — derives the subagent tool registry from src/core/operations.ts (15-name allow-list, size pinned by test/brain-allowlist.serial.test.ts). Includes add_timeline_entry (the canonical timeline write), fenced server-side by the same enforceSubagentSlugFence policy as put_page. By default put_page schema is namespace-wrapped per subagent (^wiki/agents/<subagentId>/.+). When BuildBrainToolsOpts.allowedSlugPrefixes is set, the put_page schema describes the prefix list to the model and the OperationContext is threaded with allowedSlugPrefixes — trust comes from PROTECTED_JOB_NAMES gating subagent submission (MCP cannot reach this field); only cycle.ts (synthesize/patterns) and direct CLI submitters set it. BuildBrainToolsOpts.deferEmbeds (server-side-only, set by the oneshot runner for its programmatic writes; never hydrated from any wire payload) threads OperationContext.deferEmbeds so put_page defers chunk embeddings for the phase-end backfill. Allow-list includes get_recent_salience + find_anomalies but deliberately NOT get_recent_transcripts (all subagent calls run ctx.remote === true and the trust gate rejects remote callers, so it would always reject; the cycle synthesize phase calls discoverTranscripts directly instead). paramsToInputSchema() consumes paramDefToSchema from src/mcp/tool-defs.ts; required-aggregation at the tool-def level stays here (the shared helper is per-param).

• src/mcp/tool-defs.ts — buildToolDefs(ops, opts?) helper; the stdio MCP server, the OAuth HTTP tools/list (WP3 amendment 14 unified the former inline mapper onto it), and the subagent tool registry all consume it, byte-for-byte equivalence pinned by test/mcp-tool-defs.test.ts. Default emission is byte-identical to the pre-WP3 output; opts.strictParams: true (when mcp.strict_params resolves 'reject') additionally declares the _meta/dry_run passthrough keys in properties and closes each schema with additionalProperties: false (D14.1 — schema-validating clients must not strip _meta.session_id); both emission states pinned. Exports the recursive paramDefToSchema(p: ParamDef) — single source of truth for ParamDef→JSON Schema mapping shared by buildToolDefs and src/core/minions/tools/brain-allowlist.ts (subagent registry). Recursive on items so nested array-of-arrays preserves inner shape on the wire. Key ordering (type, description, enum, default, items) is intentional so JSON.stringify output stays byte-stable. test/mcp-tool-defs.test.ts has a findArrayWithoutItems walker that fails on any type: 'array' lacking items.type.

• src/core/verbs.ts — MEMORY_VERBS v1 (Cathedral 1): the four new frozen protocol verbs (remember, entity, synthesize, forget) as first-class Operations, plus MEMORY_VERBS_VERSION (single source of truth, =1), VERB_NAMES, the hand-authored RESPONSE_SCHEMAS registry (Operation carries input params only; response shapes live here and conformance validates LIVE responses against them), and ERROR_SCHEMA. The fifth verb is the extended recall op in operations.ts. RUNTIME LEAF invariant: operations.ts spreads verbOperations into its array at module-eval time, so this file must never statically import operations.ts VALUES (type-only imports fine; handlers use dynamic import) — violating it reintroduces a TDZ crash on whichever module evaluates second. Every verb error carries a populated suggestion + protocol_version (via verbError in operations.ts). The forget verb deliberately has NO cliHints (CLI_ONLY forget dispatches first and would shadow it). Frozen contract: docs/protocol/MEMORY_VERBS_v1.md; pinned by test/memory-verbs-conformance.test.ts.

• src/core/verbs/entity-card.ts — buildEntityCard(engine, sourceId, name, {remote}): the zero-LLM sub-100ms card behind the entity verb. Resolution reuses the Retrieval Reflex arms (alias > exact title/slug > slug-suffix; exact-slug candidates include the RAW input because slugify flattens slashes in namespaced slugs); ties break on GREATEST(updated_at, last_retrieved_at). Per-arm degradation: a pre-page_aliases brain still resolves via arm 2 (aka returns empty, never throws). Card assembly is a parallel Promise.all of depth-1 indexed reads (page row, alias reverse lookup, getLinks+getBacklinks mentions-excluded cap 10, getBacklinkCounts, getTimeline(5), listFactsByEntity world-only-when-remote); deliberately NOT the recursive-CTE traversePaths — the card is a latency contract (CI gate: test/entity-card-perf.slow.test.ts, p99 < 100ms × GBRAIN_PERF_BUDGET_MULTIPLIER + 50× getPage-p50 ratio guard on a 20K corpus). summary runs through the exported safeSynopsis (the get_page fence boundary). Miss → keyword near-miss suggestions with create_safety hints.

• src/core/verbs/usage-log.ts — E4 observability sidecar: one JSONL line per verb call at ~/.gbrain/integrations/memory-verbs/usage.jsonl (gbrainPath — GBRAIN_HOME honored; brainId() = the resolved gbrain home). LOCAL ONLY, never uploaded, stats-only (lock-free 10MB rotation may drop lines; O_APPEND line-atomic, best-effort on Windows). logVerbUsage is fire-and-forget (never awaited, never throws); written from the DISPATCH layer so param-validation failures count. readVerbUsage/earliestVerbUsageTs feed gbrain protocol stats (incl. measured TTHW vs the init-stamped protocol_installed_at) and the doctor memory_verbs_usage check.

• src/core/verbs/conformance.ts + src/core/verbs/conformance-fixtures.ts — the conformance runner core (transport-agnostic: minimal ConformanceClient = list_tools + call_tool) and the embedded fixture set. Deterministic by construction: shape/enum/behavior/round-trip checks only, never ranking quality. Validation is NON-STRICT on extra fields (additive-forever means unknown fields are always legal). Entity-card cases seed via put_page when the target exposes it and skip honestly on verbs-only targets; synthesize is cost-gated behind --synthesize. validateAgainstSchema is a minimal JSON-Schema-subset validator (type unions, required, properties, enum, const, items). Fixtures mirror to test/fixtures/memory-verbs/cases.json (BrainBench seeds; drift-guarded by the conformance test). The negative self-test (test/memory-verbs-conformance.test.ts) proves the runner FAILS a lying server.

• src/core/facts/write-single.ts — writeSingleFact(fact, ctx): the zero-LLM single-fact seam behind remember [E1]. runFactsPipeline is extraction-first (LLM-gated) and cannot back a pre-formed fact; this reuses the pipeline's post-extraction stages directly: resolve → embedding-cosine dedup (same 0.95 threshold) → fence-first write with the same legacy DB-only fallbacks (thin-client, unparented, stub-guard). Supersession [X1]: deterministic rule — same entity_slug + same kind + similarity ≥ threshold + DIFFERENT text ⇒ the new fact supersedes (fence path: append new + forgetFactInFence(old) + superseded_by link; DB path: engine insertFact supersedeId). Provenance lands on NewFact.source verbatim (no FactsBackstopCtx). No embedding provider ⇒ degraded_dedup: true (near-duplicates may insert — documented).

• src/mcp/surface.ts — MCP tool-surface modes: 'verbs' (exactly the ops marked verb: true) | 'starter' (the ~27-op daily-driver set) | 'full' (default — identity; existing installs unchanged). STARTER_OPS is composed PROGRAMMATICALLY: a spread of VERB_NAMES (never a hand-count) + the FOV-6b fallback daily slice (BRAIN_TOOL_ALLOWLIST + the agent lane submit_agent/get_agent_job) + whoami + request_tools + capture (a DIRECT literal, deliberately NOT via the allowlist); re-derived from production usage via scripts/derive-starter-ops.ts (paste-in proposal, never an auto-edit). ALWAYS_INCLUDED_STARTER_OPS (verbs + whoami + request_tools + the agent lane + capture) is the exported always-set consumed by BOTH derive-starter-ops.ts and the advisor starter-fit collector, so neither re-types the composition (an out-of-sync copy in the collector once produced a perpetual bogus unused-starter finding). parseSurfaceFlag (strict, loud reject), resolveSurface (flag > config mcp_surface > full), filterOpsForSurface, allowedOpNames. Enforcement is TWO-layer and fail-closed: the advertised list AND dispatchToolCall's allowedOps set (a hidden op returns unknown_tool even when called by name) — applied on stdio (server.ts) and BOTH HTTP paths (serve-http.ts after !localOnly, and the second transport http-transport.ts). WP4 per-client ceiling machinery (OAuth transport only): effectiveSurfaceForClient is the pure composition clamp(min(server ceiling, client row surface ?? mcp.default_surface_dcr ?? ceiling)); the per-REQUEST application lives in serve-http.ts's resolveEffectiveSurface, which short-circuits a verbs ceiling (min() cannot go lower, so the config read is skipped) and, on a default-surface read failure, applies the LAST successfully read default (held per process, fail-closed) so a transient config outage cannot silently widen a NULL-surface client to the ceiling; resolveClientRowSurface ignores unknown row values with a bounded warn-once (the column's value space is documented OPEN for future tier names); resolveDefaultClientSurface reads the DCR default dual-plane (DB > file > null) and never throws; clampSurface/readForceSurfaceEnv fold in the GBRAIN_MCP_FORCE_SURFACE kill switch — NARROW-ONLY by construction (min(); can never widen past the ceiling). minSurface/surfaceWiderThan own the verbs < starter < full rank math. Pinned by test/mcp-surface.test.ts (membership, monotonicity verbs ⊆ starter ⊆ full, ceiling + force-narrow cases).

• src/commands/protocol.ts — gbrain protocol [--json] | conformance [--target <http-url|stdio-cmd>] [--token] [--synthesize] | stats [--days N]. --json emits input schemas from the LIVE Operation defs + RESPONSE_SCHEMAS (doc/code can't drift). Conformance default target self-spawns gbrain's own stdio server (dev .ts entry vs compiled binary both handled); CI certifies stdio with --synthesize (no key ⇒ asserts the clean unavailable error). Stats aggregates the usage sidecar + the measured TTHW; output states "local JSONL only — never uploaded". CLI_ONLY + SELF_HELP wired in cli.ts; no pre-bound engine.

• src/core/minions/attachments.ts — Attachment validation (path traversal, null byte, oversize, base64, duplicate detection).

• src/commands/agent.ts — gbrain agent run|logs|register dispatcher. run submits subagent (or N children + 1 aggregator) under {allowProtectedSubmit: true}; single-entry --fanout-manifest short-circuits; children get on_child_fail: 'continue' + max_stalled: 3; --follow is the default on TTY (streams logs + polls waitForCompletion in parallel; Ctrl-C detaches, does not cancel). logs delegates to agent-logs.ts; register lazy-imports agent-register.ts. Subcommand-aware help is answered BEFORE any engine or queue work and STOPS at the -- terminator (agent run -- --help submits the LITERAL prompt); on a brainless machine (null engine) help still prints while real run/logs invocations refuse with an init hint.

• src/commands/agent-logs.ts — gbrain agent logs <job> [--follow] [--since]. Merges JSONL heartbeat audit + subagent_messages into a chronological timeline. parseSince accepts ISO-8601 or relative (5m, 1h, 2d). Transcript tail renders only for terminal jobs.

• src/commands/agent-register.ts — gbrain agent register <name> --harness claude-code|codex|opencode|openclaw: mints a scoped OAuth client + access token and prints the exact harness wiring in one step (CLI-only, never an MCP op). Composes existing parts — registerScopedClient (auth.ts), exchangeClientCredentials, the mcp-registration argv builders, renderCodexHttpServerBlock, openclawThinClientBlock — no new auth machinery. Order is load-bearing: cli.ts pre-connect guards (thin-client refusal + PGLite live-serve probe) → pure parse (exit 2) → preset resolve → source validation (existence + not-archived, engine lane ANY($1::text[])) → column pre-flight OUTSIDE any tx (25P02 forbids in-tx degrade) → ONE engine.transaction (name-scoped pg_advisory_xact_lock → duplicate-name pre-check → ensureWorkspaceSource create-or-reuse-only-when-truly-empty (refuses page-, fact-, or file-bearing and archived sources) → registerScopedClient with ttl + surface) → COMMIT → post-commit fail-open surface audit → token exchange on the OUTER engine (the tx sql is dead) → serve probe (probeServeHealth + the unconditional SCOPES_MIN_SERVE_VERSION floor line): a probe-PROVEN pre-scopes serve REFUSES registration (serve_too_old) unless --allow-old-serve — such a serve verifies scoped tokens as full access; an unreachable serve stays a warning, and the reissue lane warns instead of refusing (the secret is already rotated by that point) → render + print (human, or ONE JSON doc carrying probe_note + serve_warning from the probe; secrets redacted unless --show-token). Presets: daily-driver (write one source; federated reads = SNAPSHOT of non-archived sources at registration, EXCLUDING other agents' *-workspace scratch sources — a workspace named explicitly in --federated-read is still granted, and the print counts the exclusions) and coding-agent (write-isolated derived <name>-workspace DB-only source; requires --federated-read); both default the client to the starter surface — override with --surface at registration or widen per client via gbrain auth rescope-client. Always writes token_ttl (default 30 days — the server default is 1 hour and would kill a pasted config). --url|--port required (every block embeds the brain URL). A scope blocklist keeps operator-grade scopes on auth register-client. --reissue <client-id> rotates the secret under the same advisory lock and reprints the block (headed by the stored client_name); rotation is not revocation — outstanding tokens live until expiry. Failure after COMMIT prints the client_id + the exact revoke command (never a false "nothing was created"). openclaw renders the honest thin-client CLI block (no native remote-MCP client upstream yet). Pinned by test/agent-register.test.ts.

• src/commands/jobs.ts — gbrain jobs CLI subcommands + gbrain jobs work daemon. Help is real and guarded: JOBS_HELP (full block incl. watch/stats/smoke flags + a footer naming exactly the five subcommands with dedicated help) and JOBS_SUBCOMMAND_HELP (work/supervisor/submit/watch/prune) print from a guard at the TOP of runJobs, BEFORE the thin-client refusal and the subcommand switch — jobs work --help can never start a daemon; only --help/-h are help tokens (bare help can be a job name); cli.ts routes it engine-free via SELF_HELP_WITHOUT_ENGINE + CLI_ONLY_SELF_HELP. formatJobDetail prints the effective wall-clock budget (Timeout:/Deadline: — 1x deadline kill when claimed, 2x wall-clock backstop, or which default applies) with a Date|string-defensive renderer; timeout_at is in JOB_DATE_FIELDS for thin-client rehydration. jobs stats prints a Backpressure (24h) line (per-name coalesce counts from the backpressure audit, current+previous ISO-week files, queue-filtered, best-effort) plus a suppressed-by hint naming the in-flight live-lock job when waiting=0 past the shared GBRAIN_WEDGED_QUEUE_WARN_MINUTES threshold — the read-only visibility for maxPending single-flight suppression. Pinned by test/jobs-subcommand-help.serial.test.ts, test/jobs-format-detail.test.ts, test/jobs-stats-backpressure.serial.test.ts. case 'work' wraps worker.start() in try/finally and owns engine lifecycle — calls engine.disconnect() on shutdown with loud error logging (the worker must not disconnect an engine it doesn't own; pool slots free immediately on shutdown rather than waiting for TCP keepalive). jobs submit surfaces the MinionJobInput retry/backoff/timeout/idempotency surface as flags: --max-stalled, --backoff-type fixed|exponential, --backoff-delay, --backoff-jitter, --timeout-ms, --idempotency-key, --max-waiting (maxPending is deliberately internal-only — no flag; see TODOS). jobs smoke --sigkill-rescue is the SIGKILL-rescue regression guard. registerBuiltinHandlers always registers subagent + subagent_aggregator (no env flag — ANTHROPIC_API_KEY is the cost gate, trust is via PROTECTED_JOB_NAMES) and loads GBRAIN_PLUGIN_PATH plugins at startup with a loud per-plugin line; shell handler still gated by GBRAIN_ALLOW_SHELL_JOBS=1 (RCE surface). The autopilot-cycle handler forwards job.data.phases to runCycle, validated against ALL_PHASES from src/core/cycle.ts (invalid names filtered; empty/missing falls back to the default cycle); when source_id is set it binds brainDir to that source's local_path (null for a pure-DB source, never the global repo — the #2194/#2227 mixed-scope fix) and checks isSourceInCooldown before runCycle, returning a no-op skipped (not a failure) for a source still in its failure cooldown. The sibling autopilot-global-maintenance handler runs MAINTENANCE_PHASES (mixed ∪ global) once (no sourceId, pull:false) and stamps autopilot.last_global_at on success. resolveJobPull gives both cycle and standalone sync jobs one positive-polarity pull contract while preserving queued payloads that still carry the inverse legacy noPull key; explicit pull wins. The sync handler resolves sourceId at entry from sources.local_path (mirrors cycle.ts:480) so multi-source brains read the per-source last_commit anchor; concurrency routes through autoConcurrency() in src/core/sync-concurrency.ts (PGLite stays serial); noEmbed default is true. gbrain jobs supervisor status consumes summarizeCrashes() from src/core/minions/handlers/supervisor-audit.ts for parity with gbrain doctor: JSON adds crashes_by_cause: {runtime_error, oom_or_external_kill, unknown, legacy} + clean_exits_24h; human output gains per-cause + clean-exits lines. Pinned by test/job-pull-policy.test.ts and 4 source-grep wiring assertions in test/doctor.test.ts requiring crashes_by_cause + clean_exits_24h= in both doctor.ts and jobs.ts. gbrain jobs watch decouples its two output axes: --json picks FORMAT (human default, never gated on isTTY), --follow picks LOOP (default isTTY && !json). Non-TTY with no flags prints ONE human snapshot then exits (clean for subagent/pipe/cron); --follow opts into a continuous stream (human plain per tick, or JSONL with --json); a TTY with no flags keeps the live ANSI dashboard. Resolution is the pure resolveWatchMode(opts, isTTY): {json, follow, useAnsiDashboard} in src/commands/jobs-watch.ts; the dispatch wires --follow. Pinned by test/jobs-watch-mode.test.ts (format×loop matrix incl. the TTY+--json-one-shot case) + test/e2e/non-tty-output.serial.test.ts (the cmd </dev/null non-empty-stdout contract). registers 11 Minion handlers: reindex, repair-jsonb, orphans, integrity, purge, synthesize (PROTECTED), patterns (PROTECTED), consolidate (PROTECTED), extract_facts, resolve_symbol_edges, recompute_emotional_weight. Phase wrappers delegate to runCycle({phases:[name]}) so src/core/cycle.ts stays the single source of truth for phase semantics. The standalone sync handler passes noExtract: true to match runPhaseSync's contract (doctor's remediation plan emitting [sync, extract] would otherwise double-extract). The extract handler routes {stale: true} jobs (submitted by performSync's #2849 size-gate defer branch) through extractStaleFromDB scoped to data.sourceId, chaining a continuation job (no maxWaiting — same NULL-sourceId coalesce hazard; timeout derived from STALE_TIME_BUDGET_MS) when the sweep's budget leaves staleRemaining > 0 with forward progress. parseJobIsolationFlag(args, env?) (--job-isolation, space/= forms, GBRAIN_JOB_ISOLATION fallback, default inline); case 'work' resolves + fail-fast validates the child CLI invocation and warns when --max-rss is combined with isolation (watchdog covers the worker only); case 'run-child' is the INTERNAL child entrypoint (quiet registerBuiltinHandlers incl. plugin discovery, CLI owns disconnect+exit); startup warning when a Supabase-shaped engine runs single-pool (kill-switch collapse made loud); the db_dead fatal text is verdict-aware (pool starved vs server unreachable). v0.46: the sync handler forwards job.data.github_item ({repo, number, kind}) into performSync for github-kind single-item webhook refreshes.

• src/commands/features.ts — gbrain features --json --auto-fix: usage scan + feature adoption salesman.

• src/commands/autopilot.ts — gbrain autopilot --install: self-maintaining brain daemon (sync+extract+embed). Freshness sync jobs always send an explicit positive-polarity pull value derived from the source's parsed remote_url, so local-only sources skip pull and PGLite JSON-string configs behave like Postgres objects. Consumes detectTini() from src/core/minions/spawn-helpers.ts, resolved once at startup. Composes a ChildWorkerSupervisor instance for spawn-and-respawn (no inline crashCount/startWorker/child.on('exit')); --max-rss 2048 and maxCrashes: 5 preserved. onMaxCrashesExceeded routes through autopilot's own shutdown('max_crashes') so the autopilot lockfile gets cleaned up. shutdown() drains via childSupervisor.killChild('SIGTERM') + awaitChildExit(35_000). Pinned by test/autopilot-fanout-wiring.test.ts and test/autopilot-supervisor-wiring.test.ts (6 static-shape guards: composes ChildWorkerSupervisor not legacy names, --max-rss 2048 in argv, maxCrashes: 5 literal, shutdown-via-callback, no workerProc reference). tick body invokes runNightlyQualityProbe when cfg.autopilot.nightly_quality_probe.enabled === true (default OFF — opt-in to protect API spend). NO scheduler-side rate-limit check — runNightlyQualityProbe's internal shouldRunNightly (reading the audit JSONL) is the single source of truth. Probe call wrapped in try/catch that logs via logError and does NOT bump consecutiveErrors (probe failure is informational, never crashes the loop). Default max_usd cap = 5. Pinned by test/autopilot-nightly-probe-wiring.test.ts. per-source extract_atoms auto-drain. Postgres-only block after the freshness fan-out: gated on autopilot.auto_drain.enabled (default true) AND !packDeclaresPhase(engine,'extract_atoms') (the silent-backlog condition) AND per-source countExtractAtomsBacklog > threshold (default 25) AND a daily cap floor(max_usd_per_day / ~$0.30). Enumerates loadAllSources. Submits the PROTECTED extract-atoms-drain job ({allowProtectedSubmit:true}) with a UTC-day time-sloted idempotency key autopilot-extract-atoms-drain:<src.id>:<utcDay> (a static key would block the source after the first job completed). src/core/minions/protected-names.ts adds extract-atoms-drain; src/commands/jobs.ts registers the handler (thin wrapper over runExtractAtomsDrainForSource, LockUnavailableError → {deferred:true}); src/core/config.ts adds the autopilot.auto_drain.* config keys + the autopilot. key prefix. Pinned by test/extract-atoms-drain-handler.test.ts, test/autopilot-auto-drain-wiring.test.ts. federated-brain co-existence + launchd hygiene. (1) LOCK_PATH resolves via gbrainPath('autopilot.lock') so it honors GBRAIN_HOME (two brains can run autopilot simultaneously without lock-stealing); lock file stores PID, startup checks kill -0 <pid> before refusing to start (stale lock from a crashed process no longer blocks). (2) exported classifyReconnectError(err) returns 'recoverable' | 'unrecoverable'; unrecoverable causes process.exit(0) so launchd backs off instead of looping config.database_url undefined. (3) exported pure generateLaunchdPlist(wrapperPath, home) sets ThrottleInterval=300 so launchd respects the exit-0 backoff. Pinned by test/autopilot-lock-path.test.ts + test/autopilot-reconnect-classifier.test.ts. targeted-submit loop instead of blanket autopilot-cycle dispatch. Each tick: cheap engine.getHealth() (single SQL count) + computeRecommendations(), then route by shape — score >= 95 AND no plan AND <60min since last full → sleep; score >= 95 AND >=60min → submit autopilot-cycle (60-min floor exercises phase-coupling invariants on healthy brains); plan <= 3 steps AND est <5min → submit individual handlers; plan large OR score < 70 → submit full autopilot-cycle. The gbrain-cycle lock ensures targeted submissions and the full cycle can't run concurrently. maxWaiting: 1 per submit closes the queue-fan-out vector.

• src/mcp/server.ts — MCP stdio server (generated from operations). Tool-call handler delegates to dispatchToolCall from src/mcp/dispatch.ts so stdio + HTTP transports share one validation, context-build, and error-format path. Stdin 'end' / 'close' shutdown hooks are skipped when process.env.MCP_STDIO === '1' — gateway-piped stdio MCP wrappers (OpenClaw's bundle-mcp) pipe the handshake then close their stdin half, which would otherwise kill the server before the first tool call; signal handlers (SIGTERM/SIGINT/SIGHUP) + the parent-process watchdog still cover legitimate disconnects. src/commands/serve.ts exposes ServeOptions.mcpStdio?: boolean as a test seam so the guard is exercisable without process.env mutation. Pinned by test/serve-stdio-lifecycle.test.ts.

• src/mcp/dispatch.ts — shared tool-call dispatch consumed by both stdio (server.ts) and HTTP transports. Exports dispatchToolCall(engine, name, params, opts), buildOperationContext(engine, params, opts), and re-exports normalizeOptionalParams/validateParams from src/mcp/validate-params.ts (the extracted validation module — call order normalize → validate → findUnknownParams is load-bearing). Single source of truth for (ctx, params) handler arg order and the OperationContext shape. Defaults remote: true (untrusted); local CLI callers pass remote: false. Deny layers, in order: opts.allowedOps surface enforcement (hidden op → unknownToolEnvelope, byte-identical to a nonexistent op; did-you-mean candidates drawn ONLY from the caller's visible surface minus localOnly minus gated names), unknown op, the localOnly transport backstop (op.localOnly && transport !== 'stdio' → same envelope; stdio IS the local surface, D7), param validation, strict/warn unknown-arg handling (reject mode returns invalid_params with suggestions; warn mode attaches _meta.warnings + a model-visible notice block), then enforceBoundClientOpAllowList (the bound-client fence) inside the handler try. _meta assembly per docs/protocol/MCP_META_CHANNELS.md: handler-emitted keys via ctx.emitResponseMeta (retrieval, warnings) attach first and independently of the metaHook (brain_hot_memory), each producer isolated so one failure never drops another's key; empty retrieval results get a SECOND model-visible content block via buildEmptyRetrievalBlock (D8). Exports isListLevelDenialEnvelope(parsed) — the honest-catalog metric classifier (amendment 33/D10): true for op-level denials the tools/list filter should have prevented (detail: 'config_key=...' publish-gate backstop, detail: 'fence=op' fence op-level deny), false for argument-level denials; serve-http logs matches as status='denied_after_list'. Exports requestLogStatusForResult(result) — the ONE request-log status decision (success / success_with_warnings / denied_after_list / error); BOTH HTTP transports (serve-http.ts and the legacy-bearer http-transport.ts) route every tools/call row through it so the amendment-33 honest-catalog metric sees all HTTP traffic (pinned by test/denied-after-list.test.ts + test/http-transport.test.ts). Also exports summarizeMcpParams(opName, params) — privacy-preserving redactor for mcp_request_log and the admin SSE feed, returns {redacted, kind, declared_keys, unknown_key_count, approx_bytes}. Intersects submitted top-level keys against the operation's declared params allow-list (declared keys preserved sorted; unknown keys counted but never named, closing the attacker-controlled-key-name leak). Byte counts bucketed up to nearest 1KB so an attacker can't binary-search secret-content sizes by probing. Raw payload visibility is opt-in via gbrain serve --http --log-full-params (loud stderr warning). New logging paths route through this helper, not JSON.stringify(params).

• src/mcp/validate-params.ts — param normalization + validation extracted from dispatch (WP3, direct unit surface). validateParams (required/type/enum — enum membership is a TYPE error in BOTH strict modes; the caller's raw value is never echoed into the message), normalizeOptionalParams (null/'' optional-param idioms become truly absent, copy-on-write), findUnknownParams (unknown top-level keys on the NORMALIZED object; UNKNOWN_PARAM_ALLOWLIST = _meta + dry_run; per-op did-you-mean from the op's OWN declared params only), buildUnknownParamWarnBlock (the model-visible warn notice), resolveStrictParamsMode(engine, config) (dual-plane mcp.strict_params, DB > file > 'warn'; a failed DB read applies the LAST successfully read DB mode, held per process — fail-closed, so a transient config outage on a reject-mode server cannot re-open the warn grace period; test seam resetStrictParamsModeCache()). Privacy: raw unknown key names reach the CALLER only, never mcp_request_log. Pinned by test/validate-params.test.ts.

• src/mcp/publish-gates.ts — publish-gate resolution for the honest tools/list (WP1). readPublishGate(engine, config, key): dual-plane (DB > file > false), never throws — a FAILED read resolves false (hide-on-doubt matches the default-off consent posture). disabledOpsForPublishGates(engine, config): the op-name set tools/list subtracts; one getConfig read per distinct gate key per call, deliberately NOT memoized so gbrain config set mcp.publish_skills true takes effect on the next list without a restart. Call-time gates inside the handlers stay as the fail-closed backstop (their denials carry detail: 'config_key=<key>' — the machine-readable denial grammar). Pinned by test/publish-gates.test.ts.

• src/mcp/tool-catalog.ts — renderToolCatalogMarkdown(): the docs/TOOL_CATALOG.md renderer (E6). Config-independent + deterministic (no engine/config reads, no timestamps): non-localOnly ops grouped one section per Operation.area, per-op first-sentence description (from buildToolDefs's non-strict shape), scope, STARTER_OPS membership, publish-gate key. Generated by scripts/generate-tool-catalog.ts; freshness-guarded by scripts/check-tool-catalog-fresh.sh in bun run verify (the METRIC_GLOSSARY pattern). Pinned by test/tool-catalog.test.ts.

• src/core/surface-audit.ts — writeSurfaceChangeAudit(engine, audit): the surface-mutation audit trail (amendment 32/ENG-8). Every surface mutation (rescope CLI, POST /admin/api/rescope-client, request_tools persist) writes one typed mcp_request_log row — operation='surface_change', params a RAW object {actor, client_id, old, new, via} via executeRawJsonb (never JSON.stringify into ::jsonb). Zero new DDL; rides idx_mcp_log_time_agent + the retention TODO. Best-effort: a failed audit write warns to stderr, never fails the committed mutation (callers needing fail-closed semantics inspect the returned boolean). CLI-actor rows are written even though stdio ops don't otherwise log (documented exception — audit outranks the transport-logging convention). The usage reader excludes these rows from op-call stats.

• src/core/mcp-usage.ts — readClientOpUsage(engine, {days}): the ONE shared reader over mcp_request_log (amendment 30), consumed by gbrain auth clients --usage (E4), the advisor mcp-client-fit collector (E3), and scripts/derive-starter-ops.ts. Encodes the row-hygiene rules once (normalizeLoggedOperation): JSON-RPC method rows (tools/list, initialize, …) and surface_change audit rows drop; the legacy tools/call:<name> prefix strips to the op name, and the hygiene check re-runs on the stripped name (tools/call:tools/list is still not an op call). Only status IN ('success','success_with_warnings') rows count as usage — denied or erroring traffic cannot "use" its way into starter derivation or advisor fit findings. Windows on created_at (rides idx_mcp_log_time_agent); plain SQL through engine.executeRaw, both engines. D12 behavioral automation classification: likely_automation = >90% of calls are context_pack/delta boundary verbs (the hook lane is stdio and never logs, so there is no name convention to key on). Sees HTTP clients ONLY — stdio never writes the log. Pinned by test/mcp-usage.test.ts.

