# 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`).

- `src/core/operations.ts` — Contract-first operation definitions (the foundation). 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. `put_page` enforces: when `viaSubagent` and `allowedSlugPrefixes` is set, slug must match the allow-list; else the legacy `wiki/agents/<id>/...` namespace check applies. Auto-link skipped only when `remote=true && !trustedWorkspace`. Every `Operation` carries `scope?: 'read' | 'write' | 'admin'` + `localOnly?: boolean`; `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. `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/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`. `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.
- `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 CLI disconnects." `registerBackgroundWorkDrainer({name, order, drain(timeoutMs), abort?})` + `drainAllBackgroundWorkForCliExit({timeoutMs})` over a `Map<name, BackgroundWorkDrainer>` (idempotent registration by name; `__registerDrainerForTest` returns an unregister handle). 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`. Best-effort per drainer: one sink's failure never blocks the others or the disconnect. FOUR sinks register at module import (rule-of-four): `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`). Both CLI-exit paths (`src/cli.ts` op-dispatch finally + `handleCliOnly` finally) call it before `engine.disconnect()` — closing the PGLite busy-loop where `db.close()` raced an in-flight job and pinned the single-writer lock (#1762). 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 op-dispatch + handleCliOnly force-exit timers `process.exit(process.exitCode ?? 0)` so a hung disconnect can't mask an errored op as success; `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 hanging past the 10s force-exit (#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/hybrid.ts` extension — `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.
- `src/core/search/explain-formatter.ts` — renders `SearchResult[]` as a multi-line per-result breakdown for `gbrain search --explain`. Reads every boost-stamping field. 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` extension — `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).
- `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` 0.2.0, additive — older hosts work unchanged; the plugin entry maps `ctx.resolveEntities`/`ctx.brainQuery` onto it). `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), 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). `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); synopsis runs through `stripTakesFence`/`stripFactsFence` (the same privacy boundary `get_page` applies) so private facts never reach the prompt; suppression scans `priorContextText` only; 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). `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`). Config: `retrieval_reflex` + `retrieval_reflex_max_pointers` in `src/core/config.ts`. 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/context/resolve-ipc.test.ts`, `test/doctor-retrieval-reflex.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`.
- `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-options.ts` extension — `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.
- `src/commands/search.ts:gbrain search stats` extension — `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`.
- `src/commands/doctor.ts` extension — `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`.
- `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. `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 emits an actionable error (macOS 26.3 WASM bug #223, points at `gbrain doctor`); the lock is released on failure so the next process can retry cleanly. `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. `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`) 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`. Exports `classifyPgliteInitError(message): 'bunfs' | 'macos-26-3' | 'unknown'` + `buildPgliteInitErrorMessage(verdict, original)` 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; `macos-26-3` keeps the #223 link; `unknown` falls through); Pinned by `test/pglite-init-classifier.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).
- `src/core/postgres-engine.ts` — Postgres + pgvector implementation (Supabase / self-hosted). `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. `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`); 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`.
- `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/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`. Entries: OpenAI text-embedding-3-large ($0.13/1M), 3-small ($0.02/1M), ada-002 ($0.10/1M), Voyage 3-large ($0.18/1M), 3 ($0.06/1M). `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 [--limit N] [--dry-run] [--json] [--no-embed] [--repo PATH]`. Walks `pages WHERE page_kind = 'markdown' AND chunker_version < MARKDOWN_CHUNKER_VERSION` in 100-row batches ordered by id. 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. Idempotent — partial-completion re-runs pick up via id-ordered batches. 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`.
- `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). 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/commands/sync.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.
- `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. `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 block teardown until the CLI's 10s force-exit fires and truncates stdout (#1959); it never throws. `connection-manager.ts` ends its direct + read pools concurrently through the same helper so the per-pool bounds don't stack.
- `src/commands/migrate-engine.ts` — Bidirectional engine migration (`gbrain migrate --to supabase/pglite`).
- `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`.
- `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), dot-prefix dirs, `ops/`, and `*.raw` sidecars; `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.
- `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) → `acknowledged` (human resolved via `gbrain sync --skip-failed`) or `auto_skipped` (chronic). `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/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).
- `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/git-remote.ts` — SSRF-hardened git invocations for remote-source `cloneRepo` and `pullRepo`. 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)`).
- `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/intent.ts` — Query intent classifier (entity/temporal/event/general → auto-selects detail level).
- `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 "Mingtang"). 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)` names the strongest signal (precedence: `alias_hit` > `exact_title_match` > `high_vector_match` (base ≥ `HIGH_MATCH_FLOOR=0.85`) > `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)` stamps `evidence` + `create_safety` in place once at pipeline end (after the alias hop, before slice); idempotent.
- `src/core/search/mode.ts` extension — `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`.
- `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/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-4o` / `anthropic:claude-opus-4-7` / `google:gemini-1.5-pro`. `estimateCost()` exports a small per-model pricing table (drifts; refresh alongside model-family bumps).
- `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`. 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-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).
- `src/commands/autopilot.ts` extension — 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`.
