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Commits
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d61808d806 |
v0.42.64.0 fix: harden confidential OAuth token revocation (takeover of #3017) (#3032)
* fix(oauth): validate confidential revoke secrets * fix(oauth): harden confidential token revocation * chore: bump version and changelog (v0.42.64.0) Co-Authored-By: OpenAI Codex <noreply@openai.com> --------- Co-authored-by: Robin <rayme@boltdsolutions.com> Co-authored-by: OpenAI Codex <noreply@openai.com> Co-authored-by: Garry Tan <garrytan@gmail.com> |
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60125ee626 |
feat(dream): --once for one-shot phase runs without toggling config gates (takeover of #2983) (#3031)
* feat(dream): --once for one-shot phase runs without toggling config gates Fixes the "toggle enabled true, run, toggle back to false" workaround that gbrain doctor's extract_atoms_backlog message implicitly recommends and that #2860's reporter had to script around: with an external orchestrator running `gbrain dream --phase patterns` on a cadence outside the autopilot, the only way to run patterns once was `config set dream.patterns.enabled true` -> run -> `config set ... false`. A crash between steps left the flag stuck true, and the autopilot (which polls the same flag) re-enqueued patterns every cycle -- 119 LLM jobs / ~$400 over 24h before it was caught. Root cause: `--phase X` only controls which phase FUNCTION cycle.ts calls; it does not bypass that phase's own `dream.<phase>.enabled` / `cycle.<phase>.enabled` config read. Each gated phase (patterns, synthesize, conversation_facts_backfill, enrich_thin, skillopt) reads its enabled flag internally and skips regardless of how the phase was selected -- confirmed by reading each phase module, not assumed. extract_atoms/synthesize_concepts are a DIFFERENT mechanism entirely (pack-declaration via packDeclaresPhase, not a config .enabled read) and already have a working one-shot escape hatch: `--drain`. The existing doctor message for extract_atoms already says `--phase extract_atoms --drain --window 120`, so no doctor text needed updating there -- verified by reading src/commands/doctor.ts directly rather than assuming the paraphrase in the issue was literal. Design: `gbrain dream --phase <name> --once`. Requires an explicit --phase (bare --once is a usage error, exit 2) so it can never force-enable every disabled phase at once in a full/default cycle -- that would recreate the same unbounded-spend risk the flag exists to prevent. Threaded through CycleOpts as `onceForPhase?: CyclePhase` (the literal phase name, not a boolean) so the bypass can never leak to a phase other than the one named, even if a future programmatic caller passes a wider `phases` array than the CLI does. Never reads or writes config -- the phase still evaluates its .enabled gate every call; --once only overrides the boolean OUTCOME for that one invocation, mirroring the existing --unsafe-bypass-dream-guard / --input precedents (stderr warning at the bypass point, no new config-touching code path). Rejected alternatives (documented per task instructions): - Making explicit --phase X always bypass .enabled: breaking change for existing crons that rely on the disabled flag as a cheap no-op; an upgrade would silently start running LLM/write phases. - A new subcommand: adds a whole dispatch/help/arg surface that internally routes through the same override anyway. - Extending --once to also bypass packDeclaresPhase for extract_atoms/synthesize_concepts: conflates two different gating mechanisms (config toggle vs. pack membership) under one flag; extract_atoms already has --drain, which is purpose-built for its batched/windowed execution model. Design was cross-validated by an independent second-model review (external design consultation) before implementation; its recommendation to also update the extract_atoms doctor message to `--once` was NOT adopted because that phase has no .enabled gate to bypass -- doing so would be a documented no-op, contradicted by reading src/commands/doctor.ts:3264 directly. Tests: 9 new (structural CLI-flag wiring in dream-cli-flags.test.ts; a real PGLite E2E test in dream-patterns-pglite.test.ts proving the bypass fires AND that dream.patterns.enabled is never written; 4 runCycle-level tests in cycle.serial.test.ts proving onceForPhase does not leak across phases). Verified 6 of 9 fail against the pre-fix source (via git stash of source-only changes) to confirm they're meaningful regressions, not tautologies. Closes #2860 Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> * fix(dream): --help short-circuits before --once usage validation Codex review finding (P2): `gbrain dream --help --once` (no --phase) called process.exit(2) from the new --once usage-error check inside parseArgs before runDream's documented IRON RULE ("--help short-circuits BEFORE any engine-bearing work") ever got a chance