• docs/protocol/MCP_META_CHANNELS.md — normative _meta conventions for MCP tool responses: one producer per top-level key, additive-forever within a key, producer isolation, and the registered-keys table (brain_hot_memory, retrieval, warnings). Anything the model must SEE rides a content block (mainstream harnesses don't feed _meta to the model); _meta serves structured consumers. Add a key by registering it in the table — one producer, additive-forever.

• src/mcp/rate-limit.ts — Bounded-LRU token-bucket limiter. buildDefaultLimiters() returns the two-bucket pipeline: pre-auth IP (30/60s, fires BEFORE the DB lookup so brute-force load against access_tokens is capped) + post-auth token-id (60/60s). Tracks lastTouchedMs separately from lastRefillMs so an exhausted key can't be reset by hammering past the TTL. LRU cap bounds memory under attacker-controlled key growth. refund(key) returns one consumed token (capped at the limit) — the request_tools persist path refunds when a race-lost 0-row UPDATE (concurrent operator pin) means no write actually happened; dry-run previews never draw a token at all (the limiter meters actual writes only).

• src/commands/serve-http.ts — Express 5 HTTP MCP server with OAuth 2.1, admin dashboard, and SSE live activity feed. Started via gbrain serve --http [--port N] [--token-ttl N] [--enable-dcr] [--public-url URL] [--bind HOST] [--log-full-params]. Combines MCP SDK's mcpAuthRouter (authorize/token/register/revoke), a custom client_credentials handler running BEFORE the router (SDK's token endpoint throws UnsupportedGrantTypeError for CC; custom handler falls through for auth_code / refresh_token), requireBearerAuth middleware for /mcp with scope enforcement + localOnly rejection before op dispatch, and express-rate-limit at 50 req / 15 min on /token. Serves the built admin SPA from admin/dist/ with SPA fallback. /admin/events SSE broadcasts every MCP request. cookie-parser wired (Express 5 has no built-in). Startup logging prints port, engine, issuer URL (honors --public-url), client count, DCR status, and the admin bootstrap token line — but the generated token's raw value only prints when stderr is an interactive TTY (shouldSuppressBootstrapPrint): a non-TTY (containerized/piped) start hides it so the secret never lands in centralized log storage, env-sourced tokens ($GBRAIN_ADMIN_BOOTSTRAP_TOKEN) are always hidden, --print-admin-token forces the raw value on a trusted terminal, and --suppress-bootstrap-token hides everything. The /mcp request handler's OperationContext literal sets remote: true explicitly (without it submit_job's protected-name guard at operations.ts:1391 saw a falsy undefined and a read+write-scoped OAuth token could submit shell jobs — RCE). summarizeMcpParams from src/mcp/dispatch.ts feeds both mcp_request_log writes and the SSE feed by default (raw via --log-full-params). Cookie Secure flag set behind HTTPS or a public-URL proxy; magic-link nonce store LRU-bounded; DCR disable routes through the GBrainOAuthProvider dcrDisabled constructor option (not a router monkey-patch); transport.handleRequest wrapped in try/catch to return a JSON-RPC 500 envelope; OperationError + unexpected exceptions unified through buildError / serializeError so /mcp always returns the same envelope. /health is liveness-only via probeLiveness(sql, engineName, version, timeoutMs) racing sql\SELECT 1`against the exportedHEALTH_TIMEOUT_MS = 3000(returns the sameProbeHealthResulttagged-union asprobeHealth, single timer-cleanup site, single 503 envelope); body shape {status, version, engine}only. Full stats moved to admin-only/admin/api/full-stats(gated byrequireAdmin, calls probeHealth(engine, ...)) — keeps getStats()'s 6× count(*) off the public route so a saturated pool doesn't trigger orchestrator restart cascades. Every OAuth/admin/audit SQL call routes through sqlQueryForEngine(engine)fromsrc/core/sql-query.tsso it works against PGLite; the fourmcp_request_log.paramsINSERT sites (success / auth_failed / scope_denied / server-error) go throughexecuteRawJsonb(engine, ...) so the column stores real objects (params->>'op'returnssearch, not the quoted string). --bind HOSTdefaults127.0.0.1(self-hosters pass--bind 0.0.0.0); a stderr WARN fires when --public-urlis set without--bind; the banner prints a Bind:line.AuthInfo.sourceId+AuthInfo.allowedSources+AuthInfo.takesHoldersAllowListare the typed source of truth, populated byoauth-provider.ts:verifyAccessToken(source scope from theoauth_clientsrow; takes-holders fromaccess_tokens.permissions.takes_holdersfor legacy bearer tokens). The/mcpdispatch site readsauthInfo.takesHoldersAllowList ?? ['world']— absent grants (OAuth-client tokens, pre-v29 brains) fail closed to world-only takes visibility, while an explicit[]grant is preserved as deny-all; pinned end-to-end bytest/e2e/serve-http-takes-holders.test.ts. The HTTP MCP tools/listhandler at:837-849usesparamDefToSchema(v)fromsrc/mcp/tool-defs.tsso array params keepitems(strict-mode OAuth clients otherwise reject the whole tool list).POST /ingestenforces the slug-prefix write fence at the ROUTE, not the op layer: the route hands its payload to theingest_captureminion handler, which deliberately bypassesput_page, so no OperationContextexists andenforceClientSlugFencenever runs — a slug-bound client must therefore supplyX-Gbrain-Slugand it must satisfyslugUnderBoundPrefixes, else 403 (without the check a bound client could overwrite any page, in the defaultsource, since untrusted payloads carry no source grant). confidential revoke: a pre-router/revokehandler validates the RFC 7009 body, verifies hash-only secrets for bothclient_secret_postandclient_secret_basic, rejects mixed authentication, preserves the SDK path for public clients, and separates opaque client-auth failures from retryable/backend failures. OAuth metadata advertises both confidential methods. Pinned by test/e2e/serve-http-oauth.test.ts. three admin routes: /admin/api/calibration/profile, /admin/api/calibration/charts/:type(image/svg+xml; type in {brier-trend, domain-bars, pattern-statements, abandoned-threads}),/admin/api/calibration/pattern/:id(drill-down). The manual mint route/admin/api/register-clientaccepts optionalsource+federatedReadbindings mirroring the CLI's--source/--federated-read(validated vianormalizeSourceInput/normalizeFederatedReadInputfromsrc/core/source-id.ts; omitting both preserves the default binding source_id='default'/federated_read=[source_id], invalid values return a structured 400 invalid_source), so an admin SPA or provisioning proxy can mint a source-confined client over HTTP. The route mirrors the CLI lane end to end: structured 400s for unknown_source/archived_source(one batchedANY($1::text[])existence check),invalid_token_ttl(sharedTOKEN_TTL_MIN/MAX_SECONDSbounds, integer-validated BEFORE the tx), andbrain_too_old (column pre-flight OUTSIDE the tx — a pre-scoped-clients brain refuses up front instead of aborting mid-transaction); the duplicate-name pre-check + INSERT run in ONE transaction under the SAME name-scoped advisory lock the CLI takes (registerClientNameLockKey), returning 409 duplicate_namewith the existingclient_id; the INSERT composes registerScopedClient(the CLI's registration core) so the two paths cannot drift; any post-commit failure includes the createdclient_idso the operator can revoke (never a false "nothing was created"). Pinned bytest/register-client-source-normalize.test.ts. The /mcptools/list is the WP1 honest catalog: per-request filters (token scope incl. the FOV-4agentCallablecarve-out, bound-client fence viaopAllowedForBoundClient, publish gates via disabledOpsForPublishGates) over the surface-filtered op set, schemas via buildToolDefs(strict emission whenmcp.strict_paramsresolves reject); the tools/listmcp_request_logrow records the listed size asparams.tool_count (amendment 23 stopgap). Call-time op-level denials the list should have prevented — the inline scope deny, publish-gate backstop (config_key=...), fence op-level deny (fence=op, classified via isListLevelDenialEnvelope) — log status='denied_after_list'instead of'error'(amendment 33/D10; the trend-to-zero honest-catalog metric, see docs/operations/mcp-surface-runbook.md) — every tools/call row's status resolves throughrequestLogStatusForResult(dispatch.ts) on BOTH transports. The admin health-indicators error rate countsstatus NOT IN ('success','success_with_warnings')and excludesoperation='surface_change'audit rows from numerator AND denominator (audit rows record operator/self actions, not traffic). Per-request surface resolution lives inresolveEffectiveSurface: a verbs` ceiling skips the default-surface config read, and a failed read applies the last successfully read default per process (fail-closed — a transient config outage cannot widen a NULL-surface client).

• src/core/sql-query.ts — engine-aware tagged-template SQL adapter for OAuth/admin/auth infrastructure. sqlQueryForEngine(engine) returns a SqlQuery ((strings, ...values) => Promise<rows[]>) that walks the template, builds $N positional SQL, asserts every value is a SqlValue (string | number | bigint | boolean | Date | null), and routes through engine.executeRaw(sql, params) (Postgres via postgres.js unsafe(sql, params), PGLite via db.query(sql, params)). Deliberately narrower than postgres.js's sql tag: no nested fragments, sql.json(), sql.unsafe(), sql.begin(), or array binding — the narrow scalar-only surface is the feature (keeps it from drifting into a partial postgres.js clone). JSONB writes go through executeRawJsonb(engine, sql, scalarParams, jsonbParams) which composes positional $N::jsonb casts and passes JS objects through; an object reaches the wire with the correct type oid, so executeRawJsonb is safe (verified by test/sql-query.test.ts on PGLite, test/e2e/auth-permissions.test.ts:67 on Postgres). Positional binding is NOT universally immune, though: binding a JSON.stringify(x) string to a bare $N::jsonb via unsafe() double-encodes it into a jsonb string scalar on real Postgres (the #2339 class; PGLite hides it). Fixes: pass a raw object (executeRawJsonb / sql.json), or cast through $N::text::jsonb. scripts/check-jsonb-pattern.sh (template grep) doesn't fire on executeRawJsonb(...) because it passes objects; the positional $N::jsonb + JSON.stringify form is caught by scripts/check-jsonb-params.mjs. Consumed by src/commands/auth.ts, src/commands/serve-http.ts, src/core/oauth-provider.ts, src/commands/files.ts, src/mcp/http-transport.ts so all five work uniformly against PGLite and Postgres.

• src/commands/serve.ts — gbrain serve stdio MCP entrypoint with idempotent shutdown across every parent-disconnect signal. Stdio EOF, SIGTERM, SIGINT, SIGHUP, and parent-process death (every reparent case — PID 1, launchd subreaper, systemd, tmux, or a parent shell with PR_SET_CHILD_SUBREAPER) all funnel into one cleanup(reason) that releases the engine and the PGLite write-lock dir within 5 seconds (otherwise the lock is held indefinitely after Claude Desktop / Cursor / launchd-managed gateways disconnect, forcing a 5-minute stale-lock wait on next start). Watchdog reparent check is getParentPid() !== initialParentPid (the === 1 check missed the subreaper case under launchd/systemd). Bun's process.ppid cache is stale across reparenting (oven-sh/bun#30305) so getParentPid() runs spawnSync('ps', ['-o', 'ppid=', '-p', PID]) per tick. Startup probe verifies ps is on PATH; if not (stripped containers, busybox), the watchdog skips installing AND emits a loud [gbrain serve] watchdog disabled: ps unavailable ... stderr line so operators see the degraded mode. Pinned by test/serve-stdio-lifecycle.test.ts (22 cases). Credit @Aragorn2046 + @seungsu-kr.

• src/core/oauth-provider.ts — GBrainOAuthProvider implementing the MCP SDK's OAuthServerProvider + OAuthRegisteredClientsStore. Backed by raw SQL (works on both PGLite and Postgres — OAuth is infrastructure, not a BrainEngine concern). Full OAuth 2.1: authorize + exchangeAuthorizationCode with PKCE, client_credentials, refresh_token with rotation, revokeToken, registerClient (DCR validates redirect_uri is https:// or loopback per RFC 6749 §3.1.2.1). All tokens + client secrets SHA-256 hashed before storage. Auth codes single-use with 10-minute TTL via atomic DELETE...RETURNING (closes RFC 6749 §10.5 TOCTOU); refresh rotation also DELETE...RETURNING (§10.4 stolen-token detection). pgArray() escapes commas/quotes/braces so a comma-bearing redirect_uri can't smuggle a second array element. Legacy access_tokens fallback in verifyAccessToken honors the original-schema scopes TEXT[] column via normalizeTokenScopes (NULL = grandfathered read+write+admin, so every pre-scopes token is byte-identical; an array is filtered to known scopes and honored as-is, []/all-unknown preserved as deny — a dedicated column is structurally immune to the permissions-object-replacement wipe class), and threads BOTH stored grants off the token's permissions JSONB: source_id via parseLegacyTokenScope and takes_holders via parseTakesHoldersAllowList (both in src/core/legacy-token-scope.ts, shared with the legacy HTTP transport so the two transports cannot drift; [] takes-holders preserved as explicit deny-all, missing/non-array → undefined → the /mcp dispatch site's fail-closed ['world']; OAuth-client tokens carry no takes-holders grant pending per-client storage — TODOS.md). sweepExpiredTokens() runs on startup in try/catch and returns the count via RETURNING 1 + array length. RFC hardening: client_id folded atomically into the DELETE WHERE for both auth-code exchange and refresh rotation (wrong-client paths don't burn the row); refresh-scope-subset enforced against the original grant on the row (RFC 6749 §6, so revoking a scope shrinks existing refresh tokens); client_id bound on revokeToken (RFC 7009 §2.1); /token redirect_uri validated against the /authorize value (RFC 6749 §4.1.3, empty-string treated as missing not wildcard); bare catch {} in verifyAccessToken/getClient replaced by isUndefinedColumnError from src/core/utils.ts (only SQLSTATE 42703 falls through to legacy; lock timeouts/network blips throw); dcrDisabled constructor option lets serve-http.ts disable /register without monkey-patching the router. Module-private coerceTimestamp() normalizes postgres-driver-as-string BIGINT columns to JS numbers at 5 read sites (getClient for RFC 7591 §3.2.1 numeric timestamps, exchangeRefreshToken + verifyAccessToken for the SDK's typeof === 'number' check); throws on NaN/Infinity (fail loud at boundary), returns undefined for SQL NULL (callers treat NULL as expired). Not promoted to utils.ts — generic BIGINT precision-loss risk. registerClient honors token_endpoint_auth_method: "none" (RFC 7591 §3.2.1): public PKCE clients store client_secret_hash = NULL and the response omits client_secret; confidential clients (client_secret_post / client_secret_basic) keep their one-time-reveal shape; getClient normalizes NULL client_secret_hash to JS undefined so the SDK's clientAuth path accepts public clients. verifyAccessToken JOINs oauth_clients.source_id (write scope, scalar) + oauth_clients.federated_read (read scope, TEXT[]) + oauth_clients.bound_slug_prefixes (write fence, TEXT[] — consumed by enforceClientSlugFence in operations.ts) onto the returned AuthInfo; legacy brains degrade via isUndefinedColumnError fallback, dropping the newest projection first. rescopeClient(clientId, {sourceId?, federatedRead?, boundSlugPrefixes?}) is the trusted-operator rescope (CLI gbrain auth rescope-client, admin POST /admin/api/rescope-client); boundSlugPrefixes is tri-state — undefined leaves the binding untouched, null clears it, a non-empty array replaces it (explicit empty array rejected as ambiguous deny-all) — so roster churn updates the write fence in place without rotating secrets. with src/commands/serve-http.ts: custom /token middleware that runs BEFORE the MCP SDK's clientAuth. The SDK does plaintext compare against the request's client_secret; gbrain stores SHA-256 hashes only, so every confidential-client /token request would fail. The middleware detects confidential auth via Authorization: Basic header OR client_secret_post form body (both shapes per RFC 6749 §2.3.1), verifies via verifyClient(client_id, presented_secret) (SHA-256 hash compare), and falls through to the SDK for public PKCE clients (which the SDK's clientAuth still accepts via NULL-client_secret_hash normalization). Pinned by test/oauth-confidential-client.test.ts (both client_secret_basic and client_secret_post).

• admin/ — React 19 + Vite + TypeScript admin SPA embedded in the binary via admin/dist/ served by serve-http.ts. 7 screens: Login (bootstrap token → session cookie), Dashboard (metrics + SSE feed + token health), Agents (sortable table + sparklines + Register), Register (modal with scope checkboxes + grant type selector), Credentials reveal (Copy + Download JSON + one-time-only warning), Request Log (filterable paginated), Agent Detail drawer (Details / Activity / Config Export tabs + Revoke). Design tokens: #0a0a0f bg, Inter for UI, JetBrains Mono for data, 4-32px spacing scale, rounded pill badges. HTTP-only SameSite=Strict cookie auth. 65KB gzip. Build: cd admin && bun install && bun run build; output at admin/dist/ is committed for self-contained binaries.

• src/commands/auth.ts — token management. gbrain auth create/list/revoke/test for legacy bearer tokens (create --scopes read,write narrows a token via the scopes TEXT[] column with mint-time validation — a typo'd scope refuses loudly, never silently denies or widens; list shows id + scopes columns with grandfathered rows rendered honestly; revoke --id <uuid> revokes exactly one row since names are not unique, and bulk revoke-by-name says when it hit several; permissions set-takes-holders MERGES into the permissions JSONB via COALESCE(permissions,'{}'::jsonb) || $2::jsonb — a whole-object replace would silently wipe the source_id federation grant), plus gbrain auth register-client and gbrain auth revoke-client <client_id> for OAuth 2.1 client lifecycle. revoke-client runs an atomic DELETE...RETURNING on oauth_clients; FK ON DELETE CASCADE on oauth_tokens.client_id and oauth_codes.client_id purges every active token + auth code in one transaction; process.exit(1) on no-such-client (idempotent). Legacy tokens stored as SHA-256 hashes in access_tokens; OAuth clients in oauth_clients; legacy tokens with no scopes grant grandfather to read+write+admin on the OAuth HTTP server (no migration); scoped tokens are honored at exactly their grant. Every SQL site routes through sqlQueryForEngine(engine) from src/core/sql-query.ts (and executeRawJsonb for the takes-holders permissions JSONB column) so gbrain auth works against PGLite; the takes-holders write goes through executeRawJsonb(engine, sql, [name, hash], [{takes_holders:[...]}]) which round-trips with jsonb_typeof = 'object'. register-client accepts --source <id> (write authority, scalar), --federated-read <S1,S2,...> (read scope, array), and --token-ttl <seconds> (per-client access-token TTL persisted to oauth_clients.token_ttl, bounds TOKEN_TTL_MIN_SECONDS=60 to TOKEN_TTL_MAX_SECONDS=7,776,000/90d) and prints the resolved Write source + Federated reads; pre-v0.34 clients backfill to source_id='default' via migration v60. The registration core is the exported registerScopedClient(sql, engine, name, parsed, opts) — exit-free, print-free, injected-handle (engine-bound callers like agent register pass the dispatcher's engine; a second withConfiguredSql engine self-deadlocks PGLite's single-writer lock), returns a RegisteredClient data object and throws on failure; the thin CLI wrapper owns exit/print. Its printer formatRegisterClientOutput is a BYTE-PINNED contract (connect.ts's defaultRegisterOAuthClient regex-scrapes Client ID:/Client Secret: from it in production) — pinned by test/auth-register-client-output-pin.test.ts. preflightOauthClientColumns(sql) probes information_schema.columns for the optional columns (token_ttl, surface, federated_read, source_id, deleted_at) so statement shapes are decided BEFORE any transaction — Postgres/PGLite abort the whole tx on any statement error (25P02) and SqlQuery has no savepoint seam, so "catch 42703 and continue" inside a tx is impossible; skipped optional writes surface as RegisteredClient.skipped with an apply-migrations hint. gbrain auth clients [--usage] [--days N] [--json] lists clients with scopes, per-client surface, write source (source_id), and federated reads (federated_read) — one projection-widened SELECT with a degrade ladder for pre-migration brains (drops the newest columns first, never errors); --usage joins per-client op-call counts via src/core/mcp-usage.ts. The bare gbrain auth create <name> form (no --takes-holders) mints a token via the exported pure parseAuthCreateArgs(rest) (the inline version used rest[takesIdx + 1] resolving to rest[0] when takesIdx === -1, excluding the name from the positional search). Pinned by test/auth-create-args.test.ts + test/auth-register-client-args.test.ts.

• src/core/mcp-client.ts — the thin-client transport (trust boundary). callRemoteTool(config, toolName, args, opts) with CallRemoteToolOptions {timeoutMs, signal}; buildAbortController composes an external signal with the timeout. All transport errors normalize to RemoteMcpError via the toRemoteMcpError funnel: stable RemoteMcpErrorReason union, RemoteMcpErrorDetail.kind ('timeout' | 'aborted' | 'unreachable') sub-tag, RemoteMcpErrorDetail.code carrying server-supplied error codes (e.g. missing_scope). extractToolErrorCode parses JSON error envelopes first, falls back to substring detection for legacy server messages. unpackToolResult<T>(res) parses tool-call JSON content. _clearMcpClientTokenCache() test escape. The CLI routing seam that consumes this lives in src/cli.ts (runThinClientRouted); see docs/architecture/thin-client.md.

• src/commands/connect.ts + src/core/connect-probe.ts — gbrain connect <mcp-url> [--token <bearer>] one-command coding-agent onboarding from a bearer token. Turns an MCP URL + token into a paste-ready claude mcp add ... -H "Authorization: Bearer ..." block (default) or, with --install, runs it directly and smoke-tests the token. Direct HTTP MCP — Claude Code talks straight to a remote gbrain serve --http, no local install needed. Token resolution: --token > $GBRAIN_REMOTE_TOKEN > placeholder (print) / error (install). The generated block tells the agent to call get_brain_identity + list_skills (the LEARN_INSTRUCTION export, which now names capture — a starter-surface MCP op — alongside put_page for full-control writes) with a core-tools fallback for hosts without skill publishing. URL normalization appends /mcp to a bare host but REJECTS a scheme-less host; the pure registration helpers (normalizeMcpUrl, isLinkLocalOrMetadata, buildClaudeMcpAddArgv with its optional scope param — claude's default is local, so the harness lane passes user explicitly — buildCodexMcpAddArgv, validateToken, redactToken, shellQuote/cmdString, issuerFromMcpUrl, the OAUTH_SECRET_NOTE secret-hygiene constant, and openclawThinClientBlock — the honest openclaw wiring print: a scoped gbrain init --mcp-only thin-client block, deliberately NOT a stdio mcpServers config since that grants full local DB access) live in src/core/mcp-registration.ts (core must not import from commands; connect.ts re-exports them — OAUTH_SECRET_NOTE included — so its surface and tests are unchanged) and are unit-tested. Flags: --token, --name <id> (default gbrain, validated against NAME_RE), --agent claude-code|codex|opencode|perplexity|generic, --install, --yes (required for --install in non-TTY), --force, --json (token redacted unless --show-token), --timeout-ms. connect is in CLI_ONLY + CLI_ONLY_SELF_HELP; dispatched in cli.ts:handleCliOnly with no local DB connect. AGENT_SPECS drives per-agent rendering + --install: claude-code → buildClaudeMcpAddArgv (literal -H "Authorization: Bearer <tok>"); codex → buildCodexMcpAddArgv = codex mcp add <name> --url <url> --bearer-token-env-var GBRAIN_REMOTE_TOKEN (on the CONNECT lane Codex reads the token from the env var at runtime, never written to config — the harness lane in src/core/bootstrap/harness.ts is the deliberate exception, writing an inline bearer_token managed block because framework-spawned codex inherits no shell profile; --install runs it and prints an export GBRAIN_REMOTE_TOKEN hint when missing); opencode → buildOpencodeMcpAddArgv = opencode mcp add <name> --url <url> --header "Authorization=Bearer {env:GBRAIN_REMOTE_TOKEN}" (the interpolation is stored LITERALLY and resolved by opencode at read time — token never in argv/config/--json; --install writes the entry directly through ConnectDeps.writeOpencodeRemoteEntry → opencode-json.ts in env token mode, no binary required; --force maps to the writer's allowReplaceOtherSource so an OURS entry at an old url — a rotated serve — is replaceable, mirroring the exec lanes' --force semantics, while foreign same-name entries still refuse with url-appropriate copy: pick --name); perplexity + generic are installable:false and reject --install. --oauth (supportsOAuth:true = perplexity/generic only) emits an OAuth 2.1 client-credentials connector block (Issuer URL via issuerFromMcpUrl = mcp-url minus /mcp, Client ID, Client Secret) — least-privilege scopes + short-lived rotating tokens vs a long-lived full-access secret. Creds from --client-id/--client-secret (BYO) or --register (deps.registerOAuthClient shells gbrain auth register-client <name> --grant-types client_credentials --scopes <DEFAULT_SCOPES="read write"> --token-endpoint-auth-method client_secret_post and parses Client ID:/Client Secret:); --oauth rejected for claude-code/codex and incompatible with --install. buildJson is a generic shape (agent, command/command_argv null for perplexity/generic, header, env_var, oauth fields with redaction); the codex command carries only the env-var name, never the token. cmdString(binary, argv) POSIX-single-quotes args. ConnectDeps = {isTTY, promptYesNo, hasBinary(bin), runBinary(bin, argv), probe, env(name), registerOAuthClient, writeOpencodeRemoteEntry} — binary-generic so claude and codex share the exec path while opencode rides the writer member; env injectable for tests. Security: rendered command single-quotes the token so shell metacharacters can't run code when pasted; token validated before it lands in an HTTP header; link-local / cloud-metadata addresses (incl. IPv4-mapped IPv6 ::ffff:169.254.x.x and AWS IMDSv2-over-IPv6 fd00:ec2::254) refused as a token-exfil guard while localhost/RFC1918/LAN stay allowed; token redacted from all error output. src/core/connect-probe.ts is the raw-bearer MCP smoke probe backing --install: connects the official MCP SDK Client over StreamableHTTPClientTransport with a STATIC Authorization header (no OAuth/discovery — distinct from mcp-client.ts:callRemoteTool which is OAuth-only and remote-mcp-probe.ts:smokeTestMcp which only sends initialize), runs the full initialize handshake via client.connect(), then calls get_brain_identity (read-scope, non-localOnly) to prove a tool call round-trips. Never throws — every failure maps to { ok: false, reason: 'auth' | 'unreachable' | 'timeout' | 'tool_error' | 'unknown', message } so a wrong/expired token fails at setup, not on the agent's first request. DEFAULT_PROBE_TIMEOUT_MS = 15_000 shared with connect.ts. serve-http.ts adds exported pure skillPublishStatus(publishSkills) for the startup banner Skills: published / not published line + a one-line gbrain config set mcp.publish_skills true stderr nudge when publishing is OFF. Docs: docs/mcp/CODEX.md, docs/mcp/PERPLEXITY.md, docs/mcp/CLAUDE_CODE.md, docs/tutorials/connect-coding-agent.md. Pinned by test/connect.test.ts (pure-helper + render, all five agents incl. the opencode writer-install lane) + test/e2e/connect-bearer.test.ts (raw-bearer probe + full OAuth chain register→connect→discovery→/token mint→get_brain_identity, client registered in beforeAll before serve takes the PGLite single-writer lock; drives real claude + codex binaries through connect --install with sandboxed HOME/CODEX_HOME, asserts registration + token never in Codex config, skips when a binary is absent) + test/e2e/serve-stdio-roundtrip.test.ts (spawns real gbrain serve stdio against a fresh init --pglite brain, drives the SDK client through initialize→tools/list→tools/call, asserts the advertised core-tool set including capture, a starter-surface MCP op) + test/serve-skills-publish-nudge.test.ts (the test/audit/batch-retry-audit.test.ts ENOENT case was made hermetic — it had read the real ~/.gbrain/audit).

• src/commands/upgrade.ts — self-update CLI. runPostUpgrade() enumerates migrations from the TS registry (src/commands/migrations/index.ts) and tail-calls runApplyMigrations(['--yes', '--non-interactive']) so the mechanical side of every outstanding migration runs unconditionally.

• src/commands/migrations/ — TS migration registry (compiled into the binary; no runtime walk of skills/migrations/*.md). index.ts lists migrations in semver order. v0_11_0.ts = Minions adoption orchestrator (8 phases). v0_12_0.ts = Knowledge Graph auto-wire orchestrator (5 phases: schema → config check → backfill links → backfill timeline → verify); phaseASchema has a 600s timeout for duplicate-heavy brains. v0_12_2.ts = JSONB double-encode repair orchestrator (4 phases: schema → repair-jsonb → verify → record). v0_14_0.ts = shell-jobs + autopilot cooperative (pending-host-work ping for skills/migrations/v0.14.0.md). All orchestrators are idempotent and resumable from partial status. The RUNNER owns all ledger writes — orchestrators return OrchestratorResult and apply-migrations.ts persists a canonical {version, status, phases} shape (orchestrators no longer call appendCompletedMigration). statusForVersion prefers complete over partial (never regresses); 3 consecutive partials → wedged → --force-retry <version> writes a 'retry' reset marker. Schema-only migrations v14 (pages_updated_at_index) + v15 (minion_jobs_max_stalled_default_5 with UPDATE backfill) live in the MIGRATIONS array in src/core/migrate.ts. in-process.ts exports runMigrateOnlyCore({timeoutMs?}) — single source of truth for "bring schema to head" (configureGateway → createEngine → connect → initSchema → disconnect, idempotent, 600s MIGRATE_ONLY_TIMEOUT_MS guard, throws MigrateOnlyError on no-config / timeout); the orchestrators' 9 schema phases AND init.ts:initMigrateOnly both delegate to it so schema bring-up can't drift (running in-process removes the spawn that died with getaddrinfo ENOTFOUND on Windows + bun + Supabase pooler). runGbrainSubprocess is the diagnostic wrapper for the remaining non-schema spawns (extract/repair/stats): captures child stderr (64MB buffer) into the thrown error. v0_13_1.ts:phaseCGrandfather is a CHUNKED bulk SQL pass keyed on pages.id (globally unique PK, NOT slug — slug uniqueness is (source_id, slug)), filters deleted_at IS NULL (no tombstones), chunked in CHUNK_SIZE batches (DELETE_BATCH_SIZE convention) for bounded lock-hold; the rollback log carries {id, slug, source_id, pre_frontmatter} so rollback is unambiguous across sources; idempotent + resumable (each UPDATE flips its rows out of GRANDFATHER_WHERE). Pinned by test/migration-in-process.serial.test.ts and test/migrations-v0_13_1-grandfather.test.ts.