- `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); `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 extracts `sourceScopeOpts(ctx)` to scalar `sourceId` / `allowedSources` / `remote` on `RunThinkOpts` so federated-read OAuth clients can't see trajectory rows outside their source scope. 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/core/operations.ts` extension (orphans fix) — `findOrphanPages` (both engines) filters `p.deleted_at IS NULL` on the candidate side AND adds `JOIN pages src ON src.id = l.from_page_id WHERE src.deleted_at IS NULL` to the EXISTS subquery on the link-source side, so soft-deleted pages don't appear as orphans AND links from soft-deleted source pages don't suppress live pages from orphan results. Pinned by `test/orphans.test.ts`'s soft-delete cases.
- `src/commands/eval-longmemeval.ts` + `src/eval/longmemeval/{harness,adapter,sanitize}.ts` — `gbrain eval longmemeval <dataset.jsonl>` runs the public [LongMemEval](https://huggingface.co/datasets/xiaowu0162/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.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`. 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.
- `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. `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): 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). Pinned by `test/sync-cost-preview.test.ts` + `test/embedding-signature-stale.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).
- `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). `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/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'`; `'query'` when threaded via `providerOptions.openaiCompatible.input_type`) 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 `${recipe.base_url}/models/rerank` with bearer auth, returns `RerankResult[]` sorted by relevance. `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 at `:595`, Layer 2 per-embedding base64 at `:619`) 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).
- `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.
- `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: `openai/text-embedding-3-small` at 1536 dims with Matryoshka `dims_options: [512, 768, 1024, 1536]`; `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 `isAnthropicProvider()` in `src/core/model-config.ts` which hard-pins gbrain's subagent infra to Anthropic-direct. 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. 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). Exports `AutocutConfig`, `DEFAULT_AUTOCUT` (frozen: `enabled=true, jumpRatio=0.20, minKeep=1`), `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` (conservative false, balanced/tokenmax true@0.20) 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). `KNOBS_HASH_VERSION` is 8 (title_boost claimed 7; autocut appends 8 — 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`. 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 v=8 knobsHash assertions in `test/search-mode.test.ts`.
- `src/core/ai/recipes/voyage.ts` — Voyage AI openai-compatible recipe. 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. Recipe docstring at `:7-16` names the seven hosted flexible-dim 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`) and notes `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`); 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/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 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. 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 → caller warns `BUDGET_METER_NO_PRICING` once and runs unbounded). `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/ai/gateway.ts: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.
- `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`. 8-step resolution chain: cliFlag → deprecated key → config key → `models.default` → `models.tier.<tier>` → env var → `TIER_DEFAULTS[tier]` → caller fallback. `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). `enforceSubagentAnthropic()` is the layer-2 runtime guard: when `tier === 'subagent'` resolves non-Anthropic, it emits a once-per-`(source, model)` stderr warn AND falls back to `TIER_DEFAULTS.subagent` (the Anthropic Messages API tool-loop can't run on OpenAI/Gemini). `_resetDeprecationWarningsForTest()` also clears `_subagentTierWarningsEmitted`. Pinned by `test/model-config.serial.test.ts`.
- `src/core/ai/model-resolver.ts` — Recipe-touchpoint validator. `assertTouchpoint(recipe, touchpoint, modelId, extendedModels?)` takes an optional 4th `extendedModels: ReadonlySet<string>`: when the modelId is in that set the native-recipe allowlist throw is bypassed (user explicitly opted in via config, so provider rejection surfaces as `model_not_found` at HTTP call time and `gbrain models doctor` catches it earlier). Default code paths with hardcoded model strings MUST NOT pass `extendedModels` — source typos still fail fast (the fail-fast contract for chat + expand + embed stays intact).
- `src/core/ai/gateway.ts` extension — module-scoped `_extendedModels: Map<providerId, Set<modelId>>` registry feeds `assertTouchpoint`'s 4th-arg path. `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` seam mirrors `__setEmbedTransportForTests` so tests drive `chat()` with a stubbed transport.
- `src/core/minions/queue.ts` extension — `MinionQueue.add()` rejects `subagent` jobs whose `data.model` resolves via `isAnthropicProvider()` to a non-Anthropic provider. Lazy-imports `model-config.ts` to avoid pulling engine types into queue's eager-load surface. Layer 1 of the three-layer subagent provider enforcement (layers 2+3: `model-config.ts:enforceSubagentAnthropic` runtime fallback + `src/commands/doctor.ts` `subagent_provider` check). Pinned by `test/agent-cli.test.ts`.
- `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 (11 `PER_TASK_KEYS`: `models.dream.synthesize`, `models.dream.patterns`, `models.drift`, `models.auto_think`, `models.think`, `models.subagent`, `facts.extraction_model`, `models.eval.longmemeval`, `models.expansion`, `models.chat`, `models.dream.synthesize_verdict`), 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}`. 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` + file-plane `openai/anthropic/zeroentropy_api_key` 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/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. Single owner of folding file-plane API keys (openai/anthropic/zeroentropy) into the gateway env and threading local-server `*_BASE_URL` env vars into base_urls; `process.env` wins. Pinned by `test/ai/build-gateway-config.test.ts`.
- `src/commands/doctor.ts` extension — `subagent_provider` check (layer 3 of 3). Warns when `models.tier.subagent` is explicitly set non-Anthropic (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`.