to run -- parseArgs computes ALL its validations unconditionally before runDream checks opts.help. Repo precedent for this ordering already exists as a pinned regression test (test/dream.test.ts's "--help --source whatever prints help and exits 0"). Fix: compute wantsHelp once in parseArgs and exempt the --once validation when it's set, mirroring that precedent. Added the same class of pinned tests here: bare `--once` still exits 2 with the usage hint, `--help --once` prints help and exits 0, and a real --phase patterns --once run against a PGLite engine proves the bypass actually fires (falls through to insufficient_evidence instead of disabled) without writing dream.patterns.enabled. Also fixed the structural test in dream-cli-flags.test.ts that asserted the exact pre-fix guard-condition source text. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> * fix(dream): --once must require an EXPLICIT --phase, not a derived one Codex review finding (P3): the --once validation checked the derived `phase` value, but `phase` gets defaulted implicitly by --input (implies --phase synthesize) and --drain (implies --phase extract_atoms) BEFORE that check ran. So `gbrain dream --input <f> --once` and `gbrain dream --drain --once` both slipped past the "explicit --phase required" contract silently -- and --once became a true no-op in both cases: --drain returns from runDream before onceForPhase is ever read (the drain path doesn't call runCycle at all), and --input already bypasses the synthesize enabled-gate on its own via the existing opts.inputFile check, so onceForPhase would never even be consulted. Fix: capture `phaseWasExplicit = phaseIdx !== -1` at the very top of parseArgs, before the --input/--drain defaulting blocks run, and validate --once against that instead of the derived `phase`. Updated the usage-error message and --help text to say "an explicit --phase" so a user hitting this understands why `--input ... --once` doesn't count. Tests: 2 new pins in test/dream.test.ts exercising runDream directly (--input <file> --once exits 2; --drain --once exits 2), plus a structural test in dream-cli-flags.test.ts pinning that phaseWasExplicit is captured before both implicit-defaulting blocks. Updated the two existing structural/behavioral tests whose literal guard-condition / error-message assertions changed shape. Verified: dream-cli-flags.test.ts 27/27, dream.test.ts 31/31, typecheck clean. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> --------- Co-authored-by: masashiono0611 <masashi.ono.0611@gmail.com> Co-authored-by: Claude Sonnet 5 <noreply@anthropic.com> Co-authored-by: Garry Tan <garrytan@gmail.com> |
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Anton SenkovskiyandGitHub
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a93fcf504f |
fix(chronicle): bound last-seen to <= asof/today so future events do not read as "seen today" (#2993)
getLastSeen had no upper date bound, so a future-dated chronicle event (a scheduled calendar-event, a planned milestone) became the entity's "last seen" date; finalizeLastSeen's Math.max(0, ...) then clamped the negative delta, reporting days_ago: 0 -- the entity reads as seen-today. Recording future events is intended (eligibility ELIGIBLE_TYPES includes calendar-event); the reader just needs to stop counting them as "seen". Bound the query to te.date <= COALESCE(asof, current_date) in both engines, mirroring getOnThisDay's existing te.date < target bound. asof now reaches the WHERE clause (previously it only reached finalizeLastSeen), so as-of time-travel is honored for the date filter too. Regression test added: an entity with past events plus a future event -> last seen returns the most recent PAST event, not the future one; and as-of after the future date lets it through. Fails before, passes after. |
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11eebc3605 |
fix(conversation): extract iMessage facts with real timestamps (#2756) (#2958)
Co-authored-by: Sameer Bopardikar <203024074+sameerbopardikar@users.noreply.github.com> |
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9ed53e4e1c |
fix(code-edges): per-row $n::text::jsonb binds in addCodeEdges — Bun SQL mis-encodes jsonb[] arrays (#2968) (#3020)
Bun SQL double-encodes ::jsonb[] array binds on the Postgres engine: every edge_metadata element landed as a jsonb string scalar instead of an object, so the resolver's `edge_metadata || jsonb_build_object(...)` UPDATE produced a jsonb array and resolved_chunk_id was never readable — code_callers / code_callees / code_blast returned nothing on Postgres-engine brains while the resolver logged edges_resolved > 0. PGLite was unaffected (per-row placeholders already). Rewrites both inserts (code_edges_chunk, code_edges_symbol) to per-row $n::text::jsonb placeholders via sql.unsafe — the same shape executeRawJsonb and the PGLite engine use. Adds the DATABASE_URL-gated Postgres regression test this class requires (PGLite cannot reproduce it): asserts jsonb_typeof(edge_metadata) = 'object' for resolved + unresolved inserts and that the resolver-style || UPDATE keeps object shape. Verified the test fails 3/3 against the pre-fix code and passes with the fix. Takeover of #2968 by @zsimovanforgeops with the missing regression test added. Co-authored-by: Garry Tan <garrytan@gmail.com> Co-authored-by: Forge (Ron) <forge@zsimovan.dev> Co-authored-by: Claude Fable 5 <noreply@anthropic.com> |