• src/commands/migrations/v0_46_3.ts — ZeroEntropy sunset notice migration, detect-and-notify ONLY. Detects the HOST brain's exposure via src/core/ze-exposure.ts (read-only); when exposed — or when exposure is UNKNOWN, fail-safe — prints the ACTION REQUIRED banner and appends one idempotent entry to ~/.gbrain/migrations/pending-host-work.jsonl pointing the host agent at skills/migrations/v0.46.3.0.md. Performs NO config writes, NO pinning, and never invokes migrate embeddings (the migration costs money and needs a target key — that decision belongs to the user/agent via the playbook). UNKNOWN returns complete with an exposure_unknown detail rather than partial (three consecutive partials would wedge the whole migration chain behind --force-retry); the stage-2 upgrade banner and gbrain doctor carry the ongoing nag instead. Host-scoped (apply-migrations runs once per host with a global completed.jsonl); mounted/team brains are covered by the per-brain stage-2 banner (ze_sunset_notice_v2_shown in each brain's own DB config) + doctor gates.

• src/commands/repair-jsonb.ts — gbrain repair-jsonb [--dry-run] [--json]: rewrites jsonb_typeof='string' rows in place across 8 affected columns (pages.frontmatter, raw_data.data, ingest_log.pages_updated, files.metadata, page_versions.frontmatter, subagent_messages.content_blocks, subagent_tool_executions.input, subagent_tool_executions.output). The subagent targets are jsonPayloadOnly: those columns can legitimately hold jsonb string scalars (persistToolExec binds a tool's pre-serialized string payload as-is), so their damage predicate additionally requires container-shaped content (^\s*[\[{]) that pg_input_is_valid(..., 'jsonb') (PG16+ floor, same as the IS JSON predicate updateSourceConfig relies on) actually parses — a plain-text value that merely starts with [ or { is never flagged or corrupted. Targets whose table doesn't exist on the brain are skipped via to_regclass (pre-subagent-era brains), and one target's failure is recorded on stderr while the run continues — earlier repairs are already committed and the v0_12_2 migration orchestrator JSON-parses stdout. runDoctor's jsonb_integrity check counts damage with the same predicate over the same target list. Fixes the double-encode bug on Postgres; PGLite no-ops. Idempotent. Pinned by test/repair-jsonb.test.ts + test/doctor.test.ts.

• src/commands/orphans.ts — gbrain orphans [--json] [--count] [--include-pseudo] [--source <id>]: surfaces pages with zero inbound wikilinks, grouped by domain (auto-generated/raw/pseudo filtered by default). Also exposed as find_orphans MCP op. findOrphans/getOrphansData (the canonical pure fn shared with doctor's orphan_ratio) takes { sourceId?, sourceIds? }; BrainEngine.findOrphanPages(opts?) (both engines) scopes ONLY the candidate side (p.source_id = $1 scalar, or = ANY($1::text[]) federated) while still counting inbound links from ANY source — a page in source X linked FROM source Y is reachable, so NOT an orphan of X (deliberate definition; the stricter intra-source-only reading is rejected). --source is an explicit raw-flag parse (NOT resolveSourceWithTier, which would scope bare invocations to a default). The total_linkable denominator enumerates ALL live pages (scoped) and subtracts every excluded-by-slug page (templates/, scratch/, etc.) so excluded NON-orphan pages with inbound links don't inflate it and suppress warnings. The find_orphans MCP op threads sourceScopeOpts(ctx) so a source-bound OAuth client doesn't see brain-wide orphans. gbrain doctor --source <id> scopes orphan_ratio and, under explicit --source below 100 entity pages, reports the ratio with a low-scale caveat (thin-client doctor --source orphan_ratio remains brain-wide — TODO). Pinned by test/orphans-source-scope.test.ts (PGLite) + test/e2e/engine-parity.test.ts (Postgres↔PGLite scalar + federated parity). Contributed by @knee5.

• src/commands/salience.ts — gbrain salience [--days N] [--limit N] [--kind PREFIX] [--json]: pages ranked by emotional + activity salience over a recency window. Mirrors orphans.ts shape (pure data fn + JSON formatter + human formatter). Calls engine.getRecentSalience(opts). Score formula: (emotional_weight × 5) + ln(1 + active_take_count) + 1/(1 + days_since_update).

• src/commands/anomalies.ts — gbrain anomalies [--since YYYY-MM-DD] [--lookback-days N] [--sigma N] [--json]: cohort-level activity outliers. Calls engine.findAnomalies(opts). Two cohort kinds: tag, type.

• src/commands/whoknows.ts — gbrain whoknows <topic> [--explain] [--limit N] [--json]: expertise + relationship-proximity routing. Mirrors salience/anomalies shape (pure rankCandidates() + findExperts() orchestrator + runWhoknows() CLI dispatch + thin-client routing). MCP op = find_experts (scope: read, localOnly: false). Ranking formula: score = log(1 + raw_match) × max(0.1, exp(-days/180)) × (0.5 + 0.5 × salience) where raw_match is hybridSearch's RRF+source-boost score. Filters at SQL via SearchOpts.types: ['person', 'company'] (no post-filter waste); hybridSearch's internal salience+recency boosts are intentionally disabled so the locked formula applies on a clean signal. Floors prevent multiplicative-zero edge cases (cold-start people stay visible); ties break alphabetically by slug for determinism. 16 unit tests in test/whoknows.test.ts pin the math. with src/core/operations.ts:find_experts: T1.5 wiring sites. Pack-aware via expertTypesFromPack(pack.manifest) from best-effort.ts. Pack-load failure → EMPTY filter (NOT hardcoded ['person', 'company'] defaults). A researcher type declared --expert now surfaces in whoknows results.

• src/commands/eval-whoknows.ts — gbrain eval whoknows <fixture.jsonl> [--json] [--skip-replay]: two-layer eval gate. Layer 1 quality (hand-labeled fixture, top-3 hit rate ≥ 0.8). Layer 2 regression (eval_candidates replay set-Jaccard@3 ≥ 0.4). Sparseness fallback: < 20 replay-eligible rows → Layer 2 auto-skips with stderr warning. Stable JSON envelope with schema_version: 1; exit 0/1/2 for pass/fail/usage. WhoknowsFn callable abstraction makes the gates impl-agnostic; runEvalWhoknows(engine: BrainEngine | null, args) picks the impl at entry — thin-client mode (isThinClient(cfg)) routes per-query through callRemoteTool(cfg, 'find_experts', {topic, limit}), local mode calls findExperts(engine, ...) directly. cli.ts adds a thin-client bypass before connectEngine (dispatch shape under src/commands/eval.ts); the regression gate auto-skips in thin-client mode (no DB access to eval_candidates). Public exports jaccardAtK, topKHit, readFixture, WhoknowsFn, threshold constants pinned by test/eval-whoknows.test.ts (25 cases incl. null-engine signature contract).

• test/fixtures/whoknows-eval.jsonl — 10-row synthetic placeholder demonstrating the eval-fixture schema ({query, expected_top_3_slugs, notes?} JSONL). End users replace with their own real queries; placeholder uses obviously-example slugs (wiki/people/example-alice). Drives test/e2e/whoknows.test.ts (seeds a matching synthetic brain, asserts the >=80% gate) and the whoknows_health doctor check.

• src/core/skillopt/ + src/commands/skillopt.ts + skills/skill-optimizer/ — self-evolving skill optimization grounded in the SkillOpt paper (arXiv 2605.23904). gbrain skillopt <skill> treats SKILL.md as trainable parameters of a frozen agent: validation-gated (median-of-3 + epsilon=0.05), budget-capped (preflight estimator), per-skill DB-locked (tryAcquireDbLock('skillopt:<name>', 60min)), atomic-versioned (history-intent-first 5-step commit), body-only mutations (frontmatter forbidden). Rollouts use gateway.toolLoop directly with no-op persistence callbacks (zero subagent_messages pollution) + a read-only tool allowlist derived from BRAIN_TOOL_ALLOWLIST minus put_page/submit_job/file_upload. Two reflect calls per step; rejected-edit buffer LRU-bounded to 100; bundled-skill gate; bootstrap workflow (sentinel + --bootstrap-reviewed); D_sel floor (>=5 with --split override); audit JSONL via audit-writer.ts. Added to ALL_PHASES after patterns (default OFF; opt-in via gbrain config set cycle.skillopt.enabled true); cycle phase wrapper at src/core/skillopt/cycle-phase.ts walks stale skills with per-skill ($0.50) + brain-wide ($2.00) caps. Added to PROTECTED_JOB_NAMES. Surface: dream-cycle phase wrapper; --all batch mode (src/core/skillopt/batch.ts:runBatchAll); --target-models fleet (runFleet parallel per-model receipts under skillopt/fleet/<slug>/); MCP op run_skillopt (admin scope + per-skill skillopt.allowed_skills allowlist, NOT localOnly, validates skill_name kebab-only + confines caller-supplied benchmark/held-out paths to skillsDir for remote callers); Minion skillopt handler + --background with allowProtectedSubmit: true; write-flavored optimization via src/core/skillopt/write-capture.ts:buildWriteCaptureRegistry (virtual put_page/submit_job/file_upload captured in-memory; --write-capture flag); held-out real-user test set via src/core/skillopt/held-out.ts (capture infra at ~/.gbrain/skillopt-captures/<skill>/<run>.jsonl, --held-out <path> flag, runHeldOutGate candidate >= baseline). Hermetic via DI seams (opts.chatFn for optimizer + judge; opts.toolLoopFn for rollouts; no mock.module). --bootstrap-from-skill → runBootstrapFromSkill in src/core/skillopt/bootstrap-benchmark.ts: reads SKILL.md directly (no routing-eval.jsonl), makes ONE LLM call emitting a full starter benchmark (tasks + rule judges) as JSONL, parsed line-by-line with skip-bad-line salvage and a min-2-valid-checks-per-task drop; provider/transport errors PROPAGATE (not collapsed to bootstrap_empty). --bootstrap-tasks N (default 15, capped 50); maxTokens scales min(8000, max(4000, N*220)). The stderr REVIEW line prints the literal gbrain skillopt <name> --bootstrap-reviewed --split 1:1:1 — load-bearing because the default 4:1:5 split makes a 15-task starter's D_sel = floor(15/10) = 1, below the >=5 floor, so a 15-task benchmark needs --split 1:1:1. Both bootstrap generators share assertBenchmarkAbsent + readSkillBodyOrThrow; --bootstrap-from-skill is mutually exclusive with --bootstrap-from-routing/--benchmark/--all/--target-models/--resume. Generated rule judges are explicitly WEAK DRAFTS to be strengthened during the review gate. The F11 held-out gate is wired: --held-out <path> is parsed and threaded through every caller (CLI main + --background held_out_path + batch/fleet heldOutPath + the run_skillopt held_out_path param), running at CHECKPOINT ACCEPTANCE so no-mutate/fleet paths can't promote a held-out-failing candidate. assertBundledMutationHeldOut in bundled-skill-gate.ts: bundled + --allow-mutate-bundled requires a NON-EMPTY held-out (MIN_HELD_OUT_SIZE = D_SEL_MIN_SIZE = 5, derived so they can't desync) or hard-refuses (exit 2), for ALL callers (they funnel through runSkillOpt); held-out must be task_id-DISJOINT from the benchmark (overlap rejected — can't catch overfitting). receipt.baseline_sel_score populated + a real final-test eval (test_score + baseline_test_score) scoring best + baseline on split.test; shared scoreSkillOnTasks primitive (validate-gate.ts) backs baseline/final-test/held-out scoring. --no-mutate writes proposed.md via writeProposed in version-store.ts. maxRuntimeMin ENFORCED (wall-clock deadline between steps → skillopt_runtime_exceeded → outcome aborted). Three eval-internal ablation opts on SkillOptOpts (NOT on CLI): reflectMode ('both'/'failure-only'), disableValidationGate (greedy-accept), optimizerMode ('reflect'/'one-shot-rewrite'), recorded in RunReceipt + audit run_start for replayability; ROLLOUT_SUCCESS_THRESHOLD = 0.5 named constant for the partition; one-shot fence-strip is anchored (^```...```$) so an embedded code sample isn't truncated. Budget no-pricing fix: Claude Haiku 4.5's dateless canonical id claude-haiku-4-5 is in src/core/anthropic-pricing.ts (a BudgetTracker-capped run on Haiku otherwise threw no_pricing on the FIRST chat() of every rollout); runValidationGate (validate-gate.ts) scans settled results for isMustAbortError(error) (from worker-pool.ts; BUDGET_EXHAUSTED is in MUST_ABORT_ERROR_TAGS) and re-throws so the caller aborts loudly instead of recording a hollow selScore:0 — ordinary non-abort rollout errors still fail-open to score:0 (judge-hiccup posture preserved). Pinned by 152 tests across 18 files (foundation + adversarial + v2 surface + E2E PGLite serial), test/skillopt/bootstrap-from-skill.test.ts (20 cases), test/skillopt/rollout.test.ts, test/skillopt/validate-gate-abort.test.ts (3 cases), held-out ENFORCE + one-shot-rewrite unit cases, and e2e (F11 block/allow, bundled no-mutate, runtime deadline, receipt honesty, held-out disjointness, no-DB-pollution). Drives the Track B SkillOpt benchmark suite in the sibling gbrain-evals repo.

• src/core/brainstorm/{domain-bank,orchestrator,judges}.ts + src/commands/{brainstorm,lsd,eval-brainstorm}.ts + src/core/last-retrieved.ts — bisociation-grounded idea generation pair: gbrain brainstorm <question> (defensible, cite-heavy, 4 close × 6 far, judge threshold 4.0/5, save by default) and gbrain lsd <question> (Lateral Synaptic Drift — inverted judge rejecting ideas with resistance >4.5 "too obvious", stale-page bias via pages.last_retrieved_at, 2 close × 12 far, axiomatic inversions required, ephemeral by default). The "domain bank" is prefix-stratified sampling from the user's own brain (SELECT DISTINCT substring(slug from '^[^/]+/[^/]+') cached 1h-TTL in config per source) tiebroken by JOIN page_links connection_count, with corpus-sampling fallback when fewer prefixes than M exist. Distance normalized to [0,1] via 1 - clamp(cosine_distance, 0, 2) / 2. judges.ts exports runJudge(config, ideas) + two configs (BRAINSTORM_JUDGE_CONFIG weighted originality/resistance/thesis_density/concrete_grounding/cognitive_load 0.25/0.20/0.20/0.20/0.15 vs LSD_JUDGE_CONFIG cognitive_load 0.50 + inversion rule). Calibration cold-start fallback: when calibration_profiles.active_bias_tags is empty, judge runs without anti-bias context AND stderr-warns. Op-layer write-back in src/core/operations.ts search/query/get_page handlers fires bumpLastRetrievedAt(engine, pageIds) (fire-and-forget, 5-min throttled via SQL clause, default-on with search.track_retrieval config escape hatch); internal callers (sync, migrations, dream cycle) bypass the op layer so the LSD stale signal stays clean. The fire-and-forget IIFE is tracked in a module-scoped Set<Promise<unknown>>; awaitPendingLastRetrievedWrites(timeoutMs?: number): Promise<{outcome, pending}> resolves once all tracked promises settle, bounded by a 5s Promise.race timeout that stderr-warns the pending count. src/cli.ts awaits the drain unconditionally for every op in the op-dispatch finally block BEFORE engine.disconnect(), then a fallback process.exit(0) fires ONLY when outcome === 'timeout' AND shouldForceExitAfterMain(argv) (excludes serve so daemons stay alive) — closes the PGLite CLI search/query/get-hang class where the IIFE raced disconnect and PGLite's WASM kept Bun's event loop alive. pages.last_retrieved_at TIMESTAMPTZ NULL has a full (NOT partial) B-tree index covering both NULL and range branches; full forward-reference bootstrap probe on both engines. Frontmatter mode: lsd makes the dream-cycle synthesize phase skip LSD output via isLsdOutput() in src/core/cycle/transcript-discovery.ts short-circuiting isDreamOutput(). gbrain eval brainstorm <fixture.jsonl> is a three-axis conjunctive gate (distance + usefulness + grounding — distance alone is gameable). gbrain doctor has a brainstorm_health check (migration applied, search.track_retrieval setting, calibration cold-start status). judges.ts computes the judge token budget via computeJudgeMaxTokens(ideaCount, modelId) (named constants TOKEN_BUDGET_PER_IDEA, TOKEN_BUDGET_ENVELOPE, LEGACY_MIN_MAX_TOKENS, MAX_OUTPUT_TOKENS_CEIL; ANTHROPIC_OUTPUT_CAPS map: Opus 4.7 32K, Sonnet 4.6 / Haiku 4.5 64K, legacy Claude 3.5 8K) so a large multi-call judge doesn't truncate mid-JSON; with no modelOverride the cap routes through the gateway's actual configured chat model via getChatModel(). --save for both commands persists through the canonical ingestion path: persistSavedIdea(engine, {slug, content, provenanceVia}) calls importFromContent({noEmbed:true, sourcePath}) (chunked + tagged + content_hash so search finds it, no embedding cost at save) THEN renders the saved row to disk via the shared writePageThrough helper (file rendered FROM the row so the two sinks can't diverge and gbrain sync doesn't churn it). formatSaveOutcome(outcome, ctx) returns an honest per-branch message (both-sinks, DB-only when no sync.repo_path/repo-not-a-dir, DB-saved-but-file-errored, total-failure → loud save FAILED … NOT persisted on stderr + nonzero exit) — closes the silent-false-success class where --save printed "Saved" unconditionally even when the DB write failed. buildIdeaSlug(question, label, nonce?) adds a random nonce suffix (injectable for tests) so two same-day runs sharing the first 60 slug chars don't clobber. --json callers stay DB-only. buildBrainstormFrontmatterObject(result) in orchestrator.ts returns the object form for serializeMarkdown (string buildBrainstormFrontmatter untouched). Pinned by test/last-retrieved.test.ts, test/e2e/pglite-cli-exit.serial.test.ts (IRON-RULE: real bun src/cli.ts subprocess against a hermetic PGLite tempdir asserts search/get/query exit 0 in <15s + daemon-survival), test/fix-wave-structural.test.ts (asserts the drain await is textually BEFORE engine.disconnect), test/brainstorm/{distance,lsd-mode-skip,eval-brainstorm,judges-maxtokens,save}.test.ts. Open Collider source: github.com/CL-ML/open-collider.

• src/core/write-through.ts — shared atomic disk write-through for the canonical ingestion path. writePageThrough(engine, slug, {sourceId?, frontmatterOverrides?, logger?}) resolves the disk target from the ASSIGNED source's own working tree (sources.local_path), re-reads the just-written DB row (getPage), renders it via serializePageToMarkdown, and writes the .md under that tree's root so the brain has a committable artifact that round-trips through gbrain sync. A source with its own local_path writes there; a source WITHOUT one falls back to the global sync.repo_path ONLY when this is the sole source (then that path is unambiguously this source's tree) and otherwise skips with source_has_no_local_path rather than leak into a sibling source's git repo. Rendering FROM the row means file and row cannot diverge. ATOMIC: writes to a unique temp sibling (<file>.tmp.<pid>.<rand>) + renameSync, cleaning up temp on any failure, so a crash or concurrent gbrain sync/autopilot walking the live git tree never reads a half-written .md (matches the .tmp + rename convention in import-checkpoint.ts / op-checkpoint.ts). Never throws — returns WriteThroughResult { written, path?, skipped?: 'no_repo_configured' | 'repo_not_found' | 'source_has_no_local_path' | 'page_not_found_after_write', error? } so the caller decides messaging + exit codes. Trust gating (subagent sandbox, dry-run) stays at the CALLER. On a durability-hardened repo (isDurabilityHardened — the gbrain post-commit hook is installed, i.e. the user ran gbrain sources harden), a successful write is best-effort COMMITTED via commitWriteThroughFile (path-limited git commit -- <file>, never sweeps unrelated edits; the hook then background-pushes) so write-through content reaches git instead of accumulating uncommitted forever (#2426); result carries committed?: boolean. Unhardened repos keep write-only behavior. Consumers: put_page op and gbrain brainstorm/lsd --save via persistSavedIdea. Pinned by test/write-through.test.ts + test/write-through-commit.serial.test.ts.

• src/core/model-id.ts — splitProviderModelId(input: string | null | undefined): {provider: string | null, model: string} shared parser for the pricing side. Splits on : first, then /. Defensive contract: null/undefined/empty/whitespace returns {provider: null, model: ''}. Five sites consume it (src/core/anthropic-pricing.ts:estimateMaxCostUsd, src/core/budget/budget-tracker.ts:lookupPricing, src/core/eval-contradictions/cost-tracker.ts:pricingFor, src/core/minions/batch-projection.ts at two call sites, src/core/model-config.ts:isAnthropicProvider) so the pricing + classification surface has no parallel re-implementations of provider:model splitting — slash-form ids (anthropic/claude-sonnet-4-6) classify correctly instead of falling through to "unknown model". Distinct from the gateway-side parseModelId in src/core/ai/model-resolver.ts, which throws on bare names because routing needs an explicit provider; this one returns {provider: null, model: 'bare'} because pricing lookups happen against bare model ids. Pinned by test/model-id.test.ts.

• src/commands/transcripts.ts — the transcripts command family, all local-only (ctx.remote=false by construction). recent: raw .txt corpus reads via listRecentTranscripts (same library as the gated get_recent_transcripts op). ingest <path-or-glob>: the cross-harness session importer — resolves ONE source id (6-tier chain), threads activePack once, streams progress (phase transcripts.ingest), and calls runTranscriptsIngest; embedding is OFF by default (embed backfill is the catch-up lane; the embed flag opts in); the max-bytes flag (validated size string, e.g. 4gb) overrides the per-format file/store byte caps for oversized stores while omission preserves each adapter's native default; the since-last watermark is an op-checkpoint (op transcripts-ingest, fingerprint = source + pathspec + format + adapter version + any explicit byte cap via ingestCheckpointFingerprintInput — a checkpoint written under one cap is never silently reused under another, so a capped run's skipped tail can't read as scanned; the pathspec binds the user-stated paths resolved + sorted, and the no-arg/all lane substitutes hostname + sorted harness roots so DB-backed checkpoints shared across a brain's machines never let one machine inherit another's watermark and skip sessions it never scanned) advanced ONLY after a clean, untruncated, non-dry scan; no-arg = confined discovery table, the all flag imports the discovered set. status: found-vs-imported gap table (disk scan vs ONE conversation-pages frontmatter query — executeRaw, both engines — in src/core/transcripts/discover.ts) — the correctness surface that catches late-arriving sessions no watermark can. The facts flag hands EVERY touched slug (including hash-skipped) to src/core/transcripts/ingest-facts.ts. Registered in CLI_ONLY + CLI_ONLY_SELF_HELP + SELF_HELP_WITHOUT_ENGINE (engine-free help).

• src/core/transcripts/ (directory) — the cathedral-4 transcript-adapter seam. types.ts: the TranscriptAdapter contract — parse(path): AsyncGenerator<ParsedSession, FileDiagnostics> (one FILE may hold many sessions; the generator RETURN value carries bytes/skipped-lines/zero-session diagnostics so an empty file explains itself), format-specific byte caps (JSONL 50MB hard cap — the 10MB default in claude-code-jsonl.ts belongs to the hook-lane tail reader, not imports; monolithic export JSON rejects-not-truncates at 200MB), and the ONE buildTranscriptSlug helper (per-provider dirs matching the conversation-archive layout; id suffixes are sha256 prefixes of the session id — hash12 in slugs, hash16 for the dedup identity — never a cleaned prefix of the source id, which let same-prefix session ids collide). detect.ts: adapter registry + head-sample detection (explicit format wins; symlinks lstat-rejected) + injectable harnessRoots (the confined discovery surface). Adapters, each with a DATED SPEC_TARGET + scrubbed fixture + bytes>0 && sessions==0 drift alarm: claude-code.ts (thin wrapper over the shipped claude-code-jsonl.ts, which gained the ADDITIVE full-file parseClaudeSessionFile with real per-message timestamps — hook-lane parseTranscript output is regression-pinned byte-identical), codex.ts (turn selection is STRUCTURAL: user turns from event_msg user_message, assistant from response_item output_text; role user/developer response_items are injected preambles and never leak), openclaw.ts (session header + message lines; .checkpoint.*.jsonl snapshots rejected), hermes.ts (COPY-THEN-READ of state.db + wal/shm sidecars — readonly WAL opens need -shm write access and lock against a live writer; schema from the installed hermes-agent source; PROVISIONAL), chatgpt-export.ts (the mapping-tree current_node walk; branches dropped by design, orphaned parents terminate quietly, latest-leaf fallback; extracted conversations.json only) + claude-export.ts (flat chat_messages); both export adapters load through the shared export-json.ts (monolithic JSON over the cap REJECTS with a split hint; a zip or wrong-shape file gets the unzip-first hint) and give id-less conversations content-derived fallback ids so two id-less exports cannot dedup-skip or overwrite each other. render.ts: session → part pages — imessage-slack line format with the regex IMPORTED from conversation-parser/builtins.ts (round-trip pinned), REAL timestamps (missing ones carry forward; zero-timestamp sessions refused — provenance is never fabricated), anchor-shaped BODY lines backslash-escaped (hostile message content cannot forge speakers), fail-closed redaction (secret-scan + harvest-private-patterns.txt user patterns, slack-channel default excluded because it eats issue refs; imperatives COUNTED into hash-covered transcript_import frontmatter, never content_flag), ~300KB message-boundary splitting with 2-message overlap (under the embed-skip threshold), part 1 keeps the base slug, frontmatter.id unique per part. ingest.ts: the engine-facing core — SESSION atomicity (failed sessions skip; integrity failures abort the run), stale-part reconciliation (deletes part > of leftovers), session metadata banked in the base page's raw_data as the REDACTED copy and healed by content-compare even on hash-skipped re-runs (a run that died before putRawData, or a private pattern added after first import, repairs on the next pass), cleanScan/maxSessionTs for the watermark. ingest-facts.ts: ONE runExtractConversationFactsCore invocation (batch slugs selector) inside ONE withBudgetTracker, isFactsExtractionEnabled pre-checked. Pinned by test/transcript-adapters.test.ts, test/transcript-render.test.ts, test/e2e/transcripts-ingest-pglite.test.ts, test/e2e/transcripts-writeback-fidelity.test.ts (raw files through the adapters into the gold-extractor facts path — the BrainBench bypass closer).

• src/commands/integrity.ts — gbrain integrity check|auto|review|extract: bare-tweet detection, dead-link detection, three-bucket repair (auto-repair / review-queue / skip). scanIntegrity() is the shared library function called from gbrain doctor (sampled at limit=500) and cmdCheck (full scan). Batch-load fast path on Postgres uses a single SQL query (fixes the PgBouncer round-trip timeout, ~60s → ~6s), gated by engine.kind === 'postgres' at the call site so PGLite never enters batch; fallback catch logs at GBRAIN_DEBUG=1. Batch projection is SELECT ... ORDER BY source_id, slug (NOT SELECT DISTINCT ON (slug), which collapsed same-slug-different-source pages into one scan) so multi-source brains scan each (source, slug) row independently. Sequential and auto-repair loops use listAllPageRefs() to enumerate (slug, source_id) pairs and thread sourceId to getPage; batch + sequential paths report the same page count on multi-source brains.

• src/core/timeline-dedup-repair.ts (#2038) — schema-drift self-heal for idx_timeline_dedup. The migration that widened the dedup index from (page_id, date, summary) to (page_id, date, summary, source) was renumbered during a master merge, so a brain that ran the old variant has its version counter stamped past the change while the index keeps the 3-column shape — and every addTimelineEntry batch then fails its 4-column ON CONFLICT, silently breaking timeline writes brain-wide. The version counter can't detect this, so the repair is keyed off the actual index SHAPE: checkTimelineDedupIndex(engine) returns {tablePresent, indexPresent, columns, needsRepair} (read-only; powers the timeline_dedup_index doctor check) and repairTimelineDedupIndex(engine) dedupes-then-rebuilds the index. runMigrations invokes the repair on every pass (including the no-pending early-return path); idempotent no-op when the index is already 4-column. gbrain apply-migrations --force-schema triggers it on demand. Pinned by test/timeline-dedup-repair.test.ts.

• src/core/progress.ts — Shared bulk-action progress reporter. Writes to stderr. Modes: auto (TTY \r-rewriting; non-TTY plain lines), human, json (JSONL), quiet. Rate-gated by minIntervalMs and minItems. startHeartbeat(reporter, note) for single long queries. child() composes phase paths. Singleton SIGINT/SIGTERM coordinator emits abort events for every live phase. EPIPE defense on both sync throws and stream 'error' events. Zero dependencies. emitHumanLine is prefix-aware — inside a withSourcePrefix(id, ...) scope from src/core/console-prefix.ts it prepends [id] (and TTY-rewrite mode \r\x1b[2K carries the prefix inside the clear-to-EOL escape); emitJson is intentionally NOT prefixed so NDJSON consumers don't choke on a [id] {...} shape.

• src/core/console-prefix.ts — AsyncLocalStorage<string>-backed per-source line-prefix helper. Exports withSourcePrefix(id, fn) (runs fn with id as active prefix; nested wraps replace then restore), getSourcePrefix() (read-only accessor; test seam), and slog(...) / serr(...) (prefix-aware console.log/console.error). Embedded-newline-safe: a multi-line string under prefix [foo] emits [foo] line1\n[foo] line2. Outside a wrap, slog/serr fall through to bare console.log/console.error so single-source callers see identical output (back-compat invariant). Use src.id (slug-validated by sources add) NOT src.name (free-form) to defeat log-injection through newline/control-character names. Coverage: src/commands/sync.ts performSync + callees, src/commands/embed.ts runEmbedCore + helpers, src/core/progress.ts emitHumanLine.