- `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` (regex-based, not full YAML). 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). Two ops register in `src/core/operations.ts` (`list_skills` with optional `section` filter + `cliHints:{name:'skills'}`; `get_skill` taking `name` + `cliHints:{name:'skill', positional:['name']}`) and 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`). `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`; `checkResolvable` dedupes so the reachability count counts each skill once. Pinned by `test/check-resolvable.test.ts` (11 cases: bold+plain forms, Unicode+ASCII suffix strip, ellipsis filter, empty pipe segments, mixed shapes, prose-bullet rejection) + `test/check-resolvable-openclaw-compact.test.ts` (8 cases over `test/fixtures/openclaw-compact-resolver/` and `test/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/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/{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` (Garry-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; trailing-slash normalized for unambiguous prefix matching. `isPathAllowed(candidate, config)` is the runtime per-file gate (scan_paths prefix-match with directory-boundary correctness; deny_paths overrides). Pinned by `test/archive-crawler-config.test.ts` (19 cases).
- `test/helpers/cli-pty-runner.ts` — generic real-PTY harness (~470 lines) using pure `Bun.spawn({terminal:})` (Bun 1.3.10+; engines.bun pin in package.json). Generic primitives only, no plan-mode orchestrators. Exports `launchPty`, `resolveBinary`, `stripAnsi`, `parseNumberedOptions`, `optionsSignature`, `isNumberedOptionListVisible`, `isTrustDialogVisible`. Self-tests in `test/cli-pty-runner.test.ts` (24 cases).
- `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. 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. 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. Reusable beyond sync (autopilot/cycle are follow-up adopters). Pinned by `test/process-watchdog.test.ts` (pure decision matrix + 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/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?}`. 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` (11 cases).
- `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 BOTH `lock-renewal-audit.ts` AND `batch-retry-audit.ts`. 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/minions/lock-renewal-tick.ts` — Pure extracted function from `MinionWorker.launchJob`'s setInterval body; the structural fix that closes the production unhandledRejection crash class. Exports `runLockRenewalTick(deps, state) → Promise<TickResult>` + `resolveLockRenewalKnobs(env, lockDuration) → LockRenewalKnobs`. Three env knobs, all parsed as positive integers with stderr-warn-once-per-process on bad input + default fallback: `GBRAIN_LOCK_RENEWAL_MAX_FAILURES` (default 3, audit-labeling only — abort triggering is time-based), `GBRAIN_LOCK_RENEWAL_CALL_TIMEOUT_MS` (default `lockDuration/3`, bounds the hung-renewLock vector via `Promise.race`), `GBRAIN_LOCK_RENEWAL_SAFETY_MARGIN_MS` (default `lockDuration/6`, ensures release before stall-detector reclaim). The tick checks `state.cancelled()` at three guard points (entry, after await resolves, after await throws) so a long renewLock that resolves after the job ended bails cleanly. Result type is a tagged union `{kind: 'ok' | 'cancelled' | 'lock_lost' | 'should_abort', reason?}`; all `abort.abort()` / `clearInterval` side effects live in the worker's closure scope, not the pure function. Audit calls wrapped in inner try/catch (defense-in-depth). `LockRenewalDeps` has an optional `reconnect?` callback; the renewal-tick's catch branch (after retryable-error classification + the time-based deadline check, before the inter-tick sleep) calls it ONCE, wrapped in its own try/catch. Recovers the mid-process-disconnect case (nulled `_sql`) where postgres.js auto-reconnect can't help because the engine's pool reference is gone. Deliberately NOT a background `withRetry` (a 12s background retry could refresh a lock AFTER the worker already decided `lock-renewal-failed` and another worker reclaimed it → two holders); the reconnect is bounded by the same `callTimeoutMs` race + abort signal as renewLock itself. Pinned by `test/worker-lock-renewal.test.ts` (18 hermetic state-machine cases — no fs, no PGLite, no real setInterval).
- `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.
- `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/commands/doctor.ts` extension — `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`.
- `src/commands/doctor.ts` extension — `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`.
- `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/commands/autopilot.ts` extension — 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`.
- `src/commands/doctor.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).
- `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). 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.
- `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` starts with `engine.countStaleChunks()` (single SELECT count(*) WHERE embedding IS NULL, ~50 bytes wire) so a fully-embedded brain short-circuits with no further reads. 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`. 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 unconditionally per page. 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.
- `src/core/conversation-parser/` — 14-pattern built-in chat-format registry + opt-in LLM polish/fallback. Modules: `types.ts` (PatternEntry + ParseResult + DateContext + CaptureMap + TimezonePolicy), `builtins.ts` (14 hand-vetted patterns sourced from public format docs — iMessage/Slack, Telegram bracket + text-export, bold-paren-time, 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), `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*(.*)$/`, index 3 after `bold-paren-time`) 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,telegram-bracket,whatsapp-iso,whatsapp-us,signal-export,irc-classic,irc-weechat,matrix-element,teams-export,all,adversarial,bold-name-no-time}.jsonl` with `scripts/check-fixture-privacy.sh` banning real-name leaks.