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23e0541d9b |
fix(cycle): budget the patterns subagent from remaining job time — one phase's fixed 35-min worst case defeats any interval-derived cycle budget (#2781) (#2959)
* fix(cycle): budget the patterns subagent from remaining job time, not a fixed constant (#2781) The autopilot-cycle job gets an interval-derived timeout stamped at submit, but the patterns phase submits its subagent with a fixed 30-min job timeout and waits up to 35 min — one phase's worst case exceeds ANY interval-derived budget <= 35 min, so the parent job dead-letters mid-patterns and the tail phases (consolidate -> schema-suggest) starve for days (#2781, the deeper half left open by the #2852 dispatch-floor fix). - MinionJobContext.deadlineAtMs: absolute deadline from the claim-time timeout_at stamp (the DB ground truth handleTimeouts() sweeps against; re-stamped on every claim so retries get a fresh budget). Null when the job has no per-job timeout. - worker: the per-job abort timer now derives its delay from timeout_at when present, so the in-process timer, the DB sweeper, and the handler-visible deadline agree on ONE absolute instant. - autopilot-cycle + autopilot-global-maintenance handlers thread deadlineAtMs into runCycle; CycleOpts carries it to the patterns phase. - patterns: clampSubagentBudgets() derives BOTH the child job timeout and the wait timeout from the same child deadline (parent deadline minus a 60s stop-margin reserve — enough for the wait poll + force-evict grace + cleanup, deliberately NOT a promise that tail phases complete). Under a 2-min minimum the phase skips honestly (insufficient_cycle_budget) instead of submitting a guaranteed-kill LLM call; the next cycle retries with a fresh budget. - Direct callers (gbrain dream) pass no deadline and keep the configured timeouts unchanged. Follow-up (separate PR): synthesize has the same shape plus sequential per-child waits that accumulate N x subagent_wait_timeout_ms past any parent budget; it needs per-wait remaining-time recomputation. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01RaNDjecPPvhC7LRqkxkhGF * fix(cycle): address review — cancel timed-out patterns child; thread deadline through phase-wrapper handlers - P1: the child's timeout_ms clock starts at ITS claim, so a queued child could outlive the parent deadline the wait was clamped to. On wait timeout, cancelJob strips it (waiting -> cancelled; active -> lock stripped, worker abort fires next renew tick). - P2: makePhaseHandler (standalone patterns/synthesize/... minion jobs) now threads job.deadlineAtMs into runCycle like the autopilot handlers. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01RaNDjecPPvhC7LRqkxkhGF --------- Co-authored-by: Claude Fable 5 <noreply@anthropic.com> |
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324c355318 |
test(e2e): production guard — setupDB refuses non-test databases (#2957)
setupDB() TRUNCATEs every data table on whatever DATABASE_URL points at, and run-e2e.sh deliberately preserves an exported DATABASE_URL — one stray environment variable away from wiping a production brain, with no guard of any kind (found during an independent review, 2026-07-18). assertSafeE2eDatabaseUrl (pure, unit-tested) now runs before any connection: allowed when the database name carries "test" as a word segment (the gbrain_test convention used by CI and .env.testing.example), or when GBRAIN_E2E_ALLOW_DB names the exact database intentionally. Refusal is loud and actionable. 7 unit tests, no DB required. Co-authored-by: Aleksei Razsadin <razsoc.01@gmail.com> Co-authored-by: Claude Fable 5 <noreply@anthropic.com> |
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184b6cb8a1 |
fix search: title candidate arm + gated OR fallback for lexical recall (#2956)