• src/core/cli-options.ts — Global CLI flag parser. parseGlobalFlags(argv) returns {cliOpts, rest} with --quiet / --progress-json / --progress-interval=<ms> / --brain <id> stripped. --brain is the brain-axis (which database) selector: exact-match only (--brain-* per-command flags pass through), value validated against the mount-id regex at parse time, missing/malformed value THROWS — never a silent host fallback. connectEngine in src/cli.ts feeds it (plus the ambient GBRAIN_BRAIN_ID / .gbrain-mount / mount-path tiers) through resolveBrainId → BrainRegistry.getBrain, which throws UnknownBrainError for an unregistered id; mounts get no auto-migrations and keep the host-config AI gateway. getCliOptions() / setCliOptions() expose a module-level singleton so commands reach resolved flags without parameter threading. cliOptsToProgressOptions() maps to reporter options. childGlobalFlags() returns the flag suffix to append to execSync('gbrain ...') calls in migration orchestrators (propagates --brain=<id> so children stay on the parent's brain). OperationContext.cliOpts extends shared-op dispatch for MCP callers. CliOptions gains explain: boolean. parseGlobalFlags recognizes --explain anywhere in argv (stripped before command dispatch). src/cli.ts formatResult for search + query cases routes to formatResultsExplain from src/core/search/explain-formatter.ts when CliOptions.explain is set; falls through to the existing JSON / human formatters otherwise. maybeBackground(opName, fingerprintArgs, runDirect) helper. Same semantics in TTY and cron (no --no-tty-detect flag, no surprise behavior change between contexts): when --background is passed, submits the op as a Minion job via op_checkpoints for resumability and returns the job_id. --background --follow execs gbrain jobs follow <id> so the user sees the same stderr stream they'd get from a direct call. PGLite degrades to inline execution with a clear stderr note ("PGLite worker pool not yet supported; running inline"). Returns a tagged union the caller dispatches on.

• src/cli.ts strict flag validation (#2185) + src/core/cli-flag-registry.generated.ts + scripts/generate-flag-registry.ts — pre-dispatch, pre-engine unknown-flag rejection for every command: a flag no handler consults fails loud (unknown flag --x for 'gbrain <cmd>', exit 1; --json invocations also get a structured {status:'error', reason:'invalid_flag'} on stdout) instead of being silently ignored while the un-asked-for real operation runs. validateCommandFlags(command, subArgs) runs after the --help short-circuit and before any dispatch or engine connect, in two lanes mirroring dispatch order (CLI_ONLY first — think/salience/anomalies are both ops AND CLI_ONLY members whose handlers parse flags the op contract doesn't declare): CLI_ONLY commands validate against the generated CLI_FLAG_REGISTRY (per-command legal sets derived from each command's source — case block + imported modules + one level of relative imports + EXTRA_FLAGS; deliberately over-inclusive, help-text mentions count; regenerate via bun run build:flag-registry); op commands validate via findUnknownOpFlag, which mirrors parseOpArgs's traversal (non-boolean flags consume their value token; --key=value inline form recognized) plus the CLI-local flags consumed outside the op contract (json, explain, help, source, dry-run); the CLI_ONLY token scan is the exported findUnknownFlag(args, legal). In parseOpArgs, json/dry_run are CLI-local booleans that never consume a value token, so a trailing --dry-run is a real rehearsal switch feeding makeContext's ctx.dryRun. Uppercase flag spellings are treated as unknown (every handler is case-sensitive-lowercase, so they'd be silently ignored downstream — the exact class the validator kills). Exempt by contract: call (arbitrary --param interface), config (arbitrary set values), jobs submit (handler-defined payload params); everything after a literal -- is passthrough and never validated. A command missing from the registry fails OPEN at runtime (never bricks a command); test/cli-flag-validation.test.ts pins registry freshness, per-command drift, and consumption evidence — a safety flag (--dry-run, --yes, --force) may only be advertised if the command's source actually reads it.

• src/core/source-id.ts — single canonical source_id validation, dependency-free by design (imported by both engines, cycle, source-resolver, sources-ops). SOURCE_ID_RE (strict: 1-32 lowercase alnum, interior hyphens only, no edge hyphens); isValidSourceId (boolean — for tiers that silently fall back: dotfile, brain_default) vs assertValidSourceId (throws — for tiers that must reject loudly: explicit --source, GBRAIN_SOURCE, cycleLockIdFor); ALL_SOURCES = '__all__' sentinel (#1712 — deliberately NOT a valid id so it can never collide with a real source or leak into lock ids/path joins; sourceScopeOpts translates it to an unscoped read for trusted local callers and keeps it unsatisfiable for remote callers, fail-closed). normalizeSourceInput/normalizeFederatedReadInput normalize the /admin/api/register-client HTTP body, mirroring the CLI's --source/--federated-read flags: omitted source → 'default'; omitted federatedRead → undefined so registerClientManual applies its own [sourceId] default; present-but-invalid values throw so the route returns a structured 400 (invalid_source) instead of failing at INSERT time. Pinned by test/register-client-source-normalize.test.ts.

• src/core/db-lock.ts — generic tryAcquireDbLock(engine, lockId, ttlMinutes) over the gbrain_cycle_locks table. Parameterized lock id so scopes nest cleanly: gbrain-cycle for the broad cycle (held by cycle.ts) and gbrain-sync (SYNC_LOCK_ID) for performSync's narrower writer window. UPSERT-with-TTL semantics survive PgBouncer transaction pooling (unlike session-scoped pg_try_advisory_lock); crashed holders auto-release once their TTL expires. Every handle is FENCED to its exact acquisition: DbLockHandle.acquiredAt captures the row's acquired_at as epoch-seconds text (extract(epoch from acquired_at)::text — GUC-independent, unlike timestamptz::text which varies with per-session TimeZone/DateStyle across pools) and refresh()/release()/the cleanup hook all match (id, holder_pid, fence), so a recycled PID or a superseded holder can never refresh or delete a successor's row. refresh() returns a boolean: true = still owned; false = the fenced UPDATE matched 0 rows (stolen or force-cleared — certain loss, the caller must stop relying on mutual exclusion); transient DB errors still THROW (not evidence of a steal; the TTL is the backstop). Exports LockStolenError (thrown/used as an AbortSignal reason by consumers like cycle.ts's refresher and the supervisor). It also does automatic same-host dead-pid takeover: when the upsert finds a held, NOT-TTL-expired lock whose holder is on this host and provably dead, it reclaims via a guarded DELETE WHERE id=$1 AND holder_pid=$2 + one normal-upsert retry returning the standard handle (refresh/release intact). The liveness check is the exported classifyHolderLiveness(pid, host, ageMs, opts?) / isHolderDeadLocally(...) (injectable process.kill seam; HOLDER_TAKEOVER_GRACE_MS = 60_000 PID-reuse guard; EPERM classified as alive so a live process you don't own is never stolen). TTL-expired locks stay the upsert's job; cross-host stays TTL-only. runBreakLock (src/commands/sync.ts) consumes the same predicate. Background reaper (#1972): reapDeadHolderLocks(engine) is the periodic sweep the contention path lacked — it deletes locks whose holder is isHolderDeadLocally, scoped to the gbrain-sync:* / gbrain-cycle/gbrain-cycle:* namespaces ONLY (election/supervisor/reindex locks keep TTL-only behavior, untouched), via deleteLockRowExact(engine, id, pid, acquiredAt) — a snapshot-matched delete (date_trunc('milliseconds', acquired_at) = $3, so the ms a JS Date keeps survives) that's TOCTOU-safe against a reused PID taking the lock between SELECT and DELETE. cycle.ts runs it at cycle start (before the sync phase); gbrain doctor --fix runs it for no-autopilot brains. selectLockRows(engine, opts?) + a shared row→LockSnapshot mapper are the single canonical reader now backing inspectLock + listStaleLocks + the reaper (was triplicated). isLockHolderLive(snap, ttlMinutes) (#2227) is the observability liveness predicate — freshness-keyed (ttl_expired plus the heartbeat steal-grace), never process.kill, so gbrain jobs supervisor status / gbrain doctor can report a live supervisor via its queue lock without a PID-reuse false-positive. Pinned by test/db-lock-auto-takeover.test.ts + test/db-lock-reap.test.ts + test/db-lock-fencing.test.ts. DbLockHandle.refresh(opts?) accepts {signal} (Postgres forwards to executeRawDirect; PGLite ignores); withRefreshingLock's heartbeat aborts the per-tick signal on timeout and guards re-entrancy (15s min cadence vs 30s timeout could stack ticks).

• src/core/sync-concurrency.ts — single source of truth for the parallel-sync policy. Exports autoConcurrency(engine, fileCount, override?) (PGLite always serial; explicit override clamped to >=1; auto path returns DEFAULT_PARALLEL_WORKERS=4 when fileCount > AUTO_CONCURRENCY_FILE_THRESHOLD=100), shouldRunParallel(workers, fileCount, explicit) (explicit --workers bypasses the >50-file floor), and parseWorkers(s) (rejects '0', '-3', 'foo', '1.5', trailing chars). Used by performSync, performFullSync, runImport, and the Minion sync handler so the sites can't drift. DEFAULT_PARALLEL_SOURCES = 4 is a SEPARATE constant for the per-source fan-out under gbrain sync --all — kept distinct from DEFAULT_PARALLEL_WORKERS because total live Postgres connections per wave ≈ DEFAULT_PARALLEL_SOURCES × DEFAULT_PARALLEL_WORKERS × 2 (per-file pool) = 32 at both defaults (each per-file worker opens its own PostgresEngine with poolSize = min(2, resolvePoolSize(2))); sync.ts warns when parallel × workers × 2 > 16. resolveWorkersWithClamp(engine, override, commandName, fileCount) wraps autoConcurrency with a per-command stderr clamp warning on PGLite (per-(command, requested) dedup via module-scoped warned-once set with _resetWorkersClampWarningsForTest() seam) and is the canonical surface for every bulk-command --workers N flag (extract-conversation-facts, extract, edges-backfill, reindex-multimodal, reindex, reindex-code); embed.ts deliberately bypasses it and keeps GBRAIN_EMBED_CONCURRENCY || 20. resolveMaxConnections() (reads GBRAIN_MAX_CONNECTIONS, undefined when unset) + clampWorkersForConnectionBudget(workers, perWorkerPool, maxConnections, parentPool) back the opt-in single-sync connection-footprint clamp so a big sync stays under a low pooler cap (parent_pool + workers×perWorkerPool ≤ budget); gbrain doctor's pool_budget check (computePoolBudgetCheck / checkPoolBudget in src/commands/doctor.ts) warns when the budget leaves no room for a worker, pointing at GBRAIN_POOL_SIZE=2. Pinned by test/pglite-workers-clamp.test.ts.

• src/core/worker-pool.ts — Canonical sliding-pool + bounded-semaphore primitive (extracted from src/commands/embed.ts sliding-pool sites and src/commands/eval-cross-modal.ts runWithLimit semaphore). Two exports: runSlidingPool<T>({items, workers, onItem, signal?, onError?, failureLabel?, onProgress?}) + runWithLimit<TIn, TOut>({items, limit, fn, signal?}). Atomicity invariant: const idx = nextIdx++ is one synchronous JS statement (no await between read and write — guaranteed by the single-threaded event loop), documented in the module header AND enforced by scripts/check-worker-pool-atomicity.sh (wired into bun run verify), which rejects importing worker_threads in any consuming file and inserting await between the nextIdx read and write. MUST_ABORT_ERROR_TAGS set is seeded with BUDGET_EXHAUSTED from src/core/budget/budget-tracker.ts; tagged errors (matched via err.tag === 'BUDGET_EXHAUSTED' to avoid cross-module import) bypass onError and hard-abort the pool via AbortController.abort() to in-flight onItem — the budget cap is a structural ceiling under concurrency. failures[] shape is {idx, label, error} records (NOT full items; callers supply failureLabel(item) => string) for bounded memory under huge brains. Pinned by test/worker-pool.test.ts + test/scripts/check-worker-pool-atomicity.test.ts. Drives every --workers N bulk command.

• src/core/embedding-dim-check.ts — facts.embedding dim drift surface. readFactsEmbeddingDim(engine): Promise<FactsColumnDimResult> covers both vector(N) and halfvec(N) shapes (migration v40 falls back to vector on pgvector < 0.7); regex ordering is halfvec-before-vector (substring "vec" appears in "halfvec"; naive /vector/i would shadow). buildFactsAlterRecipe(dims, configured, type) emits the paste-ready DROP INDEX IF EXISTS idx_facts_embedding_hnsw; ALTER TABLE facts ALTER COLUMN embedding TYPE halfvec(N) USING embedding::halfvec(N); CREATE INDEX idx_facts_embedding_hnsw ON facts USING hnsw (embedding halfvec_cosine_ops) WHERE ... flow (NOT bare REINDEX, which doesn't rewrite the index after a column-type change). assertFactsEmbeddingDimMatchesConfig(engine) is the preflight — throws FactsEmbeddingDimMismatchError (tagged tag: 'FACTS_EMBEDDING_DIM_MISMATCH' for parity with the worker-pool MUST_ABORT semantics) when configured dim ≠ column width; cached per-engine via WeakMap; PGLite engines silently skip. Doctor check facts_embedding_width_consistency (registered after embedding_width_consistency) reuses the same helpers with an identical ALTER recipe. Pinned by test/embedding-dim-check-facts.test.ts.

• src/core/sort-newest-first.ts — single source of truth for the descending-lex sort that gbrain import and gbrain sync both apply. Mutates in place (Array.prototype.sort semantics), returns the same array reference for fluent chaining. Empty/single-element inputs short-circuit. Future ordering changes flip one line here instead of touching two CLI commands. Pinned by test/sort-newest-first.test.ts (descending order, mixed prefixes, empty, single-element, in-place-mutation contract).

• src/core/cycle.ts — brain maintenance cycle primitive (23 phases; ALL_PHASES is the ordered source of truth). runCycle(engine: BrainEngine | null, opts: CycleOpts): Promise<CycleReport> composes phases in semantic order along the core spine lint → backlinks → sync → synthesize → extract → patterns → recompute_emotional_weight → embed → orphans, with the extraction/graph/consolidation phases (extract_facts, extract_atoms, resolve_symbol_edges, …) slotted between per the ordering comments on ALL_PHASES. synthesize runs after sync (cross-references see a fresh brain) and before extract (auto-link materializes its writes); patterns runs after extract so it reads a fresh graph (subagent put_page sets ctx.remote=true and skips auto-link/timeline by default, so extract is the canonical materialization); recompute_emotional_weight sees the union of syncPagesAffected + synthesizeWrittenSlugs incrementally, or all pages when neither anchor is set (full backfill via gbrain dream --phase recompute_emotional_weight). CycleReport.schema_version: "1" is stable; totals is additive (pages_emotional_weight_recomputed, transcripts_processed, synth_pages_written, patterns_written). Three callers: gbrain dream CLI, gbrain autopilot daemon inline path, the Minions autopilot-cycle handler. Coordination via gbrain_cycle_locks DB table + ~/.gbrain/cycle.lock file lock with PID-liveness for PGLite; the two handles compose into ONE lock whose refresh() treats the fenced DB row as the authoritative multi-writer identity and the file half as best-effort freshness — the file lock is refreshed ONLY while the fenced DB refresh reports ownership, so a losing holder can never clobber the successor's file lock on the very tick it detects the steal. A dedicated serialized refresher — startCycleLockRefresher(lock, controller, lockId) (exported; unref'd setInterval at max(15s, TTL/6), env-only override GBRAIN_CYCLE_LOCK_REFRESH_MS, in-flight guard so a slow refresh never overlaps the next tick) — heartbeats the lock through long phases (synthesis/patterns/consolidation waits routinely outlive the TTL with no other heartbeat). A fenced miss aborts the controller with LockStolenError; that steal signal combines with the worker's external signal via the exported anyAbortSignal(signals) (duck-type-tolerant — stubs without addEventListener are observed by poll; returns {signal, dispose} and dispose detaches the caller-signal listener + clears the poll timer so daemons don't leak), and the run stops at the next phase boundary with a structured partial report carrying reason: 'lock_stolen' (for the 5 long phases — synthesize / extract_atoms / patterns / synthesize_concepts / consolidate — the steal races the phase promise and stops the WAIT immediately; their in-flight work runs to its own bounded timeout because their opts can't carry a signal yet). Transient refresh errors log and retry next tick (the TTL stays the backstop). yieldBetweenPhases runs between phases; yieldDuringPhase is in-phase keepalive. Engine nullable; lock-skip on read-only phase selections. CycleOpts.signal?: AbortSignal propagates the worker's abort signal with checkAborted() between every phase. CycleOpts.deadlineAtMs (the enclosing minion job's ABSOLUTE wall-clock deadline, threaded from MinionJobContext.deadlineAtMs by the autopilot-cycle handler; null for direct gbrain dream callers) flows into patterns, propose_takes, AND synthesize (#4168) so time-spending phases derive their deadlines from the REAL remaining job budget instead of duplicated literals that collide with the job's own kill timer. Pinned by test/cycle-lock-steal.serial.test.ts (mid-run steal → partial report, no further phases, successor row intact) + test/cycle-any-abort-signal.test.ts + test/db-lock-fencing.test.ts. runPhaseSync returns pagesAffected via SyncPhaseResult (threaded to runPhaseExtract as the 4th arg) and takes willRunExtractPhase: boolean setting noExtract: phases.includes('extract') so gbrain dream --phase sync doesn't silently lose extraction. resolveSourceForDir(engine, brainDir) threads sourceId to performSync() so sync reads the per-source sources.last_commit anchor (not the drift-prone global config.sync.last_commit). CycleOpts.brainDir is string | null; when null (checkout-less postgres/Supabase brain) the 6 filesystem phases (lint/backlinks/sync/synthesize/extract/patterns) skip with details.reason: 'no_brain_dir' and the DB-only phases run; resolveSourceForDir is null-tolerant. cycleSourceId = opts.sourceId ?? resolveSourceForDir(engine, brainDir) is the canonical per-source scope for extract_facts/extract_atoms/calibration — and for synthesize (#1586: threaded as SynthesizePhaseOpts.sourceId so synthesized pages land in the cycle's resolved source, not 'default') — so gbrain dream --source repo-a reconciles repo-a's facts even with no checkout (instead of scoping to 'default' while stamping repo-a fresh). deriveStatus counts edges_resolved/edges_ambiguous as work so an edges-only cycle reports ok not clean, and scores ONLY attempted phases — the implicit source-cycle exclusion skip-records are bookkeeping and never dilute failure aggregation (pre-#4250 they turned an all-freshness-phases-failed cycle into a stampable 'partial'); the jobs.ts autopilot-cycle + phase-wrapper handlers pass null (not '.') when no repo is configured. The cycle is SPLIT for autopilot fan-out (#2194/#2227) along the PHASE_SCOPE taxonomy in src/core/cycle/phase-scope.ts (see its entry): cycle.ts derives SOURCE_PHASES / MIXED_PHASES / GLOBAL_PHASES / MAINTENANCE_PHASES (mixed ∪ global, original cycle order) plus SOURCE_FRESHNESS_PHASES (deterministic, non-LLM: lint/backlinks/sync/extract/extract_facts/recompute_emotional_weight — defined in phase-scope.ts) and SOURCE_BACKGROUND_PHASES (LLM-backed/unbounded source work = SOURCE minus FRESHNESS). resolveCyclePhases(requested, sourceId) at the shared runCycle boundary: default/no-source → requested ?? ALL_PHASES (the canonical default cycle remains full); a named non-default source with NO explicit phases → SOURCE_FRESHNESS_PHASES only (the freshness keeper's implicit dream --source X path must stamp freshness without first draining LLM-backed maintenance); explicit phase lists are honored VERBATIM — dream --source X --phase synthesize (and --input <file>, which implies synthesize) is deliberate operator intent, and --phase orphans --source X still narrows orphans via forceGlobalOrphans. The N-way duplication guard lives at the QUEUE boundary instead: the autopilot-cycle handler intersects queued per-source payloads with SOURCE_FRESHNESS_PHASES (legacy pre-v0.46.20 payloads carried mixed+background phases; an all-rejected or empty list is an explicit no-op skip with reason all_phases_rejected_by_normalization, never an implicit run, and rejected phases surface on the job result as phases_rejected_by_normalization). On the implicit path, excluded phases surface as skipped with details.reason: 'excluded_from_implicit_source_cycle' + phase_scope. Per-source autopilot-cycle jobs enqueue phases: SOURCE_FRESHNESS_PHASES and stamp last_source_cycle_at; the single autopilot-global-maintenance job runs MAINTENANCE_PHASES (no sourceId) and stamps the brain-level autopilot.last_global_at config key (LAST_GLOBAL_AT_KEY). SOURCE_BACKGROUND phases have NO automatic lane on multi-source brains (the legacy full-cycle job fires only when the brain has no sources rows) — run them explicitly (gbrain dream --source X --phase extract_atoms) until the background lane lands (see TODOS). The freshness stamp gate is opts.sourceId && phases.length > 0 && engine && !dryRun && !aborted && status ∈ {ok, clean, partial}; last_full_cycle_at is still written alongside last_source_cycle_at on a per-source success for doctor/legacy readers (no longer a gate for the brain-wide phases). Pinned by test/dream-postgres.serial.test.ts + test/jobs-autopilot-cycle-braindir.serial.test.ts + test/autopilot-global-maintenance.test.ts + test/cycle-enabled-phase-completeness.test.ts. runPhaseLint + runPhaseBacklinks carry the export keyword so behavioral tests can drive them directly (internal helpers exposed for test-only consumption; downstream code should NOT depend on them). Pinned by test/cycle-legacy-phases.test.ts (11 cases across both phases: clean run → status='ok', partial fix → status='warn' with dryRun in details, dry-run path doesn't write, throw-from-lib → status='fail' with the wrapper's try/catch envelope populated). Future phase wrappers (sync, extract, embed, orphans, extract_facts, resolve_symbol_edges, recompute_emotional_weight) land as additional describes in the same file. with src/core/cycle/extract-atoms.ts + src/core/cycle/synthesize-concepts.ts + src/commands/extract.ts + src/commands/doctor.ts + src/core/op-checkpoint.ts: six daily-driver ops fixes. (1) Batch idempotency: atomsExistingForHashes(engine, sourceId, hashes[]) (exported from src/core/cycle/extract-atoms.ts) replaces the per-hash loop (7K individual queries) with one batched SQL roundtrip returning already-extracted content_hash16 values; fail-open (SQL error → empty set, extraction proceeds); powered by migration v104 pages_atom_source_hash_idx (partial expression index on frontmatter->>'source_hash' for atom rows where deleted_at IS NULL; Postgres CREATE INDEX CONCURRENTLY with invalid-remnant pre-drop, PGLite plain). (2) Cycle lock TTL + heartbeat: LOCK_TTL_MINUTES = 5; buildYieldDuringPhase(lock, outer) (exported, with LockHandle) calls lock.refresh() + any external hook on every fire, throttled to 30s via maybeYield, firing both in the main loop AND immediately after every await chat(...); synthesize_concepts uses the same throttled hook. A crashed cycle releases its lock within one short TTL, while the dedicated startCycleLockRefresher interval (see the coordination sentence above) keeps a healthy long-running cycle alive even across a single multi-minute await chat(...) — the timer fires during awaits, so no single slow call can silently expire the lock. (3) Progress wiring: progress?: ProgressReporter opt on ExtractAtomsOpts and SynthesizeConceptsOpts; cycle.ts passes its phase-level reporter down (NOT a child reporter, which would collide on cycle.extract_atoms.extract_atoms.work); phases only call tick()/heartbeat(), cycle.ts owns start()/finish(). (4) by-mention resume: mentionsFingerprint({source, type, since, gazetteerHash}) in src/core/op-checkpoint.ts — the gazetteer hash is load-bearing (adding entity pages mid-pause shifts the hash → new fingerprint → fresh scan against the new gazetteer, never silent skip); the gazetteer itself is entity-page titles PLUS live-verified page_aliases entries joined to entity-typed pages (ambiguous aliases and alias-vs-title collisions within a source are skipped), so body mentions of a documented alias link too; gbrain extract links --by-mention resumes via op_checkpoints with flushAndCheckpoint ordering (links flush to DB FIRST, page keys commit to checkpoint SECOND, persist THIRD, so a crash mid-batch leaves the page un-checkpointed and resume re-scans it); persist every 1000 items OR 30s; clean exit clears the checkpoint; --dry-run skips both load and write. (5) sync_consolidation doctor check (multi-source brains see a paste-ready gbrain sync --all --parallel 4 --workers 4 --skip-failed; single-source "not applicable"; SQL errors return warn via the check's own try/catch). (6) Test-isolation: test/cycle-last-full-cycle-at.test.ts + test/schema-cli.test.ts use per-test GBRAIN_HOME=tempdir. Pinned by test/cycle/extract-atoms-batch.test.ts, test/cycle/cycle-lock-ttl.test.ts (regression pin on LOCK_TTL_MINUTES === 5), test/op-checkpoint-mentions-fingerprint.test.ts, test/cycle/extract-atoms-progress.test.ts, test/cycle/synthesize-concepts-progress.test.ts, test/cycle/yield-during-phase-refresh.test.ts, test/cycle/yield-during-phase-throttle.test.ts, test/extract-by-mention-resume.test.ts, test/doctor-sync-consolidation.test.ts. Companion sync --all recipe block in skills/cron-scheduler/SKILL.md. synthesize_concepts writes concept pages through importFromContent (#2163: the same parse→chunk→embed pipeline put_page uses, with put_page's isAvailable('embedding') → noEmbed gate) so concepts/ pages carry content_chunks + embeddings and are reachable by retrieval (where source-boost.ts weights them 1.3×). purge phase (soft-delete TTLs) also GCs stale op_checkpoints rows older than 7 days. Non-fatal on pre-v67 brains (DROP-target-table check before DELETE). #1737: the cycle threads its abort signal into the embed phase (runPhaseEmbed(engine, dryRun, signal)) so a timed-out cycle's long embed phase honors cancellation and releases gbrain_cycle_locks right away instead of after a full backlog run.

• src/core/cycle/phase-scope.ts — the phase-scope taxonomy: PHASE_SCOPE: Record<CyclePhase, 'source'|'mixed'|'global'> maps each of the 23 phases (source: safe to parallelize per source; global: must serialize across the brain; mixed: brain-wide read + page write, so it stays in the default/global-maintenance lane until decomposed), plus SOURCE_FRESHNESS_PHASES — the deterministic, non-LLM subset (lint, backlinks, sync, extract, extract_facts, recompute_emotional_weight) that alone defines source freshness, so LLM-backed enrichment can never hold a freshness stamp hostage. cycle.ts re-exports both and derives the scheduling lists from them (see the cycle.ts entry). Consumed by runCycle's resolveCyclePhases boundary, the autopilot fanout's per-source enqueue (src/commands/autopilot-fanout.ts), the jobs global-maintenance handler, and doctor's routing-federation phase-scope surface (src/commands/doctor/checks/routing-federation.ts). Pinned by test/autopilot-global-maintenance.test.ts (SOURCE ∪ MIXED ∪ GLOBAL == ALL_PHASES with no overlap; FRESHNESS ∪ BACKGROUND == SOURCE; resolveCyclePhases boundary semantics).