- `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 pages, splits into time-windowed segments (30-min gap or 30-msg cap), prepends a topical/temporal header, and runs through `extractFactsFromTurn()` so anchor-rich facts surface in `gbrain search`. 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); **two-phase enumeration** (paginated `listPages({type, sourceId, limit:10})`; per-page body cap MAX_PAGE_BODY_BYTES=25MB with `pages_skipped_too_large` counter surfaced in doctor); **page-global row_num accumulator** (facts unique index is `(source_id, source_markdown_slug, row_num)` per migration v51 — per-segment row_num would collide); **page-level TERMINAL audit row** to facts table after all segments commit (source='cli:extract-conversation-facts:terminal'; doctor's NOT EXISTS matches the terminal row so partial-extraction pages stay in backlog); **optional `opts.budgetTracker?`** (when present, used as-is — nested `withBudgetTracker` REPLACES; when absent, core auto-wraps with `BudgetTracker({maxCostUsd})`); **body read covers compiled_truth + timeline**; **honors `facts.extraction_enabled` kill-switch** with `--override-disabled` escape; **--types LIST allowlist** (`conversation,meeting,slack,email`) with CLI default reading `cycle.conversation_facts_backfill.types`; **fingerprint on sourceId only**; **string-encoded op-checkpoint** entries `"<sourceId>|<slug>|<endIso>"` for resume (durable audit is the facts terminal row); **`--background` via maybeBackground** (Minion handler `extract-conversation-facts` re-creates BudgetTracker from `data.max_cost_usd`; on `BudgetExhausted` mid-job catches + persists + marks `completed` with `result.budget_exhausted=true`). The companion cycle phase `conversation_facts_backfill` (default OFF) iterates `listSources(engine)`, creates ONE brain-wide tracker per tick + wraps the loop in `withBudgetTracker` + passes the tracker into every per-source call. Two-layer cost AND walltime caps: per-source (`max_cost_usd=$1`, `max_walltime_min=20`) AND brain-wide (`max_total_cost_usd=$5`, `max_total_walltime_min=30`). Pinned by `test/extract-conversation-facts.test.ts` (27 cases). Migration v94 adds partial index `idx_facts_extract_conversation_session ON facts(source_id, source_session) WHERE source LIKE 'cli:extract-conversation-facts%'` (`transaction:false` + invalid-index pre-drop on Postgres; plain CREATE INDEX on PGLite). `src/commands/doctor.ts:computeConversationFactsBacklogCheck` is 3-state (SKIPPED when disabled; OK when caught up; WARN when >10 pages lack the terminal row, with paste-ready `gbrain doctor --remediate` step). `src/commands/sources.ts:runAudit` adds `facts_backfill_estimate: {pages, est_segments, est_cost_usd, types}`. Schema-pack `gbrain-base.yaml` promotes `conversation` (temporal, extractable) + `atom` (annotation, NOT extractable) into the base seed; backstop uses hardcoded `ELIGIBLE_TYPES` in `src/core/facts/eligibility.ts:51` not pack extractable. `ALL_PAGE_TYPES` in `src/core/types.ts` extended with the two new types.
- `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`. `DIR_PATTERN` covers `people`, `companies`, `deals`, `topics`, `concepts`, `projects`, `entities`, `tech`, `finance`, `personal`, `openclaw`. 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.
- `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. `--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`.
- `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). 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`. Query path wrapped in the standard `withEngine(...)` lifecycle so `engine.connect()` runs before the first SQL call. Pinned by `test/reindex-frontmatter-connect.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`).
- `src/core/sync.ts` extension — `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'`. `src/commands/sync.ts:772` cleanup loop guards on `unsyncableReason(path) === 'metafile'` so previously-indexed metafile pages 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).
- `src/core/import-file.ts` extension — 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).
- `src/core/engine.ts` extension — 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/migrate.ts` 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)).
- `src/cli.ts` extension — `dream` dispatch at lines 1063-1080 binds the caught engine-connect error and emits `[dream] WARNING: could not connect to DB (...)` to stderr 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).
- `src/commands/autopilot.ts` extension — 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`.
- `src/core/oauth-provider.ts` + `src/commands/serve-http.ts` extension — 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`).
- `src/core/sync.ts:pruneDir` extension — `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/minions/handlers/subagent.ts` extension — 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`.
- `src/commands/doctor.ts` extension — 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`.
- `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.
- `src/commands/doctor.ts` extension — `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).
- `src/core/cycle.ts` extension — `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.
- `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`.
- `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/commands/doctor.ts` extension — 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).
- `src/commands/lint.ts` extension — 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`.
- `src/commands/embed.ts` extension — 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`.
- `src/core/import-file.ts` extension — `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. `DIR_PATTERN` covers `people`, `companies`, `deals`, `topics`, `concepts`, `projects`, `entities`, `tech`, `finance`, `personal`, `openclaw`. Used by extract.ts, operations.ts auto-link post-hook, and backlinks.ts. Pinned by `test/import-file-content-sanity.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/core/content-sanity.ts` extension — 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/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/search/hybrid.ts` + `src/core/search/sql-ranking.ts` + `src/core/operations.ts` + `src/core/types.ts` extensions — 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`.
- `src/commands/doctor.ts` extension — 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`.
- `src/commands/lint.ts` + `src/commands/sources.ts` extensions — `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/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 `maxWaiting` coalesce path uses `pg_advisory_xact_lock` keyed on `(name, queue)` to serialize concurrent submits for the same key, and filters 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, so long handlers aren't wall-clock-killed mid-progress by the short null-default; an explicit `opts.timeout_ms` always wins. 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).
- `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` + per-call `Promise.race` timeout (`GBRAIN_LOCK_RENEWAL_CALL_TIMEOUT_MS`, default `lockDuration/3`); (3) time-based abort (`Date.now() - lastSuccessfulRenewalAt >= lockDuration - GBRAIN_LOCK_RENEWAL_SAFETY_MARGIN_MS`) so we release the lock BEFORE another worker can reclaim; (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). 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 `test/worker-lock-renewal.test.ts` (18), `test/audit/lock-renewal-audit.test.ts` (11), `test/scripts/check-worker-lock-renewal-shape.test.ts` (5), `test/worker-shutdown-disconnect.test.ts` (asserts `disconnectSpy).not.toHaveBeenCalled()`), `test/worker-rss.test.ts` (11), `test/worker-supervised-db-probe.test.ts` (3).
- `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 max-crashes stay in MinionSupervisor. `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 fails past the threshold exits `LOCK_LOST` (code 4) rather than risk a split-brain. `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`.
- `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. 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/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) — per-handler default wall-clock budgets. `HANDLER_DEFAULT_TIMEOUT_MS` maps the long handlers (`subagent`, `subagent_aggregator`, `embed-backfill`, `autopilot-cycle`) to a 30-min default (the value `cycle/patterns.ts` already passed for subagents, generalized). `defaultTimeoutMsFor(jobName)` returns that default or `null` for short handlers (keep the tight null-default wall-clock). `MinionQueue.add()` stamps this onto `minion_jobs.timeout_ms` at submit time when the caller passed no `timeout_ms`, so a long job submitted without one isn't wall-clock-killed mid-progress; an explicit value always wins and already-queued jobs are NOT backfilled. Pinned by `test/minions.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.
- `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/commands/doctor.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.
- `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 at `doctor.ts:1011-1043`) and `gbrain jobs supervisor status` (`jobs.ts:803-826`) 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` coalesce events. JSONL at `~/.gbrain/audit/backpressure-YYYY-Www.jsonl`. One line per coalesce with `(queue, name, waiting_count, max_waiting, returned_job_id, ts)`. Closes the silent-drop vector the maxWaiting guard introduced.
- `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. Throws `RateLeaseUnavailableError` (renewable) when rate-lease capacity is full. 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.
- `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`). 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).
- `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 `tool_use_id`. 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` (13-name allow-list). 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. 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)` helper; MCP server + subagent tool registry both call it, byte-for-byte equivalence pinned by `test/mcp-tool-defs.test.ts`. Exports the recursive `paramDefToSchema(p: ParamDef)` — single source of truth for ParamDef→JSON Schema mapping shared by three consumers: `buildToolDefs` (stdio MCP), `src/commands/serve-http.ts:837` (HTTP MCP `tools/list`), and `src/core/minions/tools/brain-allowlist.ts:84` (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/minions/attachments.ts` — Attachment validation (path traversal, null byte, oversize, base64, duplicate detection).
- `src/commands/agent.ts` — `gbrain agent run <prompt> [flags]` CLI. 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.
- `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/jobs.ts` — `gbrain jobs` CLI subcommands + `gbrain jobs work` daemon. `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 full `MinionJobInput` retry/backoff/timeout/idempotency surface as flags: `--max-stalled`, `--backoff-type fixed|exponential`, `--backoff-delay`, `--backoff-jitter`, `--timeout-ms`, `--idempotency-key`. `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). 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` at `jobs.ts:803-826` 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 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).
- `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). 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-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).
- `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)`, `validateParams(op, params)`. Single source of truth for `(ctx, params)` handler arg order and the 5-field `OperationContext` shape (engine + config + logger + dryRun + remote). Defaults `remote: true` (untrusted); local CLI callers pass `remote: false`. 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/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.
- `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, admin bootstrap token. 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 exported `HEALTH_TIMEOUT_MS = 3000` (returns the same `ProbeHealthResult` tagged-union as `probeHealth`, single timer-cleanup site, single 503 envelope); body shape `{status, version, engine}` only. Full stats moved to admin-only `/admin/api/full-stats` (gated by `requireAdmin`, 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)` from `src/core/sql-query.ts` so it works against PGLite; the four `mcp_request_log.params` INSERT sites (success / auth_failed / scope_denied / server-error) go through `executeRawJsonb(engine, ...)` so the column stores real objects (`params->>'op'` returns `search`, not the quoted string). `--bind HOST` defaults `127.0.0.1` (self-hosters pass `--bind 0.0.0.0`); a stderr WARN fires when `--public-url` is set without `--bind`; the banner prints a `Bind:` line. `AuthInfo.sourceId` + `AuthInfo.allowedSources` are the typed source of truth, populated by `oauth-provider.ts:verifyAccessToken` from the `oauth_clients` row. The HTTP MCP `tools/list` handler at `:837-849` uses `paramDefToSchema(v)` from `src/mcp/tool-defs.ts` so array params keep `items` (strict-mode OAuth clients otherwise reject the whole tool list).