• src/core/cycle/synthesize.ts — Synthesize phase: conversation-transcript-to-brain pipeline, a two-stage cascade (#4152) where cheap scored triage gates frontier synthesis. Reads dream.synthesize.session_corpus_dir, runs runTriagePass (exported; bounded pool dream.triage.concurrency default 4, wall-clock cache-MISS budget dream.triage.max_ms default 5 min — cache hits are free and deferred files report deferred: true, never cached, so the next pass continues) whose judge judgeSignificance emits {score 0-1 ordinal salience, content_type, segments ≤8 verbatim quotes, entities ≤12, reasons} (non-overlapping bands LOW 0-0.29 / MEDIUM 0.30-0.69 / HIGH 0.70-1.0; head 50%/middle 20%/tail 30% sample within dream.triage.max_chars default 24K via safeSplitIndex; out-of-[0,1] scores are unparseable, never clamped) cached in dream_verdicts with the judging model + TRIAGE_VERSION — cache validity requires BOTH to match (switching models.dream.triage re-judges; max_chars/max_tokens deliberately excluded from validity — dream retriage --force re-judges under new sampling knobs). Degenerate verdicts (truncated/refusal/unparseable) are never cached. The gate score >= dream.triage.threshold (default 0.5) is applied at READ time in the fan-out filter, so retuning the threshold re-gates with zero re-judging; the stored worth_processing boolean derives from the fixed DEFAULT_TRIAGE_THRESHOLD constant (back-compat only, never the live dial). Passing files fan out one subagent per chunk with max_turns from dream.synthesize.max_turns (default 16) and a bounded advisory buildTriageMapBlock (exported; score/type/entities + chunk-filtered segments, '' for legacy/degraded verdicts so the prompt is byte-identical to the pre-cascade shape) spliced into buildSynthesisPrompt, with allowed_slug_prefixes (sourced from skills/_brain-filing-rules.json dream_synthesize_paths.globs; when dream.synthesize.output_root is set, loadAllowedSlugPrefixes(outputRoot) remaps the wiki/-rooted globs to the configured namespace — #2415 — and the same root drives the prompt slug templates; default 'wiki', validated against the slug grammar via the exported loadOutputRoot). The phase is source-scoped (#1586): cycle.ts threads cycleSourceId as opts.sourceId → each child's SubagentHandlerData.source_id → the subagent tool registry's OperationContext.sourceId, so put_page writes, collected refs, the summary page, and reverse-writes all target the cycle's resolved source ('default' when unscoped; reverse-writes for the cycle's own source land at brainDir/<slug>.md, foreign sources under brainDir/.sources/<id>/). Orchestrator collects slugs from subagent_tool_executions (NOT pages.updated_at) and reverse-renders DB → markdown via serializeMarkdown. Cooldown via dream.synthesize.last_completion_ts, written ONLY on success. Idempotency keys dream:synth-v2:<enc source>:filename:<enc basename>:<hash16>[:c<i>of<n>] (byte-stable, pinned by test/e2e/dream-synthesize-chunking.test.ts; grammar parsed by exported parseSynthV2Key). Fan-out self-heals idempotency-coalesced rows stranded waiting in a FOREIGN dead dream-inline-* queue (cancel releases the key slot → re-add into the live run's queue) instead of burning the 35-min wait on a row no worker will ever claim. Opt-in per-source daily submission cap dream.synthesize.max_submissions_per_source_per_day (default 0 = off; skips whole files — never partial chunk sets; bypassed for explicit --input/--date/--from/--to targets; count-query failure fails OPEN with a stderr warn). --dry-run runs triage, skips synthesis; deferral-aware headlines append "(N not yet triaged — time budget...)" so a time-boxed cold pass never reads as mass rejection. details.triage (threshold/judged/cache_hits/unreliable/degraded/deferred/below_threshold) + details.synthesis (jobs/avg_turns/max_turns_config) carry the phase telemetry. Subagent never gets fs-write access. renderPageToMarkdown (exported) stamps dream_generated: true + dream_cycle_date into every reverse-write's frontmatter; writeSummaryPage does the same on the summary index — this marker is the explicit identity surface isDreamOutput checks in transcript-discovery.ts. stampDreamProvenance (#2569) additionally persists the same marker into the pages.frontmatter JSONB row (merge via executeRawJsonb, raw object bound to $N::jsonb) for every child-written page BEFORE reverse-rendering, so generated pages are DB-queryable and a later put_page write-through (which re-renders from the DB row) can't erase the stamp. judgeSignificance, JudgeClient, runTriagePass, buildTriageMapBlock, parseSynthV2Key, loadSynthConfig, TRIAGE_VERSION, and DEFAULT_TRIAGE_THRESHOLD are exported; the triage model resolves via an explicit pre-read of models.dream.triage (preferred; through exported resolveAlias) falling back to the standard resolveModel chain (models.dream.synthesize_verdict → deprecated dream.synthesize.verdict_model → tier utility). splitTranscriptByBudget(content, contentHash, maxChars) splits oversized transcripts at paragraph boundaries (## Topic: → --- → \n ladder) using a deterministic offset seeded from the first 32 bits of contentHash so retries chunk identically; per-chunk char budget = MODEL_CONTEXT_TOKENS[resolvedModel] × 0.9 × 3.5 chars/token (non-Anthropic ids fall back to a 180K-token safe default + once-per-process stderr warn); operator overrides dream.synthesize.max_prompt_tokens (floor 100K, wins) and dream.synthesize.max_chunks_per_transcript (default 24); per-chunk subagent job/wait timeouts are dream.synthesize.subagent_timeout_ms / dream.synthesize.subagent_wait_timeout_ms (defaults 30/35 min). Legacy dream:synth: keys are never produced — completed legacy rows are read via loadSuccessfulLegacySynthesisKeys so existing brains skip with already_synthesized_legacy_single_chunk/_chunked instead of re-spending the synthesis model. collectChildPutPageSlugs raw-fetches every (job_id, slug) pair (not SELECT DISTINCT) and rewrites bare-hash6 slugs to <hash6>-c<idx> for chunked children (orchestrator-side, zero Sonnet trust). Cap-hit skips write nothing new to dream_verdicts (the pass's cached triage verdict remains — a free cache hit on retry) and record no synthesis job, so raising the cap on next run re-attempts cleanly. Bounds INITIAL prompt size only; tool-loop turn-N accumulation is caught by terminal-error classification in subagent.ts. Verdict routing is gateway-routed: makeJudgeClient(verdictModel) (exported, replacing makeHaikuClient()) mirrors tryBuildGatewayClient in src/core/think/index.ts — a construction-time provider/key probe returns null on a clear miss (unknown provider id via resolveRecipe AIConfigError, or Anthropic provider with no key via hasAnthropicKey()). The verdict loop wraps judgeSignificance in try/catch for AIConfigError so mid-run provider failures surface as per-transcript worth=false, reasons=['gateway error: ...'] instead of crashing the phase. Canonical config key models.dream.synthesize_verdict (per PER_TASK_KEYS in src/core/model-config.ts); JudgeClient signature preserved verbatim for test-seam stability; CI guard scripts/check-gateway-routed-no-direct-anthropic.sh prevents reintroducing new Anthropic() here or in think/index.ts. At the queue.add boundary a conditional anthropic: prefix is applied ONLY when the resolved model has no colon AND starts with claude- (because resolveModel returns bare ids from TIER_DEFAULTS/DEFAULT_ALIASES and the subagent validator requires provider:model form) — avoids changing the shared constants which would ripple across every resolveModel caller. Pinned by test/cycle/synthesize-gateway-adapter.test.ts, test/e2e/dream-synthesize-pglite.test.ts (gateway-adapter mid-run AIConfigError catch), test/cycle/regression-pr-wave-r1-r2-r4.test.ts. Drain-loop lock renewal runs through exported runDrainRenewalTick (per-call AbortSignal + timeout + re-entrancy guard) — a hung renewLock no longer stacks one checked-out slot per interval firing. Pinned by test/cycle-drain-renewal.test.ts. Execution mode (#4216): dream.synthesize.mode (default oneshot) threads to every child as data.mode alongside oneshot_slug_suffix (the CDX-9 structural suffix contract) and require_writes: true; details.synthesis adds mode/oneshot_jobs/fallback_jobs/agentic_jobs/fallback_reasons plus the #4194 drain telemetry (inline_concurrency_config/effective, drain_ms, queue-wait + runtime p50/p95, dead_jobs, degraded). Pre-retrieval LINK CANDIDATES manifest (link-manifest.ts, dream.synthesize.link_manifest default on) is built once per transcript from the cached triage entities/segment notes and spliced into buildSynthesisPrompt together with an ALLOWED WRITE PATHS block rendered from the trusted allow-list (the oneshot path never sees a tool schema, so the fence lives in the prompt; rule 2 points at the candidates first). Phase outcome gate (CDX-4): ALL children dead/cancelled → phase fails with SYNTH_ALL_CHILDREN_DEAD (fan-out details preserved on the failure); ANY non-completed child → the cooldown stamp is skipped so released idempotency keys retry next run; 'timeout' (parent stopped waiting) degrades but never triggers the all-dead error. Phase-end deferred-embed closure: whenever the phase wrote pages (regardless of mode — an agentic revert still sweeps debt left by earlier oneshot runs), a 120s-bounded embedStalePages (embed-stale.ts) embeds the NULL-embedding chunks of exactly the pages this phase wrote — never a source-wide sweep; the pre-existing stale backlog stays with the budget-tracked embed-backfill machinery — closing the gap on invocation shapes that never reach the global embed phase (--phase synthesize, autopilot per-source NON_GLOBAL_PHASES). Best-effort (never fails a phase that wrote its pages) and stamps the current embedding signature on fully-re-embedded pages so they stay inside the model-drift invalidation contract. The inline drain lives in src/core/cycle/inline-drain.ts (re-exported here for patterns.ts + __testing). Budget clamping (#4168): clamped to the remaining parent-job budget when opts.deadlineAtMs is threaded (#4168, via patterns.ts's clampSubagentBudgets template): the clamp re-runs against the live clock PER SUBMIT (the phase is a fan-out with claim-time-anchored child kill switches, so one phase-start clamp only bounds the first child); under the minimum child budget the phase skips honestly (insufficient_cycle_budget) or defers the remaining transcripts (details.budget_deferred_transcripts), the inline drain stops CLAIMING when the budget can't fit another child and unclaimed children are cancelled + deferred (they'd otherwise strand forever in the run's private queue), each completion wait is additionally bounded by the remaining parent budget (floored at 1s so already-terminal children still resolve), and a deferring run neither writes the 12h cooldown timestamp nor counts deferred transcripts as processed — deferral genuinely retries next cycle

• src/core/cycle/inline-drain.ts — the dream cycle's private-queue drain (peeled from synthesize.ts). runSubagentsInline(engine, queue, queueName, yieldDuringPhase?, handler?, lockMs?, concurrency?) runs N independent drainLoops (#4194; dream.synthesize.inline_concurrency, clamp [1,8], PGLite forced serial at the callsite) sharing the queue via the same SKIP-LOCKED claim fencing workers use — everything job-scoped (lockToken, abort, timeout timer, keepalive, renewTimer, outcome recording) stays loop-local. Pool hygiene: global housekeeping sweeps are leader-only (loop 0) while promoteDelayed runs in every loop; idle claim-poll backs off 1s→5s; a NON-retryable loop-level failure aborts siblings after their current child (a failing child is a job outcome, never a drain crash). Exit only when the queue holds no active/waiting/delayed child (a lease-full bounce's delayed backoff must not strand a child). Outcome routing mirrors the worker: UnrecoverableError → dead immediately; RateLeaseUnavailableError → releaseLeaseFullJob requeue without burning an attempt; timeout terminal. runDrainRenewalTick (per-call AbortSignal + timeout + re-entrancy guard) and the null-safe nearest-rank percentile() telemetry helper are exported. Pinned by test/cycle-synthesize-inline-concurrency.test.ts (loop semantics) + test/e2e/dream-synthesize-concurrency-postgres.test.ts (real-Postgres exact-once + lease-ceiling).

• src/core/cycle/link-manifest.ts — #4216 pre-retrieval LINK CANDIDATES manifest. buildManifestContext(engine, sourceId?) snapshots the source's slugs + basename index once per phase; buildLinkManifest(engine, ctx, verdict, basename, {outputRoot, sourceId}) resolves wikilink candidates ZERO-EMBED from the triage verdict's cached entities/segment notes (basename-index exact/slugified matches first, bounded searchKeyword FTS second), excludes dream-output prefixes (self-consumption guard), renders - [[slug]] — <deterministic first-two-sentence one-liner> under hard caps (20 pages / 2400 chars) with buildTriageMapBlock's injection posture (whitespace-collapse + length caps + a 'data, not instructions' header). Best-effort everywhere — any failure degrades to the manifest-less prompt. Pinned by test/cycle-link-manifest.test.ts.

• scripts/check-gateway-routed-no-direct-anthropic.sh — CI guard that fails the build if src/core/cycle/synthesize.ts or src/core/think/index.ts reintroduces a runtime new Anthropic() constructor call or a value-shaped import Anthropic from '@anthropic-ai/sdk' import. Type-only imports (import type Anthropic from '@anthropic-ai/sdk') stay allowed for adapter types; comment lines (// or * prefixes) are excluded so historical JSDoc doesn't false-fire. Mirrors scripts/check-jsonb-pattern.sh. Wired into bun run verify. Extend GUARDED_FILES when migrating another file off direct SDK construction.

• src/core/cycle/patterns.ts — Patterns phase: cross-session theme detection over reflections within dream.patterns.lookback_days (default 30). Names a pattern only when ≥dream.patterns.min_evidence (default 3) reflections support it. Reflection excerpts use the shared UTF-16-safe truncator; a raw .slice(0, 600) can split an emoji pair and make Postgres reject the subagent job's JSONB payload. Single Sonnet subagent; same allow-list path as synthesize (imports loadAllowedSlugPrefixes + loadOutputRoot from synthesize.ts — #2415: the reflections lookup, prompt slug templates, and allow-list all honor dream.synthesize.output_root, default 'wiki'). Subagent job/wait timeouts are config keys dream.patterns.subagent_timeout_ms / dream.patterns.subagent_wait_timeout_ms (defaults 30/35 min, mirroring the dream.synthesize.* pair). The phase status reflects the child outcome: non-completed outcome with zero writes → fail (error code PATTERNS_CHILD_<OUTCOME>); non-completed with partial writes → warn. Runs AFTER extract so the graph is fresh. The fan-out sets require_writes: true (#4217) so an all-writes-failed child dead-letters instead of reporting completed. Budget clamping (#4168): clamped to the remaining parent-job budget via clampSubagentBudgets when the cycle threads deadlineAtMs — the clamp template synthesize.ts reuses (#4168); MIN_PATTERNS_SUBAGENT_BUDGET_MS gates an honest skip, and CYCLE_DEADLINE_RESERVE_MS is re-exported here from its base-phase.ts home for existing imports

• src/core/cycle/extract-facts.ts — extract_facts cycle phase. Fence is canonical: per-page wipe (deleteFactsForPage) + reinsert from parseFactsFence + extractFactsFromFenceText + engine.insertFacts. #1928: the per-page wipe passes excludeSourcePrefixes: ['cli:'] so conversation facts (written by extract-conversation-facts, on pages with NO ## Facts fence to recreate them from) survive the reconcile instead of being deleted-with-nothing-to-reinsert. The destructive phase no longer inherits a failed sync's full-brain walk: slugs: [] (a real incremental no-op) is distinguished from slugs: undefined (full-walk intent) by presence, not length. runPhaseExtractFacts (cycle.ts) surfaces a warn (net_fact_deletion) when the reconcile deletes at least NET_DELETION_WARN_FLOOR (50) more facts than it reinserts — the exact signature of the conversation-facts wipe, which previously read as a silent ok. Empty-fence guard refuses when legacy rows (row_num IS NULL AND entity_slug IS NOT NULL) pend backfill (status: warn, hint: gbrain apply-migrations --yes). A phantom-redirect pre-pass runs AFTER the legacy-row guard, BEFORE the main reconcile loop: when opts.brainDir is set, runPhantomRedirectPass(engine, brainDir, sourceId, dryRun) walks unprefixed-slug pages capped by GBRAIN_PHANTOM_REDIRECT_LIMIT (default 50). The pass returns touched_canonicals — canonical slugs whose disk fence merged with phantom rows; runExtractFacts UNIONs them into the main reconcile slug set so canonical's DB facts derive from the merged fence in the same cycle (handles phantom-had-only-on-disk-fence). ExtractFactsResult gains six phantom fields: phantomsScanned, phantomsRedirected, phantomsAmbiguous, phantomsSkippedDrift, phantomsLockBusy, phantomsMorePending. Three bubble to CycleReport.totals (phantoms_redirected, phantoms_ambiguous, phantoms_skipped_drift).

• src/core/fence-shared.ts — shared pipe-table primitives for the ## Takes (takes-fence.ts) and ## Facts (facts-fence.ts) fences: parseRowCells, isSeparatorRow, stripStrikethrough, parseStringCell, escapeFenceCell. parseRowCells is escape-aware: \| stays inside its cell and decodes back to a literal | (exact inverse of escapeFenceCell), while any other backslash passes through verbatim so existing fence text (e.g. Windows paths) is byte-stable across a render → parse cycle. This matters because the fence is canonical and reconcile is wipe-and-reinsert — a pipe inside a cell shifting the column layout would corrupt every row behind it on the next reconcile. Pinned by the escape cases in test/facts-fence.test.ts + the full render → parse → reconcile round-trip in test/e2e/facts-fence-reconcile-postgres.test.ts.

• src/core/entities/resolve.ts — Free-form entity name → canonical slug resolution. resolveEntitySlug(engine, source_id, raw): exact slug → alias-exact (an unambiguous page_aliases hit via resolveAliases, verified against LIVE pages since page_aliases has no FK — a stale alias row can never point at a deleted page; fail-open on pre-v110 brains missing the table; ResolutionSource reports alias_exact) → unambiguous bare-name prefix expansion across people/<token>-% + companies/<token>-% → high-specificity fuzzy match for multi-token input (pg_trgm @ 0.7 threshold) → deterministic slugify holding fallback. Bare-name collisions never use popularity as confidence; shared-token company names below the threshold remain unresolved. Two helpers for the phantom-redirect pass: resolvePhantomCanonical(engine, sourceId, phantomSlug) SKIPS the exact-slug step (a phantom slug 'alice' would exact-match itself and no-op the redirect); returns the canonical only when non-null AND contains /. findPrefixCandidates(engine, sourceId, token) is a standalone SQL query returning ALL candidates across PREFIX_EXPANSION_DIRS (hardcoded ['people', 'companies']) via slug LIKE ANY($N::text[]) over patterns dir/token + dir/token-%, cap of 10 ordered by connection_count DESC, slug ASC. Pinned by test/entity-resolve.test.ts (explicit, unique, ambiguous-person, and shared-token-company cases) plus test/phantom-redirect.test.ts (resolvePhantomCanonical 3 cases + findPrefixCandidates 6 cases incl. multi-dir ambiguity and the people/aliceberg-doesn't-match-alice false-positive guard).

• src/core/cycle/phantom-redirect.ts — Phantom-redirect orchestrator. Exports runPhantomRedirectPass(engine, brainDir, sourceId, dryRun): Promise<PhantomPassResult> (per-cycle wrapper acquiring the gbrain-sync writer lock once for the whole pass, 30s bounded retry, walks up to GBRAIN_PHANTOM_REDIRECT_LIMIT unprefixed phantoms) + tryRedirectPhantom(engine, page, sourceId, brainDir, dryRun): Promise<RedirectResult> + stripFenceAndFrontmatterAndLeadingH1 (pure body-shape gate helper — strips facts fence incl. preceding ## Facts heading and the leading H1; zero residue = phantom). Handler order: body-shape gate → resolvePhantomCanonical (bypasses exact-self-match) → findPrefixCandidates ambiguity check → fenceDbDrift bi-directional check → dry-run early exit → materialize canonical via serializeMarkdown if DB-only → append phantom fence rows to canonical's disk fence with (claim, valid_from) dedup-guard + row_num continuation → engine.refreshPageBody with SHA-256 content_hash recomputed via the import-file shape → engine.migrateFactsToCanonical (lossless) → engine.rewriteLinks (DB FK rewrite; wiki-link text rewrite is a documented follow-up) → engine.softDeletePage + engine.deleteFactsForPage(phantom) + fs.unlinkSync(phantomPath). RedirectResult.canonical populated on 'redirected' (incl. dry-run preview) so the caller builds touched_canonicals. Idempotent on re-run: phantom soft-deleted → predicate fails (deleted_at IS NULL); migrate UPDATE matches no rows; dedup-guard prevents double-append.

• src/core/facts/phantom-audit.ts — JSONL audit at ${resolveAuditDir()}/phantoms-YYYY-Www.jsonl. Pattern copy of src/core/audit-slug-fallback.ts (ISO-week rotation, honors GBRAIN_AUDIT_DIR). Exports logPhantomEvent(record) + readRecentPhantomEvents(days) + computePhantomAuditFilename(now?). Records every outcome: redirected | ambiguous | drift | no_canonical | not_phantom_has_residue | pass_skipped_lock_busy. Best-effort writes — stderr warn on failure, never throws. Separate file from stub-guard-audit.ts (distinct consumer + lifecycle: stub-guard logs PREVENTIVE blocks; phantom-audit logs CLEANUP decisions, to be read by a future phantoms_pending doctor check).

• src/core/cycle/emotional-weight.ts — Pure function computeEmotionalWeight({tags, takes}, {highEmotionTags?, userHolder?}). Deterministic 0..1 score: tag-emotion boost (max 0.5, case-insensitive match against HIGH_EMOTION_TAGS seed list), take density (0.1/take, capped at 0.3), take avg weight (0..0.1), user-holder ratio (0..0.1 over active takes; default holder 'garry'). Total clamped to [0..1]. Anglocentric / personal-life-biased seed list intentional; override via config emotional_weight.high_tags (JSON array). userHolder overridable via emotional_weight.user_holder.

• src/core/cycle/anomaly.ts — Pure stats helpers for find_anomalies. meanStddev returns sample stddev (n-1 denominator) and (0,0) for empty input. computeAnomaliesFromBuckets(baseline, today, sigma, limit) takes densified daily-count buckets + today's counts per cohort, returns AnomalyResult[]. Zero-stddev fallback: cohort fires when count > mean + 1, with sigma_observed = count - mean as a finite sort proxy (no NaN). Brand-new cohorts (no baseline) have mean=0, stddev=0 so the fallback fires at count >= 2. Sorted by sigma_observed desc, top limit (default 20). page_slugs capped at 50 per cohort.

• src/core/cycle/recompute-emotional-weight.ts — Cycle phase orchestrator. Two SQL round-trips: engine.batchLoadEmotionalInputs(slugs?) → computeEmotionalWeight (per-row pure function) → engine.setEmotionalWeightBatch(rows). Reads config emotional_weight.high_tags (JSON array, falls back to default seed list on parse error) and emotional_weight.user_holder. Empty affectedSlugs short-circuits with zero-work success. dry-run reports the would-write count without touching the DB. Engine throw bubbles into status: 'fail' with code RECOMPUTE_EMOTIONAL_WEIGHT_FAIL so the cycle continues.

• src/core/transcripts.ts — listRecentTranscripts(engine, opts) library reused by both the gbrain transcripts recent CLI and the get_recent_transcripts MCP op. Reads dream.synthesize.session_corpus_dir + dream.synthesize.meeting_transcripts_dir config (same as discoverTranscripts); walks .txt files within days; applies the isDreamOutput guard from transcript-discovery.ts (skips dream-generated files); returns {path, date, mtime, length, summary}[] sorted newest-first. Summary mode (default true) = first non-empty line + ~250 trailing chars; full mode caps at 100KB/file. Missing/non-existent corpus dirs return [], not error. Trust gate lives in the op handler, not here: the op throws permission_denied for ctx.remote === true; this is a trusted library function used by both the gated op and the local CLI.

• src/core/operations-descriptions.ts — Constants module for tool descriptions. Pinned via test/operations-descriptions.test.ts. Houses GET_RECENT_SALIENCE_DESCRIPTION, FIND_ANOMALIES_DESCRIPTION, GET_RECENT_TRANSCRIPTS_DESCRIPTION plus LIST_PAGES_DESCRIPTION, QUERY_DESCRIPTION, SEARCH_DESCRIPTION. Stable surface for the Tier-2 LLM routing eval — extracting them keeps the test from binding to whatever was in operations.ts at test-run time.

• src/core/cycle/transcript-discovery.ts — Pure filesystem walk for synthesize. discoverTranscripts(opts) filters .txt files by date range, min_chars, and word-boundary regex excludePatterns (medical matches "medical advice" but NOT "comedical"; power users may pass full regex). readSingleTranscript(path) is the gbrain dream --input <file> ad-hoc path. Self-consumption guard: DREAM_OUTPUT_MARKER_RE (anchored at frontmatter open ---\n, optional BOM + CRLF tolerance, scans first 2000 chars for dream_generated: true with case-insensitive value and word boundary on true) drives isDreamOutput(content, bypass=false). Both functions skip matching files and emit a [dream] skipped <basename>: dream_generated marker stderr log (no silent skips). bypassGuard?: boolean on DiscoverOpts and readSingleTranscript's opts disables the guard for the explicit --unsafe-bypass-dream-guard escape hatch only — never auto-applied for --input.

• src/commands/dream.ts — gbrain dream CLI; thin alias over runCycle. Flags: --dry-run, --json, --phase <name>, --pull, --dir <path>, --input <file> (ad-hoc transcript, implies --phase synthesize), --date YYYY-MM-DD, --from <d> --to <d> (backfill range), --unsafe-bypass-dream-guard (plumbed through runCycle.synthBypassDreamGuard → SynthesizePhaseOpts.bypassDreamGuard → discoverTranscripts({bypassGuard}) / readSingleTranscript({bypassGuard}); loud stderr warning at synthesize-phase entry; never auto-applied for --input). Conflict detection: --input + --date exits 2. ISO date validation. --dry-run runs the scored triage pass but skips synthesis (NOT zero LLM calls). Exit 1 on status=failed. resolveBrainDir returns string | null (order: --dir → resolved --source's local_path → global sync.repo_path → null); a checkout-less postgres/Supabase brain runs DB-only phases (incl. resolve_symbol_edges) and skips the 6 filesystem phases with details.reason: 'no_brain_dir'; runDream owns the only hard error (no checkout AND no engine). When --source resolves but has no on-disk checkout, returns null (DB-only) rather than borrowing another source's global sync.repo_path (would mix scopes). Pinned by test/dream-postgres.serial.test.ts. --drain [--window <seconds>] for --phase extract_atoms: runDrain() bypasses the pack-gate and runs the single-hold bounded drain from src/core/cycle/extract-atoms-drain.ts under the same cycleLockIdFor(sourceId) the routine cycle uses (concurrent autopilot tick defers with cycle_already_running), reporting {extracted, skipped, remaining}. Exits EXIT_DRAIN_INCOMPLETE=3 while remaining > 0; a null backlog count (count query FAILED) is also exit 3, never a drained success; LockUnavailableError → cycle_already_running skip (also exit 3). The extract_atoms_backlog doctor check (computeExtractAtomsBacklogCheck) surfaces the silent pack-gated backlog with the exact --drain command; pack-gated cycle skips carry a greppable pack_gated:true marker. dream retriage dispatches on args[0] === 'retriage' BEFORE parseArgs (its flag set never collides with cycle flags; dream retriage --help prints subcommand help engine-free per the same IRON RULE).

• src/commands/dream-retriage.ts — gbrain dream retriage (#4152): re-scores the corpus via the shared runTriagePass (with maxMs: 0 — operator sweeps run to completion; --limit slices the discovered list caller-side) and reconciles the queued private-queue backlog: synth-v2 rows verdict-gated, plus (#4250) any row stranded in a provably-dead dream-inline-* queue regardless of key family (patterns children, legacy grammars) — doctor's orphaned_private_queue check points here, so the repair selects everything the check can flag. Liveness uses ownership correlation (mirrors the doctor check): a live gbrain_cycle_locks row suppresses conversion only for queues born at/after its acquired_at; an older crashed cycle's queue stays repairable while a new cycle runs (unknown birth/acquisition stays fail-safe possibly-live). Spend-gated (outside-voice C12): upfront estimate via canonicalLookup on the resolved triage model, confirmation above SPEND_CONFIRM_USD ($5, in dream-retriage-constants.ts; unpriced models gate on UNPRICED_CONFIRM_FILES=500) unless --yes (--json non-interactive requires --yes above the gate); --max-usd soft-stops via the pass's shouldStop seam (estimate-based). --reconcile-queue (opt-in — cancels queued work): selects waiting/delayed/paused dream:synth-v2:% jobs across ALL queues, parses keys with parseSynthV2Key, then per row: matched below threshold → cancel; matched above threshold but waiting in a stale dream-inline-* queue → cancel as converted_for_resubmit (the C1 backlog conversion — cancelled rows release their idempotency slot so the next cycle re-adds into a live drain); matched above in a live queue → keep; matched-but-unscored → keep (never cancel on missing data); unmatched → keep unless --cancel-unmatched; key-source vs data.source_id disagreement → skip + source_mismatch (C9); status re-checked immediately before each cancel (rows turned active are skipped; residual race matches cancelJob's best-effort contract). Legacy dream:synth: keys are excluded at the SQL LIKE filter — never candidates. --source scopes cancels (other_source counted); --threshold/--since/--force/--dry-run (zero judge calls, zero cancels — cached scores only, uncached files report needs_triage). --audit-rejects <n> (C6) re-judges N stride-sampled below-threshold files with the SYNTHESIS model and reports the disagreement rate — the operator calibration loop. Exit 0 success (even when nothing cancelled), 1 no engine/corpus, 2 usage or declined spend gate. Pinned by test/dream-retriage.test.ts.

• src/commands/friction.ts + src/core/friction.ts — gbrain friction {log,render,list,summary,diff} reporter. Append-only JSONL under $GBRAIN_HOME/.gbrain/friction/<run-id>.jsonl. Schema is a flat extension of StructuredAgentError; every claw-test run opens with a phase-marker/start meta record carrying agent + scenario + harness_schema (agent-name resolution depends on it). Render groups by severity → phase, defaults to --redact for md output (strips $HOME/$CWD to placeholders so reports paste safely in PRs). diff --base <run-or-agent> --compare <run-or-agent> is the cross-agent instrument: exact run-id wins, else agent name resolves to that agent's latest run; identity is (kind, phase, normalized 80-char message prefix — digit runs collapsed so durations/counts don't split identities) over kind ∈ {friction, delight} as MULTISETS (per-severity counts + totals are the compared attributes: count_changed = volume, severity_changed = distribution shape via exact integer proportion test, so a delight→friction flip or a 2×error+1×nit → 1×error+2×nit redistribution always surfaces; markers/interrupted feed the compatibility banner, which warns on scenario/version mismatch); output labels sections "unique to <run>" — an instrument, never a blame-attributor. Run-id resolves from --run-id > $GBRAIN_FRICTION_RUN_ID > standalone.jsonl. Skills the claw-test exercises gain a _friction-protocol.md callout so agents know when to log friction.

• src/commands/claw-test.ts + src/core/claw-test/ — gbrain claw-test [--scenario <name>] [--live --agent <name>]. End-to-end "fresh user" friction harness. Two modes: scripted (CI gate, agent-free) and live (real agent subprocess, $1–2 in tokens). Sets GBRAIN_HOME=<tempdir> for hermeticity and captures gbrain's --progress-json events from each child's stderr to verify expected phases ran (import.files, extract.links_fs, doctor.db_checks). Scripted phases: setup → install_brain (gbrain init --pglite) → import (--no-embed) → query → extract → verify (gbrain doctor --json; top-level status is healthy|warnings|unhealthy) → render. Live mode STAGES the scenario before the agent turn (fresh-install: brain pages + AGENTS.md stub + init; upgrade: seed-first via seed-pglite.ts, NO init — the migration is the scenario under test), prepends a per-run gbrain PATH shim so the BRIEF's bare gbrain runs this checkout, hands BRIEF.md to the agent runner, then verifies a scenario-declared success ORACLE (oracle: {query, min_results, files_exist} in scenario.json; upgrade uses a non-mutating schema-version probe via readPgliteSchemaVersion — doctor would auto-migrate and pass a do-nothing agent). Child-side friction merges into the parent's friction file before tempdir cleanup. Four runners ship (src/core/claw-test/runners/{openclaw,hermes,grok,opencode}.ts; shared detectBinary/filterAllowlistEnv live in agent-runner.ts): openclaw invokes openclaw agent --local --agent <name> --message <brief>; hermes invokes hermes -z <brief> ($HERMES_BIN > which hermes; HERMES_HOME passthrough is the env-allowlist delta; shared BASE_ENV_ALLOWLIST + validateBinPathEnv live in agent-runner.ts); grok (xAI Grok Build, observed shapes in docs/mcp/GROK-CLI-PIN.md) invokes grok -p <brief> --output-format plain ($GROK_BIN > which grok; delta GROK_HOME + XAI_API_KEY; writes a version preamble into the transcript and warns loudly when the operator's ~/.claude.json registers gbrain — grok reads vendor MCP configs for trusted folders); opencode (SST, observed shapes in docs/mcp/OPENCODE-CLI-PIN.md) invokes opencode run <brief> --format default ($OPENCODE_BIN > which opencode; delta = the EXPLICIT multi-provider keys XAI/Google/Gemini/OpenRouter — BASE carries only Anthropic+OpenAI — plus XDG dirs, OPENCODE_CONFIG(_DIR), and OPENCODE_DISABLE_AUTOUPDATE; OPENCODE_CONFIG_CONTENT deliberately absent, it is a config-shadow channel; no --auto — MCP tools fire without it; bare-semver version preamble is the SST-vs-claimant discriminator; warns loudly when the user-global opencode config carries mcp.gbrain). Live-lane posture: the OPERATOR's configured agent + hermetic brain; the fully hermetic lanes are test/e2e/install-real-hermes.serial.test.ts, test/e2e/install-real-grok.serial.test.ts, and test/e2e/install-real-opencode.serial.test.ts (split-gated a step past grok: opencode's anonymous free tier drives MCP tool calls keyless, so even the nonce SMOKE — with a STRUCTURAL gbrain_* tool_use assert via parseOpencodeJsonl — runs in the keyless tier; the paid anthropic leg self-validates its pinned model id against the authed opencode models list before any spend) (grok door is split-gated: keyless compat tier needs only the binary — mcp doctor is grok's honest discriminator, proving the seven-verb surface keyless; paid SMOKE additionally needs XAI_API_KEY and asserts a per-run nonce fact, never the committed one). Transcript capture (transcript-capture.ts) uses fs.createWriteStream with 'drain'-event backpressure (256KB-burst child-stall fix). Env knobs (harness escape hatches, all optional): GBRAIN_BIN_OVERRIDE (child gbrain binary; validated absolute/no-dotdot/no-metacharacter because it's interpolated into the PATH shim — under the bun runtime the harness otherwise synthesizes a launcher so children never exec bun itself), GBRAIN_CLAW_PHASE_TIMEOUT_MS (per-phase child wall clock, default 5 min), GBRAIN_CLAW_AGENT_TIMEOUT_MS (live agent turn wall clock, default 10 min).

• skills/_friction-protocol.md — shared cross-cutting convention skill (like _brain-filing-rules.md). Tells agents when to call gbrain friction log and how to choose a severity. Routes to friction CLI from any skill the claw-test exercises.

• scripts/check-progress-to-stdout.sh — CI guard against regressing to \r-on-stdout progress. Wired into bun run test via scripts/check-progress-to-stdout.sh && bun test in package.json.

• docs/progress-events.md — Canonical JSON event schema reference. Additive only.

• src/core/markdown.ts — Frontmatter parsing + body splitter. coerceFrontmatterString(v) coerces a non-string title/slug/type to a deterministic string at parse time so a YAML-typed value never reaches .toLowerCase() and throws (the #1939 wedge: title: 2024-06-01 parsed as a Date, title: 1458 as a number, and the throw blocked the sync bookmark from advancing); a Date becomes its UTC ISO date (2024-06-01, machine-independent and matching the on-disk token, unlike String(date)), null/undefined become '', everything else uses String(). splitBody requires an explicit timeline sentinel (<!-- timeline -->, --- timeline ---, or --- immediately before ## Timeline/## History). Plain --- in body text is a markdown horizontal rule, not a separator. inferType auto-types /wiki/analysis/ → analysis, /wiki/guides/ → guide, /wiki/hardware/ → hardware, /wiki/architecture/ → architecture, /writing/ → writing (plus existing people/companies/deals/etc heuristics).

• scripts/check-jsonb-pattern.sh — CI grep guard. Fails the build if anyone reintroduces (a) the ${JSON.stringify(x)}::jsonb interpolation pattern (postgres.js v3 double-encodes it), or (b) max_stalled INTEGER NOT NULL DEFAULT 1 in any schema source file (must be DEFAULT 5 to preserve SIGKILL-rescue). It also invokes scripts/check-jsonb-params.mjs and propagates its exit code. Wired into bun test.

• scripts/check-getpage-scoped-write.mjs — CI scanner for the unscoped-check/scoped-write source-isolation bug class: flags any non-test src file containing BOTH a getPage( call with no second argument (or the X ? {sourceId} : undefined any-source-when-unset ternary) AND a write-path call (putPage(/importFromContent(/importFromFile(). Fix pattern: getPage(slug, { sourceId: x ?? 'default' }) (mirror the write's schema default); opt-out marker gbrain-allow-unscoped-getpage: <reason> for documented read-only first-match sites (span, preceding lines, or trailing same-line comment). Grandfathered allowlist is EMPTY. Comment/string-aware balanced-paren span walker (same skeleton as check-jsonb-params.mjs); argv-overridable roots; wired as check:getpage-scope in verify CHECKS + guards-manifest + test/fixtures/guards/check-getpage-scoped-write.mjs/{bad,good}/ + test/check-getpage-scoped-write.test.ts.

• scripts/check-jsonb-params.mjs — AST-lite CI guard for the POSITIONAL jsonb double-encode form the template grep above misses: an executeRaw/executeRawDirect/.unsafe() call whose balanced arg span binds JSON.stringify(x) into a bare $N::jsonb cast (the #2339 class). Walks each call's balanced span respecting strings/templates/comments, handles generic-typed calls (executeRaw<T>(), and allows the sanctioned forms ($N::text::jsonb, $N::text[], executeRawJsonb, sql.json, an inline jsonb-guard-ok comment). PGLite's native db.query is deliberately not scanned (it parses text→jsonb, so the bug can't occur there). Heuristic by design (whole-span correlation; can't see a JSON.stringify assigned to a variable before the call) — the real backstop is the DATABASE_URL-gated e2e parity tests. Scan roots overridable via argv for its self-test (test/check-jsonb-params.test.ts).

• scripts/check-source-id-projection.sh — CI grep guard for the multi-source bug class. Greps src/core/postgres-engine.ts + src/core/pglite-engine.ts for SELECT.*FROM pages projections matching the rowToPage feeder shape (id + slug + type + title) and fails if source_id is missing. Page.source_id is required at the type level; a projection dropping the column produces Page rows with source_id: undefined while TypeScript's : string lies about it. Wired into bun run verify.

• scripts/guards-manifest.tsv + scripts/guard-self-test.sh — THE single registry of scripts/check-* CI guards (52 guards) and its self-test harness. Every guard is classified scanner (greps/parses repo sources — must eventually carry fixtures), buildfresh, or repostate (exempt-with-reason, not fixture-tested). guard-self-test.sh (bun run check:guard-self-test, wired into bun run verify) runs each selftest=yes scanner against known-bad (must exit non-zero) and known-good (must pass) fixture trees under test/fixtures/guards/<guard>/{bad,good}/ via the GBRAIN_GUARD_ROOT env seam, and fails the build when a new scripts/check-* script is missing from the manifest — so a guard whose pattern rots into a permanently-green no-op fails CI instead of masquerading as coverage. The manifest replaces the second hand-synced REGISTRY copy (package.json's check:all chain — deleted); it registers and classifies guards but does not itself schedule them — run-verify-parallel.sh's CHECKS array remains the execution list, and a registered guard is not automatically wired into verify. New guard = new manifest row (+ fixtures if scanner) + a CHECKS entry if it should gate pushes.

• scripts/merge-lcov.ts + scripts/coverage-diff-gate.ts + scripts/coverage-baseline-gate.ts + scripts/update-coverage-baseline.ts + scripts/render-coverage-summary.ts + scripts/coverage-gate-exemptions.txt + scripts/coverage-baseline.json — the coverage measurement + gating cluster; the operating guide is docs/TESTING.md "Coverage lanes and gates". merge-lcov.ts walks artifact dirs for lcov.info + lane-manifest.json, sums DA hits per file:line, normalizes paths repo-relative, and emits a merged lcov + summary JSON (src-only totals/per-dir/per-file, the lineHits extension the diff gate consumes, and never-loaded src files as count + sorted list — deliberately never a percentage, since physical lines ≠ executable lines); --manifest-expect pins the lane set, and a missing/incomplete lane or a shard lane with lcovCount != 1 (the xargs-batching tripwire) marks the summary degraded: true — still exit 0 (degraded is data, and both gates go report-only on it). coverage-diff-gate.ts gates added/changed gate-scoped lines (non-test, non-generated src/**.ts) at ≥80% covered plus zero changed-but-never-loaded files; report-only unless COVERAGE_GATE_ENFORCE=1; a [coverage-exempt: reason] commit trailer passes with a loud warning; coverage-gate-exemptions.txt rows (exact path or trailing-/ prefix; SHRINK-ONLY — additions need a graduation review) are excluded from the gate but still reported ([e2e-exempt] / [subprocess-undercount]); exit contract: 0 = pass or report-only, 1 = fail while enforcing, 2 = infrastructure error (never conflated with a coverage verdict). coverage-baseline-gate.ts reads the baseline via git show origin/master:scripts/coverage-baseline.json (never the working tree, so a PR can't weaken its own bar) and compares corpus-matched sections only (--corpus prCorpus|fullCorpus), failing on >0.5pp global or >1.0pp per-dir drops; provisional: true in the baseline (the current state — both corpus sections unseeded) keeps it report-only regardless of enforcement; update-coverage-baseline.ts writes the working-tree baseline (per-file detail limited to the committed watchlist) and --promote flips provisional: false. render-coverage-summary.ts renders the summary JSON as markdown on stdout for $GITHUB_STEP_SUMMARY, including the behavioral-vs-structural counts from scripts/structural-suites.tsv. Wiring: 13 PR-corpus lanes in test.yml (10 matrix shards + serial + the two dedicated slow jobs) upload coverage-* artifacts and the advisory coverage-report job merges + renders + runs both gates report-only (deliberately absent from test-status/cache-write until graduation); schedule-only coverage-full-{unit,serial,slow,e2e} + coverage-full-report in e2e.yml produce the self-contained nightly fullCorpus number (full e2e glob included) and the coverage-full-merged trend artifact. Collection is COVERAGE_DIR-opt-in in test-shard.sh/run-serial-tests.sh/run-e2e.sh — unique coverage dir per bun process (a reused dir overwrites lcov.info), lane manifest written only on a green run, run-e2e.sh requires an ABSOLUTE COVERAGE_DIR and honors E2E_FILE_TIMEOUT_SECS (both deliberately non-GBRAIN_-prefixed to survive the hermetic env scrub). Bun/JSC emits line records only (function coverage is informational) and no subprocess coverage, so src/cli.ts undercounts. Pinned by test/scripts/merge-lcov.test.ts, test/scripts/coverage-diff-gate.test.ts, test/scripts/render-coverage-summary.test.ts.

• scripts/check-module-size.sh + scripts/module-size-limits.tsv — the module-size ratchet (bun run check:module-size, wired into bun run verify). The TSV commits a per-file wc -l ceiling (path max_lines policy note); four rules, all violations reported before a single exit 1: a file above its ceiling fails (raise a ceiling only as a conscious TSV edit); a ceiling more than 50 lines above the measured size fails (stale slack after a shrink — lower it so the ratchet holds); a TSV row whose path no longer exists fails (remove the row); an unlisted src/**/*.ts (excluding *.generated.ts/*.test.ts) above the 1500-line new-file cap fails (split it or add a row). Policy region-exempt (only src/core/migrate.ts) counts lines OUTSIDE the append-only export const MIGRATIONS = [ … ]; region, so the migrations array grows freely while the surrounding runner logic stays ratcheted. Self-test seams: GBRAIN_GUARD_ROOT, GBRAIN_MODULE_SIZE_SLACK, GBRAIN_MODULE_SIZE_NEWFILE_CAP.

• scripts/classify-tests.ts + scripts/structural-suites.tsv — suite-level behavioral-vs-structural test classification (the intent axis described in docs/TESTING.md "File taxonomy"). Content-based detectors — repo-anchored readFileSync/Bun.file readers, exec-scan grep windows over src|scripts|docs, and the doctorSource()/doctorFileSource() helpers — mark a suite STRUCTURAL when its assertions read repo source/doc text rather than executing product code; tmpdir-anchored reads don't count, and files with detectors but no attributable suite land in an unknown bucket emitted as comment rows (surfaced, never silently dropped). Modes: bare = rewrite the TSV; --check = byte-for-byte regenerate-and-diff freshness (wired as bun run check:structural-manifest in bun run verify via scripts/check-structural-manifest.sh); --summary = counts only. Fix misclassifications in the detector list, never by hand-editing the TSV. render-coverage-summary.ts consumes the TSV for the behavioral-vs-structural line in the CI coverage report.

• scripts/build-pglite-snapshot.ts — bun run build:pglite-snapshot: bakes a post-initSchema() PGLite data dir into test/fixtures/pglite-snapshot.tar + a version file (schema hash line, then dims=/model= lines recording the embedding shape it was baked with). Idempotent (hash short-circuit ~40ms when fresh; rebuilds stale) and concurrency-safe (atomic mkdir lock at test/fixtures/.pglite-snapshot.lock with staleness-verified takeover — a live lock is never stolen; tar written first, version file last, so a crash can't leave a fresh-looking torn fixture; waiter bounded by GBRAIN_SNAPSHOT_LOCK_TIMEOUT_MS, default 120000; an exhausted waiter facing a still-live lock proceeds unlocked as a last resort — the loader's hash/shape gate validates the version file, not the tar bytes). Called through the shared ensure_pglite_snapshot helper in scripts/lib/test-env.sh (also home of detect_cpus + detect_available_mem_mb; sourced by run-unit-parallel.sh, test-shard.sh, run-slow-tests.sh, run-serial-tests.sh, and run-verify-parallel.sh — default-on, opt out GBRAIN_NO_SNAPSHOT=1, no-op when a parent already exported the path, non-fatal on build failure with a one-line "active" echo so a silent cold-init fallback stays visible) and directly by scripts/ci-local.sh; every caller exports GBRAIN_PGLITE_SNAPSHOT. The loader side is tryLoadSnapshot + computeSnapshotSchemaHash (exported from src/core/pglite-engine.ts): the hash folds PGLITE_SCHEMA_SQL, every migration's sql + sqlFor.pglite, AND each migration handler's function source (handler-only migrations are invisible to a sql-only hash); any hash or embedding-shape mismatch warns once and falls through to normal cold init — the snapshot is an optimization, never authoritative. The loader memoizes per process: the schema hash computes once (MIGRATIONS + PGLITE_SCHEMA_SQL are static for the process lifetime) and the version file + ~42MB tar are read once per (path, process) instead of once per engine construction (a full suite constructs 600+ engines); a terminally-unusable path (missing/stale/torn) memoizes as null and is never retried, the tar blob loads lazily only after the FIRST caller passes the shape gate, and the dims/model shape gate itself is deliberately NOT memoized (tests reconfigure the gateway mid-process — a mismatched engine must still fall back to cold init). Accepted limitation: a snapshot rewritten mid-process is not observed; the only writer runs before test fan-out. Test seams __snapshotMemoStatsForTests/__resetSnapshotMemoForTests. Pinned by test/snapshot-shape-guard.test.ts.

• docker-compose.ci.yml + scripts/ci-local.sh — Local CI gate. bun run ci:local spins up four pgvector/pgvector:pg16 services (postgres-1..4) + oven/bun:1 with named volumes (gbrain-ci-pg-data-{1..4}, gbrain-ci-node-modules, gbrain-ci-bun-cache), runs gitleaks on host, smoke-tests scripts/run-e2e.sh argv handling, runs guards + typecheck, then the Tier 1 default: 4-shard parallel unit + E2E (xargs -P4, one Postgres per shard; unit phase keeps DATABASE_URL unset). --no-shard falls back to the legacy unsharded sequential flow (debug aid); --diff runs the diff-aware selector unsharded. Also runs a pgbouncer service (edoburu/pgbouncer, POOL_MODE: transaction, AUTH_TYPE: plain — pg16 stores SCRAM verifiers, so the userlist must hold the plaintext password; IGNORE_STARTUP_PARAMETERS whitelists gbrain's statement_timeout/idle_in_transaction_session_timeout startup params the way the Supabase pooler does) fronting postgres-1 on host port GBRAIN_CI_PGBOUNCER_PORT (default 6543); every E2E invocation exports GBRAIN_PGBOUNCER_URL (pooled; dedicated gbrain_pgbouncer database so it never races the gbrain_test TRUNCATE fixtures) + GBRAIN_PGBOUNCER_DIRECT_URL, consumed by test/e2e/pgbouncer-teardown.test.ts — the transaction-mode teardown bug class (#1972/#2015/#2084) reproduced in the local gate instead of only in production. --no-pull skips upstream pulls; --clean nukes named volumes. Postgres host port defaults to 5434; override with GBRAIN_CI_PG_PORT=NNNN. Stronger gate than PR CI's 2-file Tier 1 set.

• scripts/select-e2e.ts + scripts/e2e-test-map.ts — Diff-aware E2E test selector. Reads three git sources (committed origin/master...HEAD, working-tree HEAD, and git ls-files --others --exclude-standard for untracked NOT-gitignored files), classifies as EMPTY / DOC_ONLY / SRC. Fail-closed: EMPTY → all files; DOC_ONLY (every path matches the README/CLAUDE/AGENTS/CHANGELOG/TODOS allowlist) → empty stdout; SRC → escape-hatch paths (schema, package.json, skills/) trigger all, else the hand-tuned E2E_TEST_MAP glob narrows, and an unmapped src/ change still emits ALL files (never silently nothing). Pure-function exports selectTests, classify, matchGlob. bun run ci:select-e2e prints the current selection on stdout. test/select-e2e.test.ts covers all 4 branches plus 3 regression guards (skills/, untracked files, unmapped src/) — 24 cases.

• scripts/run-e2e.sh — Sequential E2E runner. Accepts an optional argv-driven file list (used by ci:local:diff) and a --dry-run-list flag that prints the resolved file list and exits (used by ci-local.sh's startup smoke-test). Falls back to test/e2e/*.test.ts plus test/phantom-redirect-engine-parity.test.ts when invoked with no args (the phantom-redirect Postgres arm is only reachable through a DATABASE_URL-bearing lane; the unit wrappers strip the URL per #3485, so this lane must carry it). This wrapper is the database-URL opt-in boundary (#3485): it exports GBRAIN_TEST_ALLOW_DATABASE_URL=1 so the bunfig preload guard (test/helpers/database-url-guard-preload.ts) lets the run start, unsets GBRAIN_DATABASE_URL (the e2e suite runs on DATABASE_URL only — an ambient GBRAIN_DATABASE_URL would pass the opt-in yet reach CLI-subprocess paths with no name floor), and its GBRAIN_* env scrub preserves GBRAIN_E2E_ALLOW_DB so the name-floor escape hatch the guard's own error message names stays usable. It also exports GBRAIN_TEST_KEEP_PROVIDER_KEYS=1 so the unit-lane provider-key strip preload (test/helpers/provider-keys-preload.ts) leaves the real keys that live embed/parity e2e tests skip-gate on. Each file runs under a gtimeout/timeout wedge backstop (default signal: SIGTERM — the bun test child installs no JS-level handler for it, so kernel-default termination applies) — 180s default, with a per-file override for known-slow files (skills.test.ts gets 420s: the real ingest-skill run replays every migration, so its floor grows as master adds migrations); the cap is a wedge backstop, not a per-test budget, and bare bun (no outer cap) is the fallback when neither timeout binary is installed.

• scripts/llms-config.ts + scripts/build-llms.ts — Generator for llms.txt (llmstxt.org-spec web index) + llms-full.txt (inlined single-fetch bundle). Curated config drives both. Run bun run build:llms after adding a new doc. LLMS_REPO_BASE env lets forks regenerate with their own URL base. FULL_SIZE_BUDGET (600KB) caps the inline bundle; generator WARNs if exceeded. Committed output has no runtime consumer; committed for GitHub browsing and fork-safe fetching.

• AGENTS.md — Local-clone entry point for non-Claude agents (Codex, Cursor, OpenClaw, Aider). Mirrors CLAUDE.md intent via relative links. Claude Code keeps using CLAUDE.md.

• docs/UPGRADING_DOWNSTREAM_AGENTS.md — Patches for downstream agent skill forks to apply when upgrading. Each release appends a new section; includes diffs for brain-ops, meeting-ingestion, signal-detector, enrich.

• src/core/schema-embedded.ts — AUTO-GENERATED from schema.sql (run bun run build:schema)

• src/schema.sql — Full Postgres + pgvector DDL (source of truth, generates schema-embedded.ts)

• src/core/search/expansion.ts — Multi-query expansion via Haiku. Exports sanitizeQueryForPrompt + sanitizeExpansionOutput (prompt-injection defense-in-depth). Sanitized query is only used for the LLM channel; the original query still drives search.

• recipes/ — Integration recipe files (YAML frontmatter + markdown setup instructions)

• docs/guides/ — Individual SKILLPACK guides (broken out from monolith)

• docs/integrations/ — "Getting Data In" guides and integration docs

• docs/architecture/infra-layer.md — Shared infrastructure documentation

• docs/ethos/THIN_HARNESS_FAT_SKILLS.md — Architecture philosophy essay

• docs/ethos/MARKDOWN_SKILLS_AS_RECIPES.md — "Homebrew for Personal AI" essay

• docs/guides/repo-architecture.md — Two-repo pattern (agent vs brain)

• docs/guides/sub-agent-routing.md — Model routing table for sub-agents

• docs/guides/skill-development.md — 5-step skill development cycle + MECE

• docs/guides/idea-capture.md — Originality distribution, depth test, cross-linking

• docs/guides/quiet-hours.md — Notification hold + timezone-aware delivery

• docs/guides/diligence-ingestion.md — Data room to brain pages pipeline

• docs/designs/HOMEBREW_FOR_PERSONAL_AI.md — 10-star vision for integration system

• docs/mcp/ — Per-client setup guides (Claude Desktop, Code, Cowork, Perplexity)

• BrainBench retrieval benchmark (P@5/R@5 corpus + harness): lives in the separate gbrain-evals repo. Not installed alongside gbrain. Distinct from the in-repo cross-harness memory conformance suite (gbrain eval brainbench — src/eval/brainbench/, corpus at evals/brainbench/, methodology in docs/eval/BRAINBENCH.md).

• skills/_brain-filing-rules.md — Cross-cutting brain filing rules (referenced by all brain-writing skills)

• skills/RESOLVER.md — Skill routing table (based on the agent-fork AGENTS.md pattern) with skills/manifest.json: schema-author wired into the dispatcher with the full functional-area trigger list (compressed routing pattern per the dispatcher convention).

• skills/conventions/ — Cross-cutting rules (quality, brain-first, model-routing, test-before-bulk, cross-modal)

• skills/_output-rules.md — Output quality standards (deterministic links, no slop, exact phrasing)

• skills/signal-detector/SKILL.md — Always-on idea+entity capture on every message

• skills/brain-ops/SKILL.md — Brain-first lookup, read-enrich-write loop, source attribution

• skills/idea-ingest/SKILL.md — Links/articles/tweets with author people page mandatory

• skills/media-ingest/SKILL.md — Video/audio/PDF/book with entity extraction

• skills/meeting-ingestion/SKILL.md — Transcripts with attendee enrichment chaining

• skills/citation-fixer/SKILL.md — Citation format auditing and fixing

• skills/repo-architecture/SKILL.md — Filing rules by primary subject

• skills/skill-creator/SKILL.md — Create conforming skills with MECE check

• skills/daily-task-manager/SKILL.md — Task lifecycle with priority levels

• skills/daily-task-prep/SKILL.md — Morning prep with calendar context

• skills/cross-modal-review/SKILL.md — Quality gate via second model

• skills/cron-scheduler/SKILL.md — Schedule staggering, quiet hours, idempotency

• skills/reports/SKILL.md — Timestamped reports with keyword routing

• skills/testing/SKILL.md — Skill validation framework

• skills/soul-audit/SKILL.md — 6-phase interview for SOUL.md, USER.md, ACCESS_POLICY.md, HEARTBEAT.md

• skills/webhook-transforms/SKILL.md — External events to brain signals

• skills/data-research/SKILL.md — Structured data research: email-to-tracker pipeline with parameterized YAML recipes

• skills/minion-orchestrator/SKILL.md — Unified background-work skill (consolidation of the former minion-orchestrator + gbrain-jobs split). Two lanes: shell jobs via gbrain jobs submit shell --params '{"cmd":"..."}' (operator/CLI only; MCP throws permission_denied for protected names) and LLM subagents via gbrain agent run (user-facing entrypoint). Shared Preconditions block, parent-child DAGs with depth/cap/timeouts, child_done inbox for fan-in, PGLite --follow inline path for dev. Triggers narrowed to "gbrain jobs submit" + "submit a gbrain job" so stats/prune/retry questions fall through to gbrain --help.

• templates/ — SOUL.md, USER.md, ACCESS_POLICY.md, HEARTBEAT.md templates

• skills/migrations/ — Version migration files with feature_pitch YAML frontmatter

• src/commands/publish.ts — Deterministic brain page publisher (code+skill pair, zero LLM calls)

• src/commands/backlinks.ts — Back-link checker and fixer (enforces Iron Law)

• src/commands/lint.ts — Page quality linter (catches LLM artifacts, placeholder dates). runLintCore(opts) walks the tree ONCE; --fix applies fixes during that same scan and reports per-page results through the onPageIssues(relPath, issues, fixedCount) callback (issues = what remains after this run's fix attempt for the page; fixedCount = fixes actually applied), so the summary's auto-fixed count is the true count — a second scan run after fixing would see already-fixed files and report zero. onScanStart fires once with the collected page count for progress wiring. Pinned by test/lint-fix-single-pass.test.ts. Lint rules huge-page (flags pages exceeding content_sanity.bytes_warn) and scraper-junk (flags pages matching any junk pattern). Both reuse assessContent() from src/core/content-sanity.ts so lint, doctor, and ingest share one assessor. lint.ts lifts DB config when ~/.gbrain/ is reachable; falls back to file/env on CI. Pinned by test/lint-content-sanity.test.ts. with src/commands/sources.ts: gbrain lint gains a markup-heavy rule (flags pages whose prose-vs-markup ratio exceeds content_sanity.max_markup_ratio, reusing assessContentSanity so lint/gate/scan share one assessor); pinned by test/lint-content-sanity.test.ts. gbrain sources audit <id> becomes disposition-aware: its dry-run disk scan reports would-quarantine / would-reject / would-flag counts driven by the effective content_sanity.junk_disposition + markup config, so an operator previews the gate's verdict before sync. The content-sanity-audit JSONL (src/core/audit/content-sanity-audit.ts) records the new quarantine/flag dispositions.

• src/commands/report.ts — Structured report saver (audit trail for maintenance/enrichment)

• src/core/destructive-guard.ts — three-layer protection against accidental data loss. assessDestructiveImpact(engine, sourceId) counts pages/chunks/embeddings/files/facts for a source (a fact-only source — a revoked agent's workspace, since facts are the primary agent write lane — is data at stake, not empty; pre-facts brains degrade to 0), plus oauthClientCount — OAuth clients whose source_id references it. checkDestructiveConfirmation(impact, opts) is the fail-closed gate (--confirm-destructive required when data is present; --yes alone is rejected). FK-RESTRICT lifecycle: clientsReferencingSource(engine, sourceId) lists ALL physical OAuth-client rows referencing a source via oauth_clients.source_id — the FK is PHYSICAL (ON DELETE RESTRICT ignores deleted_at), so soft-deleted (revoked-but-retained) rows BLOCK a hard delete too and come back tagged deleted; pre-migration brains without deleted_at fall back to untagged referents (42703-retry idiom) and brains without the table have none by construction. formatClientReferentsBlock renders the shared refusal sources remove/sources purge print (naming each client — [revoked, retained] for soft-deleted rows — + the revoke command) so the raw Postgres FK violation never reaches the operator. softDeleteSource / restoreSource / listArchivedSources / purgeExpiredSources drive the source-level archive lifecycle via sources.archived BOOLEAN, archived_at TIMESTAMPTZ, archive_expires_at TIMESTAMPTZ; purgeExpiredSources SKIPS client-referenced sources via a physical NOT EXISTS (soft-deleted clients count) so recurring maintenance keeps sweeping the rest instead of aborting. Page-level analog: BrainEngine.softDeletePage / restorePage / purgeDeletedPages plus pages.deleted_at TIMESTAMPTZ and a partial purge index. The MCP delete_page op rewires to softDeletePage; ops restore_page (scope: write) and purge_deleted_pages (scope: admin, localOnly: true) round out the surface. Search visibility (buildVisibilityClause in src/core/search/sql-ranking.ts) hides soft-deleted pages and archived sources from searchKeyword / searchKeywordChunks / searchVector in both engines. The autopilot cycle's purge phase calls purgeExpiredSources + engine.purgeDeletedPages(72) so the 72h TTL is real.

• src/commands/pages.ts — gbrain purge-deleted [--older-than HOURS|Nd] [--dry-run] [--json] operator escape hatch. Mirror of gbrain sources purge for the page-level lifecycle. Hard-deletes pages whose deleted_at is older than the cutoff; cascades to content_chunks/page_links/chunk_relations.

• src/core/op-checkpoint.ts — DB-backed checkpoint primitive for long-running ops. Migration v67 introduces op_checkpoints (op TEXT, fingerprint TEXT, completed_keys JSONB, updated_at TIMESTAMPTZ, PK(op, fingerprint)). Per-op fingerprint helpers (embedFingerprint, extractFingerprint, reindexFingerprint, integrityFingerprint, purgeFingerprint) compute sha8(canonical-JSON(relevant-params)) so re-running with the same params resumes from completed_keys and re-running with different params (e.g. --limit 100 vs --limit 200) starts fresh. Cross-worker safe on Postgres (DB row, no file-lock race); PGLite degrades gracefully. Replaces per-op file-backed JSON checkpoints scattered across import.ts, embed.ts, reindex.ts. The 7-day TTL GC runs in the cycle's purge phase. All writes (recordCompleted, clearOpCheckpoint) route through engine.executeRawDirect + withRetry(BULK_RETRY_OPTS) so they survive Supavisor pool exhaustion, and recordCompleted returns boolean (banked vs failed-after-retries) — the 9 non-sync consumers keep its REPLACE-into-completed_keys semantics. Resumable sync uses the additive appendCompleted(key, deltaKeys) / appendCompletedOnce (the latter no-retry for the SIGTERM path) which INSERT a delta into the op_checkpoint_paths child table (migration v115: (op, fingerprint, path) PK, FK to op_checkpoints ON DELETE CASCADE) via a single writable-CTE unnest($3::text[]) write — O(delta), killing the old O(N²) full-set rewrite. loadOpCheckpoint returns the UNION ALL of legacy completed_keys + child-table paths (deduped in JS), so an in-flight upgrade loses nothing. The legacy arm is gated on jsonb_typeof(completed_keys) = 'array' so a non-array (scalar) parent row can't make jsonb_array_elements_text throw "cannot extract elements from a scalar" and take down the whole union (which would discard the valid child rows and lose all banked progress for the key); a third union arm flags the corruption so the loader logs it once and keeps the child rows. Migration v119 adds the op_checkpoints_completed_keys_array CHECK (jsonb_typeof(completed_keys) = 'array') — a DB-enforced, always-on guard that makes the scalar-corruption class structurally impossible going forward; the migration repairs any pre-existing scalar to '[]' under LOCK TABLE ... IN SHARE ROW EXCLUSIVE MODE and src/core/schema-embedded.ts + src/core/pglite-schema.ts ship the same CHECK on fresh installs (a loader hit now implies schema drift, a disabled constraint, or an out-of-band writer). recordCompleted binds its array through $3::text::jsonb (NOT a bare $3::jsonb) so postgres.js .unsafe() doesn't double-encode JSON.stringify(sorted) into the scalar string that CHECK rejects — the #2339 bug that aborted every multi-source sync at the first pin write (PGLite parsed it silently, so it shipped). A DATABASE_URL-gated test/e2e/op-checkpoint-jsonb-parity.test.ts (its own CI job) asserts the array shape on real Postgres. syncFingerprint({sourceId, lastCommit}) keys the sync rows. Pinned by test/op-checkpoint.test.ts (incl. delta-append, union read, cascade clear, durable-write boolean, and the scalar-parent guard). import-checkpoint.ts was NOT migrated to this primitive — both checkpoint systems coexist without conflict; migrating requires async-propagating 4 sync call sites in src/commands/import.ts and rewriting 18 tests, deferred.