- `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; the double-encode bug class doesn't apply because positional binding through `unsafe()` reaches the wire protocol with the correct type oid (verified by `test/sql-query.test.ts` on PGLite, `test/e2e/auth-permissions.test.ts:67` on Postgres). `scripts/check-jsonb-pattern.sh` doesn't fire because `executeRawJsonb(...)` is a method call, not the banned literal-template-tag interpolation. 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](https://github.com/oven-sh/bun/issues/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` grandfathers pre-v0.26 bearer tokens as `read+write+admin`. `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[]) onto the returned `AuthInfo`; legacy brains degrade via `isUndefinedColumnError` fallback.
- `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, 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 grandfather to `read+write+admin` scopes on the OAuth HTTP server (no migration). 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) and `--federated-read <S1,S2,...>` (read scope, array) and prints the resolved `Write source` + `Federated reads`; pre-v0.34 clients backfill to `source_id='default'` via migration v60. 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`.
- `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 names `put_page` not `capture` since `capture` is CLI-only, not an MCP tool) with a core-tools fallback for hosts without skill publishing. URL normalization appends `/mcp` to a bare host but REJECTS a scheme-less host; pure helpers (`isLinkLocalOrMetadata`, URL parse, render) are unit-tested. Flags: `--token`, `--name <id>` (default `gbrain`, validated against `NAME_RE`), `--agent claude-code|codex|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` (Codex reads the token from the env var at runtime, never written to config; `--install` runs it and prints an `export GBRAIN_REMOTE_TOKEN` hint when missing); `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)}` — binary-generic so `claude` and `codex` share the path; `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 four agents) + `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 and that `capture` is NOT advertised) + `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/repair-jsonb.ts` — `gbrain repair-jsonb [--dry-run] [--json]`: rewrites `jsonb_typeof='string'` rows in place across 5 affected columns (pages.frontmatter, raw_data.data, ingest_log.pages_updated, files.metadata, page_versions.frontmatter). Fixes the double-encode bug on Postgres; PGLite no-ops. Idempotent.
- `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.
- `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?})` reads `sync.repo_path`, re-reads the just-written DB row (`getPage`), renders it via `serializePageToMarkdown` + `resolvePageFilePath`, and writes the `.md` under the repo so the brain has a committable artifact that round-trips through `gbrain sync`. 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' | 'page_not_found_after_write', error? }` so the caller decides messaging + exit codes. Trust gating (subagent sandbox, dry-run) stays at the CALLER. Consumers: `put_page` op and `gbrain brainstorm/lsd --save` via `persistSavedIdea`. Pinned by `test/write-through.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/core/ai/model-resolver.ts:parseModelId` — gateway-side resolver accepts both colon and slash form (`provider:model` and `provider/model`) so a slash-form id resolves to the same recipe at every gateway entry point (chat / embed / rerank) instead of throwing `AIConfigError: model id must be in format provider:model`. Bare names without ANY separator still throw — gateway routing always needs an explicit provider. Pinned by `test/ai/model-resolver-slash.test.ts` including a `resolveRecipe` round-trip asserting slash form resolves to the same recipe object as colon form.
- `src/commands/transcripts.ts` — `gbrain transcripts recent [--days N] [--full] [--json]`: recent raw `.txt` transcripts from the dream-cycle corpus dirs. Imports `listRecentTranscripts` from `src/core/transcripts.ts` (the same library the gated `get_recent_transcripts` MCP op uses). Local-only by construction — the CLI always runs with `ctx.remote=false`.
- `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/commands/doctor.ts` — `gbrain doctor [--json] [--fast] [--fix] [--dry-run] [--index-audit]`: health checks. 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. 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).
- `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).
- `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>` stripped. `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. `OperationContext.cliOpts` extends shared-op dispatch for MCP callers.
- `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. 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). Pinned by `test/db-lock-auto-takeover.test.ts` + `test/db-lock-reap.test.ts`.
- `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/commands/embed.ts` extension — 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).
- `src/commands/extract-conversation-facts.ts` extension — `--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.
- `src/core/embedding-dim-check.ts` extension — 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/postgres-engine.ts` extension — `insertFact` + `insertFacts` no longer hardcode `tx.unsafe(\`'${embedLit}'::vector\`)` for the embedding column. `resolveFactsEmbeddingCast()` (private) probes `pg_attribute` once 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.
- `src/core/cycle.ts` + `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` extensions — 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) Shorter cycle lock TTL + active in-phase refresh: `LOCK_TTL_MINUTES = 5` (was 30); `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 6x faster while a healthy long-running cycle keeps it alive (residual: a single `await chat()` past 5 min can expire the lock mid-await — TODO-OPS-2). (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); `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`.