• src/core/brain-score-recommendations.ts — pure data layer consumed by both gbrain doctor --remediation-plan / --remediate and gbrain features. computeRecommendations(checks, opts) returns Remediation[] with stable id, content-hash idempotency_key, severity, est_seconds, est_usd_cost, depends_on (references stable ids, not check names — so plan order is reproducible). classifyChecks(report) triages every doctor check three-state into remediable | human_only | blocked (human_only covers RLS warnings and other human-judgment gates; blocked covers dependency chains where a parent check failed). maxReachableScore(checks) computes the ceiling for empty/under-configured brains (no entity pages → graph_coverage caps at 70; no embedding key → embedding_coverage caps at 60). Cost estimates pull from anthropic-pricing.ts (synthesize/patterns/consolidate) and embedding-pricing.ts (embed jobs). Pinned by test/brain-score-recommendations.test.ts (~27 cases incl. determinism, content-hash idempotency, DB-backed checkpoint provenance, three-state triage).

• src/core/abort-check.ts (#1737) — one canonical place for cooperative-abort checks across gbrain's long loops. isAborted(signal?) → boolean (for loops that break and return partial progress). throwIfAborted(signal?, label?) throws an AbortError (name === 'AbortError') at phase boundaries, preferring the signal's reason ('wall-clock'/'lock-lost'/'shutdown') so the unwind self-describes. anySignal(internal, external?) composes two signals into one that fires when EITHER does (platform AbortSignal.any with a manual-relay fallback), returning the internal unchanged when there's no external so non-aborting callers pay nothing. The fix for the #1737 cycle-wedge: the embed phase ignored its abort signal and ran to completion, so gbrain_cycle_locks stayed held and later autopilot cycles skipped with cycle_already_running; threading these checks through runPhaseEmbed → runEmbedCore → embedAll(Stale)/embedPage lets the phase bail and release the lock immediately. Coverage now spans every long cycle-reachable phase (#1972), not just embed: extract (incremental extractForSlugs + the full-walk extractLinksFromDir/extractTimelineFromDir, all via runSlidingPool's signal), extract_facts (per-page loop + the per-page embed signal + runPhantomRedirectPass's 30s lock-retry), consolidate's bucket loop, and lint (which is synchronous, so it awaits a periodic yield to let the signal land). runCycle adds a terminal abort check before stamping last_full_cycle_at so a cancelled cycle never reports a completed full run, plus a per-phase duration_ms warning that names any phase overrunning the worker's 30s force-evict deadline. Pinned by test/abort-check.test.ts + test/cycle-abort.test.ts.

• openclaw.plugin.json — ClawHub bundle plugin manifest

• .codex-plugin/plugin.json + .codex-plugin/mcp.json + .agents/plugins/marketplace.json — the Codex plugin lane: manifest (skills → the committed plugin/ tree; mcpServers → the NON-root mcp.json), the MCP declaration (serve --surface starter --source-guard, code-derived env_vars passthrough), and the codex-native marketplace. Version lockstep with package.json + the claude/openclaw manifests pinned by test/codex-plugin-manifest.test.ts.

• .claude-plugin/plugin.json + .claude-plugin/marketplace.json — the Claude Code plugin lane: inline MCP declaration (command/args/cwd via ${CLAUDE_PLUGIN_ROOT}; no env block — Claude passes the parent env through); the Claude marketplace carries the full plugin PLUS the persona variant entries (gbrain-coding/gbrain-daily → plugin-variants/), while the codex marketplace intentionally stays single-entry until codex's multi-entry handling gets its observation run — variant names are pinned to skills/plugin-lanes.json#personas by test/codex-plugin-manifest.test.ts.

• .agents/gbrain-launcher — shared plugin MCP launcher (sh, Unix-only): GBRAIN_BIN → PATH → ~/.bun/bin resolution, one stderr resolution line, GBRAIN_SURFACE substitute-or-append override for serve argv, actionable exit-127 recovery copy, no auto-install by design. Behavioral branches all pinned in the manifest test.

• skills/plugin-lanes.json — curation record for the plugin lanes: lane set = (openclaw bundle ∖ base_exclusions) ∪ additions, a reason per entry; starter_gaps is the generated snapshot of per-skill beyond-starter MCP ops (refresh via --write-gaps). The openclaw lane's own curation is untouched — plugin users ARE the brain host (the downstream-vs-host inversion).

• scripts/generate-plugin-tree.ts + scripts/check-plugin-tree.sh + plugin/ — generator, byte-diff drift gate (in the skills commit gate), and the committed curated skill tree both plugin lanes ship (65 skills + shared conventions/_*.md deps + a generated README carrying the CLI-primary starter note).

• test/e2e/codex-plugin-install-real.serial.test.ts + test/e2e/claude-plugin-install-real.serial.test.ts — the plugin doors: clean-tree staging (git archive HEAD), real marketplace add/plugin add, snapshot + exec-bit + non-root-mcp.json pins, tools/list starter-surface oracle, cold-home fast-fail, --source-guard block/allow, coexistence + removal probes, auth-gated SMOKE turns. CI: the plugin-doors job in heavy-tests.yml (pinned binary provisioning + expected-pass-count refuse-green).

• src/commands/capture.ts + src/commands/serve-http.ts + src/core/{operations,import-file,types,utils,facts/absorb-log,brainstorm/{orchestrator,error-classify},scope,postgres-engine,pglite-engine}.ts — ingestion-cathedral productionization after a smoke test against Supabase+PgBouncer. Capture frontmatter merge via mergeCaptureFrontmatter (uses gray-matter directly, NOT the lossy parseMarkdown); /ingest null-guard + outer try/catch envelope with !res.headersSent guard; dedup via separate normalize-for-hash (normalizeForHash strips BOM/CRLF/whitespace/NFKC) + body-after-frontmatter-strip on the DB hash (excludes captured_at + ingested_at so capture-cli timestamp variations don't invalidate the chunk cache); friendly pages_source_id_fk rewrite via maybeRewriteSourceFkError on BOTH local + thin-client callRemoteTool catch blocks; facts:absorb 'No database connection' suppression via typed instanceof GBrainError && e.problem check + first-occurrence stack-trace info log (module-scoped _hasLoggedDisconnectedFactsAbsorb flag, test seam _resetFactsAbsorbDisconnectedFlagForTests); CLI help discoverability (capture added to CLI_ONLY_SELF_HELP + pre-engine-bind --help short-circuit in handleCliOnly + a BRAIN section in printHelp); binary-file guard via detectBinaryNullByte(buf) first-8KB NUL scan on --file (Buffer-read, no encoding) and --stdin (readStdinBuffer accumulator); provenance write-through — put_page accepts 3 optional params (source_kind, source_uri, ingested_via; ingested_at server-stamped) + trust gate (when ctx.remote !== false IGNORE client params, server stamps mcp:put_page, fail-closed) + COALESCE-preserve UPDATE semantics (omitting params on a later put_page preserves prior values; first-write-wins); /admin/api/register-client scopes normalization via normalizeScopesInput(raw: unknown) in src/core/scope.ts (accepts string/string[]/missing; rejects ['read write'] space-in-element shape, non-string elements, empty array, unknown scopes; deduped + sorted); brainstorm timeout surfacing via an orchestrator-level try/catch at runBrainstorm entry (single-point wrap covers every internal SQL site, classifies SQLSTATE 57014 via postgres.js .code / .sqlState / message fallback into StructuredAgentError code brainstorm_timeout with a hint covering all 3 PG cancel sub-causes); read-path surfaces all 4 provenance columns via getPage projection + rowToPage 3-state optional read + Page interface; canonical source resolver routes capture through resolveSourceWithTier(engine, parsed.source, cwd); thin-client --source rejection (server-side OAuth client registration owns source scope); the source_kind taxonomy is closed (capture-cli | put_page | mcp:put_page | webhook | file-watcher | inbox-folder | cron-scheduler), --source maps to source_id only. Tests: test/capture-build-content.test.ts, test/capture-runcapture.test.ts, test/put-page-provenance.test.ts, test/scope-normalize.test.ts, test/cli-help-discoverability.test.ts, test/brainstorm-timeout.test.ts; extended test/facts-absorb-log.test.ts, test/import-file.test.ts, test/e2e/engine-parity.test.ts, test/e2e/serve-http-ingest-webhook.test.ts. Report at docs/v0.38-smoke-test-report.md. Follow-ups in TODOS.md: SQL-shape rewrite of listPrefixSampledPages for PgBouncer, magic-byte allowlist for binary detection, --source-kind override flag, ingest_capture handler migration, provenance-history table, facts:absorb root-cause trace.

BrainBench — in a sibling repo

The retrieval-quality BrainBench — the public benchmark for personal-knowledge agent stacks (P@5/R@5/MRR/nDCG corpus + harness) — lives in github.com/garrytan/gbrain-evals. It depends on gbrain as a consumer; gbrain never pulls in the ~5MB eval corpus or the pdf-parse dev dep at install time. The name "BrainBench" now primarily refers to the in-repo cross-harness memory conformance suite (gbrain eval brainbench — see the src/eval/brainbench/ and evals/brainbench/ entries above and docs/eval/BRAINBENCH.md); this section covers the older retrieval benchmark, which stands unchanged.

gbrain's public API surface (the exports map in package.json) is what gbrain-evals consumes: gbrain/engine, gbrain/types, gbrain/operations, gbrain/pglite-engine, gbrain/link-extraction, gbrain/import-file, gbrain/transcription, gbrain/embedding, gbrain/config, gbrain/markdown, gbrain/backoff, gbrain/search/hybrid, gbrain/search/expansion, gbrain/extract. Removing any of these is a breaking change for the gbrain-evals consumer.

Hindsight calibration wave (key files cluster)

The wave that taught gbrain to know how the user tends to be wrong + use that knowledge at every advice surface. Six-migration schema (v67-v72), three new cycle phases, eight expansions, one admin tab. Convention skill at skills/conventions/calibration.md has the agent- facing rules.

Hotfix (migration v80): takes_resolution_consistency CHECK widened to accept quality='unresolvable' AND outcome=NULL as the 4th valid resolution state. The column-level CHECK on resolved_quality (takes_resolved_quality_values) enumerates all 4 states. Take.resolved_quality, TakeResolution.quality, and takes-fence.ts:TakeQuality are 4-state. TakesScorecard gains unresolvable_count

• unresolvable_rate; resolved stays 3-state (correct+incorrect+partial) so historical comparisons hold. finalizeScorecard: unresolvable_rate = unresolvable_count / (resolved + unresolvable_count), NULL when both 0. Spec doc at docs/architecture/calibration-quality-gate-spec.md (falsifiability + per-category calibration ship on top in a follow-up). Pinned by R1-R5 in test/takes-resolution.test.ts and test/migrate.test.ts's v80 structural + PGLite round-trip suite (CHECK admits unresolvable+NULL, still rejects partial+true and unresolvable+true|false, pre-v80 NULL/NULL rows survive).

• src/core/cycle/base-phase.ts — abstract BaseCyclePhase class. Enforces sourceScopeOpts(ctx) threading at the type level; closes the source-isolation leak class structurally for every new phase. Inherits source-scope, budget meter, error envelope, progress reporter. propose_takes / grade_takes / calibration_profile all extend it. The ONE home of CYCLE_DEADLINE_RESERVE_MS (60s carved out of the enclosing job's remaining wall-clock — wait-poll + worker force-evict grace + cleanup headroom; patterns.ts re-exports it, #4168) and of BasePhaseOpts.deadlineAtMs (the enclosing minion job's absolute deadline, threaded via runCycle; null/unset for direct gbrain dream callers — phases then fall back to their derived defaults).
• src/core/cycle/propose-takes.ts — LLM scans markdown prose, proposes gradeable claims to the take_proposals queue. Idempotency cache on (source_id, page_slug, content_hash, prompt_version) composite unique index. Fence-dedup: existing canonical takes passed to the extractor as context. Ships a stub prompt; tuned prompt arrives via the synthetic corpus build. Per-page extractor failures log a warning and continue, but a whole-run condition (per classifyGlobalLlmError in src/core/ai/errors.ts) breaks the page loop with a single combined warning line, sets aborted_global_error, and records a halt in the rollup — auth/billing on the first hit, bare rate_limit only after RATE_LIMIT_HALT_STREAK (3) consecutive hits (a successful call resets the streak). Status: fail when the halt happened with ZERO successful extractor calls (the whole LLM lane is down), otherwise any warnings fold into warn + (N warning(s)) summary suffix, so swallowed failures can't read as a clean ok. llm_calls_succeeded/llm_calls_failed/halted land in details. The phase wall-clock deadline is DERIVED, never a literal (#4168 — the old 30-min literal was bit-identical to the autopilot-cycle handler anchor with non-co-started clocks, making the clean deadline_hit partial-completion path structurally unreachable in production): explicit opts.deadlineMs wins (test seam), else resolveProposeTakesDeadlineMs(deadlineAtMs, now) = PHASE_DEADLINE_FRACTION_OF_JOB (0.8, headroom for grade_takes + calibration_profile which run after it with no deadline of their own) × (remaining job budget − CYCLE_DEADLINE_RESERVE_MS), clamped to the fallback (0.8 × the autopilot-cycle entry in HANDLER_DEFAULT_TIMEOUT_MS — a missing anchor throws at module LOAD, failing the whole cycle visibly). A fractioned value under MIN_PROPOSE_TAKES_BUDGET_MS (2 min) resolves to null and the phase returns an honest skipped with reason: 'insufficient_cycle_budget' (after the cheap provider probe, before any rollup/DB write — records neither a halt nor a completed round; next cycle retries with a fresh budget). Pinned by test/propose-takes.test.ts + test/cycle-phase-deadline-drift.test.ts.
• src/core/cycle/grade-takes.ts — walks unresolved takes older than 6 months, retrieves evidence, asks judge model, caches verdict. Auto-resolve DISABLED by default. Conservative thresholds: >=0.95 single OR >=0.85 ensemble 3/3 unanimous. aggregateEnsemble reuses the cross-modal substrate; fires on the borderline 0.6-0.95 band. Writes to take_grade_cache. Same global-error posture as propose-takes: a judge failure that classifies as a whole-run condition breaks the take loop with aborted_global_error (auth/billing first hit; rate_limit after 3 consecutive takes; fail status when zero judge calls succeeded, else warn + warning count; judge_calls_succeeded/judge_calls_failed/halted in details). Rejected ensemble judges are classified the same way — Promise.allSettled no longer flattens a revoked key or exhausted spend limit into a silent null verdict. Per-take auto-apply failures stay per-take.
• src/core/cycle/calibration-profile.ts — aggregates resolved takes into 2-4 narrative pattern statements + active bias tags. Voice-gated via gateVoice(). Cold-brain skip when <5 resolved. Writes to calibration_profiles with audit columns (voice_gate_passed, voice_gate_attempts, grade_completion).
• src/core/calibration/voice-gate.ts — single gateVoice() function, mode parameter (pattern_statement | nudge | forecast_blurb | dashboard_caption | morning_pulse). 2 regens then template fallback from src/core/calibration/templates.ts. Haiku judge with mode-specific rubrics; all rubrics structurally forbid clinical/preachy voice.
• src/core/calibration/cross-brain.ts — 4-rule contract for cross-brain calibration reads. Local-first → mount-fallback (only with canReadMountsForCtx(ctx) true) → cross-brain attribution via source_brain_id + from_mount → subagent prohibition closes the OAuth-token-to-cross-brain-leak surface. All 4 rules pinned in test/cross-brain-calibration.test.ts.
• src/core/calibration/nudge.ts — real-time pattern surfacing. evaluateAndFireNudge(opts): threshold check (conviction > 0.7, holder match, slug-derived domain hint matches active bias tag) → cooldown probe (14d via take_nudge_log) → fire + log. STDERR-only output; multi-channel deferred.
• src/core/calibration/take-forecast.ts — Brier-trend at write time. Pure math over existing TakesScorecard; no LLM. Returns predicted_brier, bucket_n, overall_brier. Insufficient-data branch at MIN_BUCKET_N = 5. batchForecast memoizes per (holder, domain) tuple.
• src/core/calibration/gstack-coupling.ts — outcome-driven learnings coupling. writeIncorrectResolution(opts) shells out to the gstack-learnings-log binary. Config gate cycle.grade_takes.write_gstack_learnings (default false for external users). Namespace prefix gbrain:calibration:v0.36.1.0: so --undo-wave can scrub.
• src/core/calibration/svg-renderer.ts — server-rendered SVG for the admin SPA Calibration tab. Pure functions: data → SVG string. Inlines design tokens; XSS-safe via escapeXml(). Four renderers: renderBrierTrend, renderDomainBars, renderAbandonedThreadsCard, renderPatternStatementsCard. SPA renders via <TrustedSVG> wrapper behind requireAdmin.
• src/core/calibration/undo-wave.ts — undoWave reverses the wave's mutations: unsets takes.resolved_* for wave-applied resolutions (cross-checks resolved_by so manual writes persist), deletes calibration_profiles, purges nudge logs, marks grade-cache rows applied=false. --dry-run shows counts without writing. Idempotent on wave_version match.
• src/core/calibration/think-ab.ts — A/B harness. runAbTrial calls thinkRunner twice (baseline + with-calibration), records preference to think_ab_results. buildAbReport aggregates over a 30-day window; flags calibration_net_negative when n>=20 + win rate < 45% on decisive trials.
• src/core/calibration/recall-footer.ts — formatter for the morning-pulse calibration block. Cold-brain branch when <5 resolved. Opt-in via the wiring layer.
• src/core/eval-contradictions/calibration-join.ts — cross-reference. tagFindingWithCalibration(finding, profile) returns bias-tag context for contradictions matching active patterns. Returns null when profile missing (output byte-identical to the pre-calibration baseline).
• src/core/think/prompt.ts — anti-bias rewrite. withCalibration option on buildThinkSystemPrompt adds anti-bias rules. buildCalibrationBlock() emits the <calibration> XML. buildThinkUserMessage has TWO shapes: default (question first), and with-calibration (retrieval → calibration → question) when opt-in. Wired into runThink via opts.withCalibration + opts.calibrationHolder.
• src/commands/calibration.ts — CLI: gbrain calibration (read + print), --regenerate, --undo-wave <ver>, ab-report. MCP op get_calibration_profile (scope: read) backs the same data path. Source-scoped via sourceScopeOpts(ctx).
• src/core/owner-holder.ts — single source of truth for "the brain owner" holder string. DEFAULT_OWNER_HOLDER = 'self' (matches the consolidate facts→takes writer + docs/takes-vs-facts.md); resolveOwnerHolder({override, configValue}) returns override > emotional_weight.user_holder config > 'self'. Consumed by the calibration_profile cycle phase, gbrain calibration CLI, the get_calibration_profile op, think's calibration block, emotional-weight's DEFAULT_USER_HOLDER, and doctor's calibration_freshness. Pure; unit-tested in test/owner-holder.test.ts. Does NOT unify owner-identity fragmentation (self/brain/people-<owner>) — tracked separately.
• src/commands/takes.ts — gbrain takes revisit <slug> opens $EDITOR on the source page with a <!-- gbrain:revisit --> cursor marker.
• admin/src/pages/Calibration.tsx — Calibration tab. Single-column layout. <TrustedSVG> wrapper handles dangerouslySetInnerHTML for the server-rendered SVG.
• admin/src/index.css — --text-muted: #777 (WCAG AA contrast bump to ~5.5 on the #0a0a0f bg).
• test/fixtures/calibration/extract-takes-corpus/ — synthetic prompt-tuning corpus. Ships 5 representative pages; full 50-page + 10-page holdout generated by gbrain calibration build-corpus. All anonymized per CLAUDE.md placeholder list.
• scripts/check-synthetic-corpus-privacy.sh — CI guard in bun run verify. Greps for explicit dollar amounts + verifies non-essay fixtures reference at least one placeholder name.
• test/regressions/v0.36.1.0-iron-rule.test.ts — R1-R5 regression inventory; pins all 5 IRON-RULE regressions in one place for future bisects.
• DESIGN.md — repo-root design system. Formalizes the de facto admin tokens. Calibration target for future /plan-design-review and /design-review.

Schema Cathedral v3

The schema-pack mutation surface (the production rebuild of community PR #1321, credit @garrytan-agents): six foundation modules + a mutate skeleton + stats/sync data plane + CLI verbs + MCP ops + a first-class agent skill.

Key files (v0.40.7.0 additions):

• src/core/atomic-write.ts — the shared atomic file writer for brain-repo markdown writers: unique tmp sibling (.tmp.<pid>.<rand>) → write loop until every byte lands (writeSync may legally short-write under disk pressure; a silent short write could atomically install truncated content) → fsync → close → optional verify(onDiskBytes) callback (throw = abort, tmp removed, target untouched) → mode-preserving atomic rename → best-effort parent-directory fsync (rename durability). Born from the backlinks frontmatter-corruption incident; currently consumed by src/commands/backlinks.ts (which verifies with parseMarkdown({validate:true}) before the rename). Rename prevents torn writes, NOT lost updates — read-modify-write callers pair it with withPageLock (backlinks does). Migrating the older per-module copies (skillopt/apply-edits, write-through, lint) is a filed TODO.
• src/core/schema-pack/pack-lock.ts — Atomic O_CREAT|O_EXCL per-pack lock. DELIBERATELY NOT the existsSync + writeFileSync TOCTOU shape from src/core/page-lock.ts. Default 60s TTL, refresh every 10s while withPackLock(fn) runs, --force semantics = "steal stale lock" NOT "skip locking." Lock path per-pack so two packs never block each other.
• src/core/schema-pack/mutate-audit.ts — ISO-week JSONL at ~/.gbrain/audit/schema-mutations-YYYY-Www.jsonl. Privacy-redacted: type names → sha8, prefixes → first slug segment only, matches candidate-audit.ts privacy posture. Logs BOTH success AND failure events so the schema_pack_writability doctor check has signal. summarizeMutations() is the cross-surface parity primitive.
• src/core/schema-pack/registry.ts — resolvePack walks the extends chain (depth cap via EXTENDS_DEPTH_WARN / EXTENDS_DEPTH_HARD_CAP), RETAINS each ancestor manifest, materializes borrow_from, and composes all of it into resolved.manifest through mergeInheritedManifest. Every downstream consumer reads resolved.manifest, so doing the merge here is what makes inheritance visible without per-consumer wiring. borrow_from is selective (only the named types / link_types, and only from the target's OWN declarations), non-transitive, and fail-closed — a missing target throws UnknownPackError via loadByName, matching the extends path; an omitted category borrows none of it. The alias graph + closure hash are computed on the MERGED manifest, so a cross-pack alias cycle surfaces as AliasCycleError at resolve. manifest_sha8 / packIdentity stay the CHILD's own bytes — a parent edit does not move the child's identity, so the invalidation path is what keeps a child honest. invalidatePackCache(name?) walks the extends-chain reverse-graph (editing a parent pack must not leave children stale). tryCachedPack(name) TTL-gated fast path: inside STAT_TTL_MS (default 1000ms, env GBRAIN_PACK_STAT_TTL_MS) returns cached without statting; outside the window it stats every TRACKED file — the extends chain PLUS every borrowed pack — and cascade-invalidates on mtime change (cross-process detection), so editing a borrowed pack invalidates its borrowers. Pinned by test/schema-pack-registry.test.ts + test/schema-pack-merge.test.ts.
• src/core/schema-pack/merge.ts — the pure child-wins composition helper behind resolvePack. mergeInheritedManifest(ancestorsBaseFirst, child, borrowed) returns the fully-composed manifest; precedence is child → borrowed → nearest parent … → base. SIX ingest/query-shaping fields inherit: page_types, link_types, frontmatter_links, enrichable_types, filing_rules, takes_kinds. phases + calibration_domains are DELIBERATELY child-only — they gate real cycle execution (cycle.ts packDeclaresPhase), so inheriting them would silently run phases a pack never declared; mapping_rules, migration_from, extends, borrow_from, and the identity fields are child-only too (all ride the ...child spread). mergePageTypes carries the ordering contract inferTypeFromPack depends on (first-path_prefix-match-wins, array order): the BASE (root, extends: null) pack is the ordered foundation/tail; an override of a base type keeps the base POSITION (Map.set updates the value, keeps insertion order) so base's curated priority survives; a genuinely-new type from ANY non-base layer — child, borrowed, or a middle pack — is PREPENDED nearest-first, so a more-derived prefix wins regardless of chain depth. mergeByKey keeps the first occurrence per key walking highest-precedence-first (the order-insensitive keyed fields); frontmatter_links keys on page_type\x00link_type — a NUL, not a space, because both are unconstrained strings and a space-join would collide {"a b","c"} with {"a","b c"}. mergeUnion backs takes_kinds: UNION not replace, because the Zod default makes an omitted field indistinguishable from an explicit one — so a child can ADD kinds but CANNOT narrow below base ∪ parent. Pure + deterministic: no disk, no engine. Pinned by test/schema-pack-merge.test.ts.
• src/core/schema-pack/best-effort.ts — loadActivePackBestEffort(ctx) returns ResolvedPack | null. Single source of truth for the T1.5 wiring sites. null means EMPTY FILTER (NOT hardcoded defaults — closes the silent-violation bug class).
• src/core/schema-pack/type-usage.ts — stored-type classifier behind the alias-footgun visibility surfaces: classifyStoredType(type, pack) → canonical | alias_of (with the canonical type + path_prefixes[0] filing directory) | undeclared, over a STRUCTURAL pack shape so import-file's thin activePack and the full manifest both satisfy it. sanitizeTypeForDisplay strips control chars + caps length (type strings come from frontmatter and get echoed into terminals); renderTypeWarningSummary renders the once-per-type-per-run lines. Consumers: importFromContent (advisory ImportResult.type_warning at the typeExplicit site — the type is still stored literally, zero filing change), sync/import summary aggregation (+ SyncResult.type_warnings so worker-driven syncs surface counts in job results), the stored_type_is_alias/stored_type_undeclared data-plane lint rules, all gated by config schema.type_warnings (default on; lint rules always active). Pinned by test/schema-type-usage.test.ts.
• src/core/schema-pack/lint-rules.ts — 14 pure rule functions. withMutation's pre-write validation gate composes the 10 file-plane rules; the 4 DB-aware rules (extractable_empty_corpus, mutation_count_anomaly, stored_type_is_alias, stored_type_undeclared) need an engine (CLI --with-db; the stored-type pair accepts LintOpts.sourceId scoping, not yet threaded from the CLI). Single source of truth consumed by CLI lint + MCP schema_lint + the pre-write validation gate. New file-plane rule link_regex_catastrophic_backtrack — advisory ReDoS pre-screen flagging the classic nested-quantifier shapes ((a+)+, (a*)*, (a+)*, (\w+)+) in a link_type's inference.regex via NESTED_QUANTIFIER_RE. WARNING not error: a hard reject would disable the whole pack on upgrade (pages fall back to legacy typing). The runtime input-length cap in redos-guard.ts is the actual safety net; this rule tells the pack author to fix the pattern.
• src/core/schema-pack/redos-guard.ts + src/core/schema-pack/link-inference.ts — ReDoS hardening for pack inference regexes. redos-guard.ts adds MAX_REGEX_INPUT_CHARS (default 64_000, env GBRAIN_MAX_REGEX_INPUT_CHARS) — a hard input-length cap, the real runtime safety net (catastrophic backtracking needs a long input; a link-extraction context is normally a sentence or short paragraph). Over the cap, runRegexBounded throws the tagged RegexInputTooLargeError and the regex is skipped (degrade-to-mentions) without entering the node:vm. link-inference.ts:inferLinkTypeFromPack no-budget branch (test contexts) now routes through runRegexBounded so the input-length cap + per-regex vm timeout (PER_REGEX_TIMEOUT_MS = 50) apply on every path (previously this branch ran new RegExp(pattern).test(context) unbounded — the one ReDoS hole with no timeout). Defensive hardening + diagnostics; the deterministic ~3100-file sync-wedge root cause remains open. Pinned by test/redos-hardening.test.ts + test/schema-pack-lint-rules.test.ts.
• src/core/schema-pack/query-cache-invalidator.ts — invalidateQueryCache(engine, sourceId?) DELETEs query_cache rows so cached search results bound to old page types don't survive a schema mutation.
• src/core/schema-pack/mutate.ts — 8-step withMutation skeleton (bundled-guard → lock → read → mutator → validate → atomic write → audit → invalidate) backs the 11 single-mutation primitives: addTypeToPack, removeTypeFromPack (with reference check), updateTypeOnPack, addAliasToType, removeAliasFromType, addPrefixToType, removePrefixFromType, addLinkTypeToPack, removeLinkTypeFromPack, setExtractableOnType, setExpertRoutingOnType. Each primitive's business-rule validation + transform is factored into a build*Mutator(...) pure (manifest) => manifest function shared with applyMutationsAtomic (the schema_apply_mutations batch entry point) so single-call and batched mutations can never validate differently. applyMutationsAtomic locks + reads the pack file ONCE, applies + lint-validates every mutation in the batch against an in-memory manifest, and calls writePackManifest at MOST ONCE — only after the whole batch checks out — so a batch that fails partway leaves the pack file byte-identical to its pre-batch state. Atomic single write via .tmp + fsync + rename — the pack file on disk is NEVER partial, for either a single mutation or a batch. Inline minimal JSON→YAML emitter so YAML packs stay YAML (does NOT preserve comments — pin pack.json if you care about layout).
• src/core/schema-pack/stats.ts — runStatsCore(engine, opts) returns per-source + aggregate page counts + coverage % + dead_prefixes (declared prefixes with zero matching pages — agent drilldown signal). Multi-source aware (sourceIds[] federated, sourceId single, or whole-brain). PGLite + Postgres parity via executeRaw. Empty brain → coverage:1.0 (vacuous truth).
• src/core/schema-pack/sync.ts — runSyncCore(engine, opts) chunked UPDATE in 1000-row batches per declared prefix. Concurrent writers never block on a single row >100ms. Write-side scoping via ctx.sourceId directly (NOT sourceScopeOpts, which inherits OAuth read federation). Idempotent on --apply re-run.
• src/commands/schema.ts — 14 CLI verbs in the dispatch table: add-type, remove-type, update-type, add-alias, remove-alias, add-prefix, remove-prefix, add-link-type, remove-link-type, set-extractable, set-expert-routing, stats, sync, reload. withConnectedEngine routes loadConfig() through the canonical toEngineConfig() helper and passes the complete result (database_url and database_path) to factory construction and connect, so PGLite schema commands open the configured brain. Lifecycle-grouped help text (Inspection / Activation / Authoring / Discovery+repair). Pinned by test/schema-cli-database-path.serial.test.ts.
• skills/schema-author/SKILL.md — Agent dispatcher for "evolve the schema pack." Triggers: 15+ phrasings incl. "add a page type", "my brain has untyped pages", "propose new types from my corpus", "backfill page types". Explicit Non-goals callout to brain-taxonomist (files one page) and eiirp (schema-check during iteration) so agents pick the right surface. 7-phase workflow: brain → assess → propose → apply → sync → verify → commit. Lists every gbrain schema CLI verb + every MCP op the skill uses. brain_first: exempt frontmatter. Required conformance sections: Contract, Anti-Patterns, Output Format.
• skills/conventions/schema-evolution.md — Canonical convention: "when to add a type vs alias vs prefix." Decision tree: <20 pages → don't pack-codify; 20-100 → alias or narrow prefix on existing type; 100+ → first-class type. Don'ts section + "when to remove a type" + "when to commit the pack" all answered in one place.