- `src/commands/sync.ts` — `gbrain sync` CLI + the `performSync` / `performFullSync` library entrypoints (consumed by the autopilot cycle and the Minion sync handler). `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 `resumeFilter`s 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` reject when combined with `--parallel > 1` (the brain-global `sync-failures.jsonl` has no per-source scope); 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}` on stdout; human banners route to stderr via `humanSink` so `jq` parses cleanly. Exit matrix: 0 all ok, 1 any error, 2 cost-prompt-not-confirmed. 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. `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 `sync --all` cost gate is mode-aware via `willEmbedSynchronously` + `shouldBlockSync` from `src/core/embedding.ts` (federated_v2 resolved once up front): 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 `sumStaleChunkChars({signature})` priced via `estimateCostFromChars` at `currentEmbeddingPricePerMTok()` + queued-job count, NEVER exits 2); the INLINE path BLOCKS only when the new-content estimate exceeds `sync.cost_gate_min_usd` (default $0.50). The new-content estimate (`estimateInlineNewTokens`) contributes ZERO for sources provably unchanged since last sync (`isSourceUnchangedSinceSync` HEAD==last_commit + clean tree AND `chunker_version === CURRENT`) and the full-tree ceiling for changed sources; the pre-existing stale backlog is shown informationally but NEVER gated on (sync doesn't sweep it inline). Helpers `resolveCostGateFloorUsd(engine)` (fail-open $0.50, accepts 0) + `resolveBackfillCapUsd(engine)`. JSON envelopes gain `mode` + `gate` discriminators (`dry_run | deferred_notice | below_floor | confirmation_required`); `SyncStatusReportSource` gains `backfill_queued`/`backfill_active`/`backfill_last_completed_at`; cost previews read `getEmbeddingModelName()` (no hardcoded OpenAI). `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`).
- `src/commands/import.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).
- `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/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 (9 phases). `runCycle(engine: BrainEngine | null, opts: CycleOpts): Promise<CycleReport>` composes phases in semantic order: lint → backlinks → sync → synthesize → extract → patterns → recompute_emotional_weight → embed → orphans. `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. `yieldBetweenPhases` runs between phases; `yieldDuringPhase` is in-phase keepalive (synthesize/patterns renew the cycle-lock TTL during long waits). Engine nullable; lock-skip on read-only phase selections. `CycleOpts.signal?: AbortSignal` propagates the worker's abort signal with `checkAborted()` between every phase. `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 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`; the `jobs.ts` `autopilot-cycle` + phase-wrapper handlers pass `null` (not `'.'`) when no repo is configured. Pinned by `test/dream-postgres.serial.test.ts` + `test/jobs-autopilot-cycle-braindir.serial.test.ts`.
- `src/core/cycle/synthesize.ts` — Synthesize phase: conversation-transcript-to-brain pipeline. Reads `dream.synthesize.session_corpus_dir`, runs a cheap Haiku verdict (cached in `dream_verdicts`), then fans out one Sonnet subagent per worth-processing transcript with `allowed_slug_prefixes` (sourced from `skills/_brain-filing-rules.json` `dream_synthesize_paths.globs`). 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 key `dream:synth:<file_path>:<content_hash>`. `--dry-run` runs Haiku, skips Sonnet. 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`. `judgeSignificance` and `JudgeClient` are exported; `judgeSignificance` takes a `verdictModel` param loaded from `dream.synthesize.verdict_model` via `loadSynthConfig`. `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 idempotency keys `dream:synth:<filePath>:<hash16>:c<i>of<n>`; single-chunk transcripts preserve the legacy `dream:synth:<filePath>:<hash16>` key byte-for-byte so existing brains skip with `already_synthesized_legacy_single_chunk` instead of re-spending Sonnet. `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 don't write to `dream_verdicts` 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 (lines 395-404) 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`.
- `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` and `bun run check:all`. 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. Single Sonnet subagent; same allow-list path as synthesize. Runs AFTER `extract` so the graph is fresh.
- `src/core/cycle/extract-facts.ts` — extract_facts cycle phase. Fence is canonical: per-page wipe (`deleteFactsForPage`) + reinsert from `parseFactsFence` + `extractFactsFromFenceText` + `engine.insertFacts`. 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/entities/resolve.ts` — Free-form entity name → canonical slug resolution. `resolveEntitySlug(engine, source_id, raw)`: exact slug → fuzzy (pg_trgm @ 0.4 threshold) → bare-name prefix expansion (`people/<token>-%` then `companies/<token>-%`, `connection_count` correlated-subquery tiebreaker) → deterministic `slugify` fallback. 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` — NOT a wrapper around `tryPrefixExpansion` (that path returns per-dir top-1 and suppresses ambiguity by design). Pinned by `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 Haiku significance verdict but skips Sonnet 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.
- `src/commands/friction.ts` + `src/core/friction.ts` — `gbrain friction {log,render,list,summary}` reporter. Append-only JSONL under `$GBRAIN_HOME/friction/<run-id>.jsonl`. Schema is a flat extension of `StructuredAgentError`. Render groups by severity → phase, defaults to `--redact` for md output (strips `$HOME`/`$CWD` to placeholders so reports paste safely in PRs). 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 openclaw]`. End-to-end "fresh user" friction harness. Two modes: scripted (CI gate, agent-free) and live (real openclaw 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`, asserts `status: 'ok'`) → render. Live mode hands `BRIEF.md` from `test/fixtures/claw-test-scenarios/<name>/` to the agent runner. Ships with the OpenClaw runner only (`src/core/claw-test/runners/openclaw.ts`, invokes `openclaw agent --local --agent <name> --message <brief>`); hermes runner deferred. Transcript capture (`transcript-capture.ts`) uses `fs.createWriteStream` with `'drain'`-event backpressure (256KB-burst child-stall fix). Upgrade scenario seeded via `seed-pglite.ts` SQL replay.
- `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). Wired into `bun test`.
- `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` + `bun run check:all`.