T1.5 wiring is partial in v0.40.7.0. Three follow-ups filed in TODOS.md under "v0.40.7.0 Schema Cathedral v3 follow-ups (v0.40.7+)" — enrichment-service.ts union widening ('person' | 'company' → string), facts/eligibility.ts pack-aware ELIGIBLE_TYPES wiring, and 3 doctor checks (schema_pack_coverage, schema_pack_writability, schema_pack_mutation_audit).

• src/core/vector-index.ts + src/commands/doctor.ts:embedding_column_registry — shared pgvector HNSW eligibility policy. hnswIndexExpected(columnType, dims) derives the answer from the canonical vector/halfvec dimension caps already used by migration index generation. Doctor reports an HNSW-less active embedding column as a healthy exact-scan configuration when its declared width exceeds the applicable pgvector cap, and only emits the index repair recipe when an index is actually supported. Pinned at both cap boundaries by test/vector-index-lifecycle.test.ts.

Agent bootstrap cluster (the paste-in desktop-agent install)

Normative docs: docs/designs/AGENT_BOOTSTRAP_DESIGN.md (scope) + docs/designs/AGENT_BOOTSTRAP_PLAN.md (implementation, review-finding IDs inlined). User-facing contract: docs/guides/bootstrap.md. Runbook the paste block fetches: BOOTSTRAP_FOR_AGENTS.md (root; carries a version stamp CI pins to VERSION).

• src/commands/bootstrap.ts — the gbrain bootstrap {status,interview,render,repo,hooks,verify,uninstall,attach} dispatcher. Engine-free everywhere except verify (which opens/closes its own engine — safe because verify runs with no live serve, before host registration). Mutating subcommands run under the workspace bootstrap lock; render is gated on interview complete && confirmed and hard-refuses when the workspace origin is a PUBLIC remote (identity files must never land in a public repo — the same template-door gate status enforces; unverifiable visibility warns and proceeds, treating the origin as public); the provider key routes to the 0600 config sink and never touches interview state; every subcommand appends a line to <home>/bootstrap/install.jsonl. uninstall's opencode teardown sweeps BOTH merged global filenames (under the opencode config-dir bootstrap lock) plus the project opencode.json, expectation-keyed on this workspace's source id (skipOtherSource) — a gbrain entry from a different workspace is skipped with a note, never silently deleted. GBRAIN_BOOTSTRAP_ABORT_AFTER is the deterministic kill-mid-phase test seam.
• src/core/bootstrap/format.ts — agent.json manifest (format_version 1, provisional; initialized sentinel distinguishes a template clone from a bootstrapped workspace) + the machine-local install receipt (<home>/bootstrap/receipt.json) that proves THIS machine ran bootstrap; uninstall is keyed to the receipt, never the repo manifest. Atomic writes; readManifest never throws (typed states incl. conflict markers).
• src/core/bootstrap/assets.ts — every template + the question bank embedded via Bun with { type: 'file' } imports (the chunkers/code.ts pattern) so the compiled binary renders with no repo checkout; DERIVED_TOKENS (GITHUB_REPO_URL, CORPUS_RETENTION_DAYS) is the non-bank half of the template token set the CI bijection guard checks.
• templates/bootstrap/ — the ten {{TOKEN}} identity templates (AGENTS/CLAUDE/SOUL/USER/MEMORY/HEARTBEAT/ACCESS_POLICY/GITHUB/memory-README/gitignore), questions.json (12 asked / 6 required; consent keys; persist:false sink keys), and template-repo/ — the VENDORED deterministic render the release job diffs against before publishing the public template repo. Generic placeholder content only (privacy iron rule; CI-asserted).
• src/core/bootstrap/interview.ts — interview state at <ws>/state/interview.json (committed; multi-device re-render source). Read-back confirm hash: --confirm must present the hash of the exact answer set shown to the human, and ANY later answer change clears the confirmation — the single-batch self-confirm attack is structurally impossible. Set-time enforcement: length caps, reject-lists, allowed-lists, control-char strip, {{ escaping. Conflict-markered files return agent-readable errors, not stack traces.
• src/core/bootstrap/render.ts — token substitution with interview values treated as data (line-leading #/<!--/fence escaping), hard-fail on unresolved tokens, never-clobber + timestamped backups on --force, blank-line collapse, byte floors scaled to answered count. --minimal is the deterministic placeholder mode the template-repo generator uses (byte-identical across runs; leaves required tokens as literal fill-me markers; writes initialized:false). --only never writes agent.json.
• src/core/bootstrap/lock.ts — the bootstrap-run mutex (atomic mkdir + pid liveness + age guard + ownership token; steal requires dead pid AND stale age) and the family's shared typed BootstrapError (GH_MISSING/GH_AUTH carry exit 2 = human action needed).
• src/core/bootstrap/repo.ts / attach.ts / uninstall.ts — private-repo lifecycle. createPrivateRepo: gh gates, slugified name probe, gh repo create --private --source --push, privacy verified via gh api .private (rate-limit/5xx is VERIFY_UNAVAILABLE, distinct from not-private) before any push, idempotency keyed off the remote URL. A pre-existing origin is adopted (disposition 'adopted') when the authed gh user owns it, there's no recorded repo_url, and it is SAFE — empty or already carrying our history (assertAdoptableOrigin; a foreign-content repo is refused ORIGIN_NOT_EMPTY, never a silent no-op); this is the create-repo-first path. Org-owned origins and anything else are refused and pointed at attach. Repo-local git identity is set in both create and adopt paths before commit; repo_url is recorded only after a successful push. attachWorkspace (machine two): requires an initialized manifest, writes this machine's receipt, returns structured wiring steps. uninstallWorkspace: receipt-keyed, refuses under a live serve (read-only lock probe — never opens the engine), removes exactly receipt-recorded paths + marker-keyed host entries, keeps the brain unless --delete-brain AND bootstrap created it; never wholesale-deletes the gbrain home. All gh/git through an injectable ExecRunner seam.
• src/core/bootstrap/hooks.ts + host-specs.ts — host wiring. host-specs.ts is the ONE module owning host-format assumptions (dated spec targets with verifiedAt + doc references: claude-code hooks/settings shapes incl. the 10,000-char hook-output cap and the five hook events; codex mcp-add argv, the streamable-HTTP url+bearer_token config shape verified against codex-cli 0.147.0, codexConfigPath() honoring CODEX_HOME, claudeUserSettingsPath() honoring CLAUDE_CONFIG_DIR/$HOME explicitly — Bun's homedir() ignores a remapped HOME, which would point sandboxed writers at the operator's real settings; the shared resolution lives in the private claudeConfigBase() (CLAUDE_CONFIG_DIR-else-$HOME-else-homedir(), the directory playing the role of ~/.claude — NOT for claudeUserMcpConfigPath, whose default lives at the HOME level as ~/.claude.json), which also feeds claudeUserSkillsDir()/claudeProjectSkillsDir() (native SKILL.md discovery, the harness-bridge install targets; user scope attested, project scope provisional-from-docs) — and the opencode shapes: opencodeConfigDir/opencodeGlobalConfigPath (XDG-only resolution; the .jsonc name preferred for parity with opencode mcp add; OPENCODE_CONFIG/_CONFIG_DIR/_CONFIG_CONTENT deliberately NOT honored — observed INERT in opencode 1.18.18, honoring them would write registrations into a file opencode never reads), opencodeProjectConfigPath, opencodeGlobalSiblingPath (the OTHER member of the global filename pair — writers reconcile mcp.<name> across it because opencode merges both), and OPENCODE_HAS_HOOKS=false — 'gbrain does not wire opencode's plugin/event system yet', not 'opencode has no hooks'). The settings writers are path+marker parameterized: writeClaudeHooksAt/removeClaudeHooksAt take an explicit settings file and a marker VALUE (workspace installs stamp bootstrap-v1 in .claude/settings.local.json; harness installs stamp bootstrap-harness-v1 in user-scope settings or a --project dir — the two coexist and each removal strips only its own; refuseOnForeignGbrainMarker blocks same-file double-wiring), fail-closed on broken JSON (a settings file that doesn't parse THROWS with the path — a writer must never relocate or overwrite a config it can't read), mode-preserving realpath-resolved atomic writes (dotfile symlinks survive), and fixed-or-timestamped backups. addPermissionsAllowEntry/removePermissionsAllowEntry manage the harness lane's mcp__<name> headless pre-approval with set semantics and NO marker (ownership rides the harness receipt; foreign entries always survive); the add path fails CLOSED when an existing permissions key or permissions.allow carries a shape it doesn't understand (host security policy is never rewritten on a guess), while removal leaves shapes it can't read untouched and reports nothing-to-remove. registerClaudeMcp/registerCodexMcp build argv only (Claude Code takes --scope, project default; Codex has no scope flag — codex mcp add is always user-global; -e/--env GBRAIN_SOURCE so MCP writes land in the workspace source, and serve --surface full pinned so a pre-existing mcp_surface: verbs config row can't silently narrow the bootstrap op surface). The opencode workspace lane execs NOTHING — registration is the direct opencode-json.ts write with an INVERTED scope default (user-global; opencode spawns project-config servers with no trust prompt, so MCP_SCOPE=project is an explicit opt-in that writes the committed-candidate opencode.json with a PATH-resolved command and prints the sharing warning), verification is config parse-back + a best-effort opencode mcp list --pure probe — the probe spawns via a held Bun.spawn handle from a fresh EMPTY temp-dir cwd (never the invoking cwd: opencode merges a project opencode.json from cwd and spawns its servers with no trust prompt), is SKIPPED entirely for project scope (printed note; parse-back is authoritative) and on plugin-bearing configs (mcp list is a code-execution surface), and on timeout actually kills the child (SIGTERM → SIGKILL, bounded pipe drain, code 124 into the could-not-confirm branch; probeSpawn is the injectable seam). User-scope writes also reconcile the SIBLING global filename first (ours → removed with a note; foreign → refuse naming both files) so a merge-shadow registration can never survive. detectHarness probes OPENCODE/OPENCODE_PID (set in opencode's bash-tool children, observed 1.18.18). writeCommittedClaudeHooks is the second, COMMITTED hook carrier: it writes marker-keyed entries into the workspace's checked-in .claude/settings.json using buildPortableClaudeHookCommand (PATH-resolved gbrain, fail-open when the binary is absent) so teammates cloning the repo inherit the hooks; committedHookEvents(ws) feeds the local writer's carriedEvents so the two carriers never double-wire an event, and removeClaudeHooks strips both.
• src/core/bootstrap/codex-toml.ts — the ONE direct codex-config writer (the CX2-17 revisit, fired by #4043: codex mcp add cannot express an inline bearer_token, and framework-spawned codex inherits no shell profile for the env-var lane). One [mcp_servers.<name>] table between full-line markers; everything outside survives byte-for-byte. Foreign-server detection PARSES the config (Bun.TOML.parse, no dependency) with our block stripped — a header-only regex would false-negative inline-table/dotted/quoted spellings into a codex-bricking duplicate table; rewrites re-anchor at EOF; renders are parse-validated with an ours-keys-exactly assert before rename; damaged markers refuse; 0600 tmp/target/.bak (the .bak carries the previous token on re-runs); CRLF preserved, missing trailing newline repaired. Also exports renderCodexHttpServerBlock({name, url, bearerToken}) — a MARKER-FREE, parse-validated [mcp_servers.<name>] TOML render for paste-into-config surfaces (gbrain agent register's codex block); rendering only, never writes a file. Pinned by test/codex-toml.test.ts.
• src/core/bootstrap/serve-health.ts — serve /health probe + scopes version-skew floor, peeled from harness.ts (which re-exports the entire surface — import sites never chase the peel). probeServeHealth(mcpUrl, fetchFn, timeoutMs=3000) GETs <base>/health and returns {ok, version?, engine?, detail?}, never throws; fetchFn is an explicit argument (no ambient fetch, no engine, no config). isServeOlderThanScopes(v) compares against the PINNED SCOPES_MIN_SERVE_VERSION constant — a comparison against the moving CLI VERSION would false-flag every scope-aware serve on the next release. An older serve verifies scoped tokens as FULL ACCESS, so callers print the floor line unconditionally.
• src/core/bootstrap/opencode-json.ts — the ONE direct opencode-config writer (workspace stdio lane, harness remote lane, connect --install). ALL edits ride jsonc-parser modify/applyEdits (comments/formatting/EOLs survive byte-for-byte outside the edited range — opencode's own mcp add preserves comments, and JSONC is its effective grammar for BOTH .json and .jsonc filenames, which MERGE when both exist). Ownership is a 4-state STRUCTURAL FINGERPRINT (opencodeEntryKind → ours-same-source | ours-other-source | foreign | absent; GBRAIN_SOURCE EQUALITY for local entries, receipt-url match or the {env:GBRAIN_REMOTE_TOKEN} interpolation for remote), never a marker key (a future strict-schema flip must not brick the host). Distinct read-failure classes (ENOENT create / empty-as-{} / unreadable refuse); foreign refusal on write AND remove; post-render validation (our entry round-trips + every other key survives) keeps the original on failure; 0600 for inline-bearer targets; backups are UNIQUE per operation (<config>.bak-<hex>, returned in the result with writtenText, the exact rendered bytes) so overlapping runs can never clobber each other's snapshot, and a backup is chmod'd 0600 whenever the COPIED content carries an inline bearer (write AND remove paths); the ours-other-source refusal is caller-appropriate (url + --force wording on the remote/expect-url path, GBRAIN_SOURCE wording on the local path); removeOpencodeMcpEntry takes a caller expectation + optional skipOtherSource — the uninstall lane passes THIS workspace's source id so an ours-other-source match becomes a calm skip-with-note (another workspace's registration is never deleted; foreign still refuses); reconcileOpencodeSiblingGlobal clears a same-name gbrain entry from the OTHER global filename before a global write (foreign → refuse naming both files) — opencode merges both, so a leftover sibling entry is a shadow registration; the bun-run ownership lane is ANCHORED (an exact gbrain/gbrain-* path segment in some arg — a gbrainy-fork cli path is NOT ours, fail-closed); parseOpencodeEntryBearer recovers the harness --status token url-matched only; opencodeRemoteEntryExists is the stdio-lane ownership arbiter (codexBlockOwnsName analog). Callers hold acquireBootstrapLock (config-dir → opencode-dir ordering). Pinned by test/opencode-json.test.ts (incl. the fingerprint truth-table suite).
• src/core/bootstrap/atomic-write.ts — the ONE atomic config-file writer for bootstrap host surfaces (rule-of-three extraction): symlink-target-resolving, mode-inheriting (freshMode for new files, forceMode for secret-bearing targets), random-suffix tmp + rename, tmp unlinked best-effort when write/chmod/rename throws (ENOSPC/EACCES never strand .tmp- litter), and the existsSync→realpathSync race falls back to fresh-path resolution instead of throwing raw ENOENT. hooks.ts (JSON), codex-toml.ts (TOML+EOL), and opencode-json.ts (JSONC) all swap through it; serialization and EOL policy stay caller-side.
• src/core/bootstrap/harness.ts — gbrain bootstrap harness (#4043): machine-level wiring of framework-spawned Claude Code/Codex/opencode sessions to a RUNNING gbrain serve --http, no agent.json. The opencode target mirrors the codex posture: forced-wire on explicit --harness opencode (the JSONC writer needs no CLI), one managed mcp.<name> remote entry with the inline bearer header (0600) via opencode-json.ts, rotation across a url change recognized through the PRIOR receipt's url, failed-smoke rollback restoring the run's UNIQUE backup or removing a fresh entry — guarded by a content compare against the exact text this run wrote, so a NEWER registration that landed after the lock released is never clobbered (rollback skips with a note; the fresh mint is revoked either way), with the backup unlinked once consumed or once the smoke verifies — --remove classifying against the receipt url (not-ours skips with a note), and --status bearer recovery via parseOpencodeEntryBearer (url-matched). Consent block in the #4029 honesty register (reach as fact, transcript capture its own numbered item + --no-capture, off-ramps in the same breath; non-TTY requires --yes); /health probe with a loopback guard on --url (remote brains are gbrain connect's charter; --token makes it a pure registrar); mint-first rotation (previous token revoked BY ID only after every target confirms + the bearer smoke passes — clients are never dead mid-swap; revoke-by-name never happens); the smoke is canary-gated: a random same-format bearer must FAIL auth before the real token is sent, so a loopback impostor is caught whichever way it answers, and ANY failed smoke rolls back symmetrically — fresh registrations removed, replaced ones restored (an unrestorable replacement fails the target honestly), the freshly-added pre-approval stripped, and the fresh mint revoked immediately so nothing live stays pointed at an unverified endpoint; the permissions.allow pre-approval only lands after the MCP registration itself confirms; stale prior-target cleanup runs AFTER the smoke passes, so a run that failed to establish its replacement never unwires working prior wiring; write-ahead harness receipt (targets persist as pending at mint time and flip per-target, so a crash leaves consumable state); registration ownership checks (--force to replace a foreign-url server; --remove skips what it no longer owns); user-XOR-project hook scopes; GBRAIN_HOOK_LANE=harness on hook commands so gbrain hook yields to a workspace bootstrap install in the cwd (Claude Code merges settings scopes — same event must not fire twice); Postgres degradation + serve-version-skew honesty lines (isServeOlderThanScopes pinned to SCOPES_MIN_SERVE_VERSION, the first scope-aware release, so later CLI bumps never re-trigger the warning); --status probes the live truth with host-config token recovery (redacted; the Claude Code lane recovers a bearer ONLY from a registration whose URL matches the receipt — never another install's credential; the codex fallback reads OUR managed block at the receipt-recorded path, its url key not yet compared — TODOS.md; the opencode fallback IS url-compared inside parseOpencodeEntryBearer) and honest verify: unavailable degrades, with a cron-honest exit contract: 0 only when serve + token + every target verify and the rotation has converged (honest degrades count), 1 on an unreachable serve, a failed token verify, failed/pending targets, unconverged rotations, or a half-removed receipt (zero targets, minted token awaiting deferred revoke — also a doctor FAIL); no receipt prints honestly and exits 0 in plain mode, 2 under --json; --json on apply emits ONLY the final JSON document on stdout (prose → stderr); --remove is engine-free-first and defers the token revoke with exact instructions under a live PGLite serve. Locks on the gbrain HOME, plus the host config dir around codex/opencode writes, removals, rollbacks, and stale cleanup (stale prior-target cleanup nests the codex/opencode config-dir lock inside the held claude config-dir lock — same claude-first ordering as apply/remove, same-dir skip — so its read-modify-write can't interleave with a concurrent config-dir-locked writer); bootstrap uninstall holds the HOME lock across the whole teardown and runs harness removal FIRST (revoke needs the DB alive; --delete-brain would destroy harness.json) and treats NO_RECEIPT/HOME_GUARD/RECEIPT_MISMATCH as "no workspace install" once harness wiring is cleared. Pinned by test/bootstrap-harness.serial.test.ts + test/e2e/bootstrap-harness-lifecycle.serial.test.ts.
• src/core/token-mint.ts — programmatic legacy-token mint/revoke for the harness lane: mintLegacyToken (scopes → the TEXT[] column; required takesHolders per-token allow-list, harness default ['world']; optional permissions.source_id federation array mirroring the stdio lane's localFederatedSourceIds grant, element 0 = write floor; RETURNING id) and revokeLegacyTokenById (never touches same-name siblings). Exports TOKEN_ID_RE, the canonical token-id shape shared with the auth revoke --id CLI gate. Canonical hashToken/generateToken from src/core/utils.ts. Pinned by test/token-mint.test.ts.
• src/commands/hook.ts — engine-free gbrain hook {session-start,user-prompt,stop,session-end,compact} (zero engine modules in the import graph; a hook must NEVER contend for the PGLite writer lock). When GBRAIN_HOOK_LANE=harness (set on harness-mode hook commands), each event PARSES the cwd's workspace settings carriers — .claude/settings.local.json AND the committed .claude/settings.json — and yields silently only when a live bootstrap-v1 hook entry wires THAT event: the workspace install wins over user-scope harness wiring so the merged settings scopes can't fire the same event twice, unwired events still run, and a repo committing marker-lookalike strings in unrelated fields can't disable the machine-wide capture lane (#4043; fail-open — a read/parse hiccup means the event runs normally). user-prompt: stdin hook JSON → transcript-path confinement → last-4-turns window + cross-turn dedupe (the transcript's hook_additional_context attachments — the blocks WE previously injected — ride priorContextText, deduplicated and capped at PRIOR_CONTEXT_MAX_BYTES (32KB, so the advisory payload can never blow the IPC message cap; one oversized block is skipped without evicting smaller ones), so a page is volunteered once per session, not once per mention; structured extraction only, never raw-turn substring matching) → IPC turn_context (with a feedback-loop channel, --harness <claude-code|codex>, default claude-code) → hookSpecificOutput.additionalContext under an 800ms self-deadline; every path fails open (exit 0, empty stdout) with a typed reason in the heartbeat. Listed in cli.ts's STARTUP_HOOK_SKIP_COMMANDS (per-prompt invocations must never spawn a detached check-update child; membership is pinned by a source grep — the runtime path no-ops under NODE_ENV=test). session-start: file-plane digest (allowlisted MEMORY.md sections, push staleness, prior failures) + crashed-session recovery push gated on an initialized manifest. session-end: confined full-transcript parse → redacted corpus write (session-id filename dedup, retention prune) → parser-drift detection (bytes>0 && turns==0 is loud) → best-effort workspace push. session-start recovery + session-end pushes run in a DETACHED child so the hook returns immediately (a synchronous inline push previously blocked harness startup on a dirty tree); the corpus write is atomic and clears the stale ingested/in-progress sidecars so a resumed session re-ingests its appended transcript. Heartbeat JSONL is counters/reasons only by construction; readHeartbeatTail feeds doctor. GBRAIN_HOOKS=0 kills all events.
• src/core/transcripts/claude-code-jsonl.ts — the Claude Code transcript parser as a dated spec-target (tool_use/tool_result/thinking/image/sidechain/summary/compact-boundary shapes; placeholders for non-text content); also extracts injectedContextBlocks — the hook_additional_context attachment lines a gbrain hook previously injected (verified live against claude CLI 2.1.224; marker-filtered, so a foreign hook's blocks are excluded and another tool's output can't suppress volunteering — a same-user mislabeling guard, not an authenticity check), the user-prompt hook's cross-turn dedupe input; confineTranscriptPath (contained under ~/.claude/projects, .jsonl, lstat-rejects symlinks, byte cap). Fixtures: test/fixtures/conversation-formats/claude-code.jsonl (synthetic, privacy-guarded) + test/fixtures/hook-transcript.jsonl (real captured hook round-trip).
• src/core/context/turn-context.ts — server-side per-turn assembly: reflex pointers + volunteered pages (≤3) + hot facts (always visibility=['world'] — the IPC path never widens what MCP would return) under a "data, not instructions" envelope, trimmed to ≤8KB (the harness caps hook output at 10,000 chars). The result exposes pointers AND post-trim volunteered — exactly what the rendered text carries — so the IPC delivery point can log the feedback loop without ever counting a trimmed-out page. Reuses the hot-memory cache keyed by typed sessionId. Engine-agnostic.
• src/core/context/resolve-ipc.ts (IPC v2) — discriminated-union requests (absent kind = legacy resolve; turn_context carries protocol: 2 + a shared secret from a 0600 file in the data dir, plus an additive channel for feedback-loop attribution — wire channel claims are validated to the harness channels at the logging site, anything else logs as the default hook channel), handler map, named response types, per-kind timeouts/size caps, socket + parent dir permissions set before exposure, server-side source binding (cross-source requests rejected), protocol echo (a response without it = stale serve → loud degradation). The connection handler processes exactly ONE request per connection (trailing bytes mid-await never double-process a line or double-log a delivery); the client clamps a too-big request below the message cap by dropping the advisory priorContextText BEFORE any conversation turn. Delivery seams: onDelivered (resolve kind) and onTurnContextDelivered (turn_context kind) both fire ONLY after the response write succeeds — a block abandoned before the serve responded is never counted (serve's callback logs the delivered block's volunteered pages + pointers to context_volunteer_events under the request channel); write-accept still isn't proof of injection (the client can trim/drop after receipt), which is why the volunteer_channels doctor check reconciles counts against the hook heartbeat. v1 clients and servers interoperate untouched.
• src/core/facts/visibility.ts — resolveDefaultVisibility(engine) / resolveVisibilityParam: the ONE resolver behind all four facts-visibility default sites (facts.default_visibility config key; explicit caller value always wins; invalid values fail closed to private). Bootstrap sets the workspace brain's default to world so the principal's own sessions can recall their facts — a documented, security-relevant knob.
• src/core/sweep.ts + src/commands/sweep.ts — the serve-resident maintenance sweep (the lock owner closes the persistence loop): facts-fence reconciliation (zero-LLM, reuses the cycle extractor with a slug subset), deterministic link/timeline extraction over recent workspace pages (the same cores as gbrain extract — remote put_page deliberately skips these, the sweep is where the graph compounds), and spend-gated corpus ingest (skipped keyless; sidecar-marked exactly-once). Bounded, fail-soft, never throws; armed at serve startup (3s, best-effort) and on 10-min idle ticks through the injectable timer seam, everything unref'd; GBRAIN_SWEEP=0 kills it. gbrain sweep --once is the trusted CLI seam bootstrap verify uses (CLI-only, never over MCP).
• src/core/capability.ts — config-plane keyless/keyed detection + the honest capability report (per-provider keyless banner: OpenAI = semantic search + auto-extraction, Voyage = semantic search, Anthropic = auto-extraction) rendered by verify and the runbook. The extraction probe resolves through the SAME shared resolveEffectiveChatModel the gateway's reconfigure fallback uses (GBRAIN_MODEL > servable file pin > key-aware tier default), so a stale unservable pin degrades identically in the report and at runtime. Key/env fold comes from mergedProviderEnv (src/core/ai/provider-env.ts). Accepted limitation (documented in the module): DB-plane overrides (models.default, facts.extraction_model) are invisible to this engine-less probe; the runtime gate in facts/extract.ts and the engine-aware pre-enqueue gate in facts/backstop.ts are the backstops.
• src/core/secret-scan.ts — pattern scanner for USER workspaces (own minimal allowlist + <ws>/.gbrain-scan-allow per-finding overrides — deliberately NOT the repo's .gitleaks.toml, which is a public-repo CI fixture policy); redacted previews only; redactFindings is the corpus-write mode.
• src/core/workspace-push.ts — gbrain sources push: deny-glob backstop (tracked *.pglite/.env* refused regardless of .gitignore state) → stage FIRST → secret-scan the STAGED index blobs via git cat-file (closes the scan-then-stage TOCTOU — scanned bytes == committed bytes) → commit FIRST → divergence-safe pull → push, under one cross-platform lock (mkdir-atomic; flock is not a dependency — macOS). The pre-push secret gate FAILS CLOSED: an unreadable, oversized (> PUSH_MAX_SCAN_BYTES), or otherwise unscannable staged blob returns blocked_unscannable (nothing committed) instead of sailing through — only a confirmed staged deletion is skipped, and binary/NUL-sniffed blobs are scanned anyway. Statuses map to exit codes in src/commands/sources.ts: pushed/skipped_in_flight → 0; blocked_secrets/blocked_tracked_deny/blocked_unscannable/refused_visibility → 5; pull_conflict/push_failed/other → 1. Refuses public AND unverifiable remotes (never fail-open); pushes even on clean trees; writes <home>/bootstrap/push-status.json. Parent-repo-aware (a source may be a subdirectory of the workspace repo).
• src/core/gbrain-home.ts — the single GBRAIN_HOME resolution choke point (delegates to config's parent-dir semantics; 0700 on create) — durability, push, hooks, and bootstrap all route through it so home semantics cannot drift.
• src/core/bootstrap/verify.ts + status.ts — verify is the definition of done: fail-soft check suite over the REAL write path (put_page op → write-through file under brain/ → in-process sweep → graph floor via link tables → recall), the keyless magic-moment check (## Facts fence → zero-LLM reconciliation → world-visibility read-back), source_id collision resolution (as the one bootstrap subcommand holding an engine: a manifest source_id already registered to a DIFFERENT checkout → derives a stable workspace-<8char-path-hash>, persists it to agent.json, names the re-register steps — every consumer reads manifest.source_id), token sweep, byte floors, secret scan, deny globs, repo privacy, hooks smoke (in-process IPC), capability report, first-run tour; snapshots kept last-5 under <home>/bootstrap/. status owns the ordered PHASES list (the runbook defers to it), artifact-first detection, install.jsonl, the runbook version-stamp skew check, and the support blob doctor/agents relay verbatim.
• src/core/bootstrap/template-repo.ts + scripts/generate-template-repo.ts — deterministic public-template generation (render --minimal + placeholder manifest + stamped README); published only by the release workflow after diffing against the vendored tree.
• scripts/check-bootstrap-tag.sh / scripts/check-bootstrap-templates.sh — CI guards: sanctioned distribution ref only (latest-stable; the release job advances it after assets publish) + runbook stamp == VERSION; template↔question-bank token bijection + placeholder-only assertion + offline generator↔vendored byte-diff + runbook-phase↔status.ts consistency. Both skip gracefully when their subjects are absent.
• src/core/cycle/synthesize-concepts.ts concept-quality addendum — eligible groups are processed deterministically by tier, descending atom count, then concept slug so the fixed LLM budget reaches the strongest evidence first regardless of database row order. Every page and phase receipt distinguishes llm, intended deterministic_tier, budget_fallback, and error_fallback synthesis modes.