- `docker-compose.ci.yml` + `scripts/ci-local.sh` — Local CI gate. `bun run ci:local` spins up `pgvector/pgvector:pg16` + `oven/bun:1` with named volumes (`gbrain-ci-pg-data`, `gbrain-ci-node-modules`, `gbrain-ci-bun-cache`), runs gitleaks on host, smoke-tests `scripts/run-e2e.sh` argv handling, runs unit tests with `DATABASE_URL` unset, then runs all 29 E2E files sequentially. `--diff` swaps in the diff-aware selector; `--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 29 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` when invoked with no args.
- `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/commands/integrations.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/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 (benchmark suite + corpus): lives in the separate [gbrain-evals](https://github.com/garrytan/gbrain-evals) repo. Not installed alongside gbrain.
- `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)
- `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)
- `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 for a source. `checkDestructiveConfirmation(impact, opts)` is the fail-closed gate (`--confirm-destructive` required when data is present; `--yes` alone is rejected). `softDeleteSource` / `restoreSource` / `listArchivedSources` / `purgeExpiredSources` drive the source-level archive lifecycle via `sources.archived BOOLEAN`, `archived_at TIMESTAMPTZ`, `archive_expires_at TIMESTAMPTZ`. 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 pages 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. `syncFingerprint({sourceId, lastCommit})` keys the sync rows. Pinned by `test/op-checkpoint.test.ts` (incl. delta-append, union read, cascade clear, durable-write boolean). `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/commands/doctor.ts` extension — `--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`.
- `src/commands/jobs.ts` extension — 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).
- `src/core/minions/protected-names.ts` extension — `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/commands/autopilot.ts` extension — 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/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 `await`s 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`.
- `src/core/cycle.ts` extension — `purge` phase (the cycle's 9th phase, for 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/commands/embed.ts` extension — 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`.
- `src/core/cli-options.ts` extension — `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.
- `openclaw.plugin.json` — ClawHub bundle plugin manifest
- `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` extensions — 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 (v0.20+)

BrainBench — the public benchmark for personal-knowledge agent stacks — lives in
[github.com/garrytan/gbrain-evals](https://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.

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.

## v0.36.1.0 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. Plan persisted
at `~/.claude/plans/system-instruction-you-are-working-rippling-knuth.md`.
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.
- `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.
- `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`.
- `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` extension — 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/commands/serve-http.ts` extension — 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).
- `src/commands/takes.ts` extension — `gbrain takes revisit <slug>` opens $EDITOR on the source page with a `<!-- gbrain:revisit -->` cursor marker.
- `src/commands/doctor.ts` extension — 4 checks: `abandoned_threads`, `calibration_freshness`, `grade_confidence_drift` (mitigation surface; math ships later), `voice_gate_health`.
- `admin/src/pages/Calibration.tsx` — Calibration tab. Single-column layout. `<TrustedSVG>` wrapper handles `dangerouslySetInnerHTML` for the server-rendered SVG.
- `admin/src/index.css` extension — `--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 (v0.40.7.0)

The schema-pack mutation surface shipped in v0.40.7.0 as the production rebuild of
closed community PR #1321 (`@garrytan-agents`). Six new foundation modules + a
mutate skeleton + stats/sync data plane + 14 CLI verbs + 9 MCP ops + a first-class
agent skill. See `~/.claude/plans/system-instruction-you-are-working-recursive-thacker.md`
for the full plan + 21 captured design decisions.

Key files (v0.40.7.0 additions):
- `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` extensions — `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 file in the chain and cascade-invalidates on mtime change (cross-process detection).
- `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/lint-rules.ts` — 12 pure rule functions. `withMutation`'s pre-write validation gate composes the 10 file-plane rules; the 2 DB-aware rules (`extractable_empty_corpus`, `mutation_count_anomaly`) need an engine. 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). 11 mutation primitives: `addTypeToPack`, `removeTypeFromPack` (with reference check), `updateTypeOnPack`, `addAliasToType`, `removeAliasFromType`, `addPrefixToType`, `removePrefixFromType`, `addLinkTypeToPack`, `removeLinkTypeFromPack`, `setExtractableOnType`, `setExpertRoutingOnType`. Atomic write via `.tmp + fsync + rename` — the pack file on disk is NEVER partial. 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` extension — 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` defensive fix retained. Lifecycle-grouped help text (Inspection / Activation / Authoring / Discovery+repair).
- `src/core/operations.ts` extension — 9 MCP ops: `get_active_schema_pack`, `list_schema_packs`, `schema_stats`, `schema_lint`, `schema_graph`, `schema_explain_type`, `schema_review_orphans` (all read-scope, NOT localOnly), plus `schema_apply_mutations` (admin scope, NOT localOnly so remote agents can author packs over HTTPS MCP — batched, one MCP tool taking a `mutations[]` array atomically inside ONE `withPackLock`, audit log captures `actor: mcp:<clientId8>`) and `reload_schema_pack` (admin, NOT localOnly). Trust posture: per-call `schema_pack` opt STAYS rejected for remote callers via `op-trust-gate.ts`.
- `src/commands/whoknows.ts` + `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.
- `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.
- `skills/RESOLVER.md` + `skills/manifest.json` — schema-author wired into the dispatcher with the full functional-area trigger list (compressed routing pattern per the dispatcher convention).

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).