Pages were unreachable by their own exact titles: FTS indexed only chunk body text while the title-weighted pages.search_vector (GIN-indexed since its introduction) was never queried by any search path, and websearch_to_tsquery AND-at-chunk-grain semantics meant one non-matching token zeroed keyword recall with no fallback — long or acronym-bearing titles (e.g. "IAWG ... AAR-LL deck") fell through to the vector arm alone and missed. - searchTitles (both engines): page-grain candidate arm over pages.search_vector (title 'A' + compiled_truth 'B' + timeline 'C'), ts_rank_cd ranked, representative-chunk LATERAL join, full filter parity with searchKeyword (visibility, soft-delete, source grants, hard-excludes, dates, types); fused as a weighted RRF list at the keyword arm's intent-effective k on all three hybrid return paths; fail-open with warnOncePerProcess. No schema changes — the index already existed, dark. - AND->OR one-retry fallback for the keyword arm, gated behind SearchOpts.orFallback (only hybridSearch opts in; countMentions, link resolution, eval, and keyword-only MCP callers keep the strict-AND contract). Refused for queries carrying websearch operators (negation, quoted phrases). searchTitles carries its own page-grain fallback. - Lexical arms parallelized (Promise.all) on the main path. Verified: typecheck clean; 18 hermetic PGLite tests + 2 engine-parity e2e cases (CI Postgres); consumer regression enrichment 18/0 + link-extraction 127/0; independent live QA on a 10,664-page brain — exact-title target miss -> rank 1 (exact_title_match), controls held, negation/quoted guards proven, strict-consumer contract pinned. Diagnosed from a 3-lane read-only diagnostic; adversarial review round closed findings on fallback scope, Postgres test coverage, and operator handling before this commit. Co-authored-by: Aleksei Razsadin <razsoc.01@gmail.com> Co-authored-by: Claude Fable 5 <noreply@anthropic.com> |
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42375bded5 |
fix(sync): stop the sync data-loss family — ops/ prune, DB-only write-through, full-sync gate drift (#2404, #2426, #2607) (#2938)
Three verified-open defects, one family: sync silently destroying or diverging on content it should preserve. #2404 (P0) — 'ops' was hardcoded in PRUNE_DIR_NAMES (a v0.2.0-era carve-out), so any path with an ops segment was 'pruned-dir': committed ops/*.md never imported, and modified ops/* files hit the unsyncableModified delete loop (whose #1433 guard only spared 'metafile'), silently deleting put-created pages like the bundled daily-task-manager's canonical ops/tasks on every sync. Fix: remove 'ops' from the prune list (ordinary user content; the vendor/generated entries stay), and harden the delete loop to also skip 'pruned-dir' — a page under a pruned dir can only exist via a deliberate put_page. #2426 (P0) — write-through content stayed DB-only and was deleted by sync --full. All three compounding bugs fixed: 1. writePageThrough now best-effort commits the artifact (path-limited git commit) on durability-hardened repos, so the post-commit hook can push it; result carries committed?: boolean. 2. scripts/brain-commit-push.sh stages+commits BEFORE any pull — the old fetch+pull-rebase-first order aborted on any dirty tree, so the helper could never commit a MODIFIED page; brain_push's rebase-on-reject already handles an advanced remote. 3. The full-sync delete-reconcile partitions stale pages by git history (listEverCommittedPaths): never-committed source_paths are DB-only write-through — pages are KEPT and re-exported to the working tree instead of soft-deleted. Builds on the #2828 mass-delete valve (covers the below-valve cases). #2607 — the sync --full git ls-files fast path bypassed pruneDir, so a full pass imported (and resurrected soft-deleted) pages under dot-dirs and vendored trees that incremental sync excludes. Fix: isCollectibleForWalker applies the same segment-level pruneDir gate as classifySync, so full and incremental enumeration agree. One regression test per defect (all verified failing against master src): test/sync-ops-pages.serial.test.ts, test/write-through-commit.serial.test.ts, the #2426 helper-order test in test/brain-durability-hook.serial.test.ts, test/sync-reconcile-db-only.serial.test.ts, test/import-git-fastpath-prune.test.ts. Fixes #2404 Fixes #2426 Fixes #2607 Co-authored-by: Sinabina <sinabina@Sinabinas-MacBook-Pro-4.local> Co-authored-by: Claude Fable 5 <noreply@anthropic.com> |
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a0ef951586 |
fix(dream): gate patterns phase on gateway provider reachability, not ANTHROPIC_API_KEY (takeover of #2279) (#2936)
Absorbs PR #2279's intent (drop the hardcoded ANTHROPIC_API_KEY gate) with the end-state the gateway world actually wants: the patterns phase now probes the RESOLVED patterns model through probeChatModel(normalizeModelId) — the same semantics as think/index.ts and synthesize's makeJudgeClient. Fixes two misclassifications of the old env gate: - Non-Anthropic stacks (litellm, deepseek, openrouter, ...) were skipped as "no upstream" even though the subagent routes them through the gateway (agent.use_gateway_loop). They now pass the gate; their auth is checked lazily at dispatch and surfaces in the job outcome. - Anthropic keys set via `gbrain config set anthropic_api_key` (stdio MCP launches without shell env) were treated as missing. hasAnthropicKey inside probeChatModel reads both sources. Skip reason renames no_api_key → no_provider (carrying the probe's detail). Both pinning tests updated: the structural test asserts the probe wiring; the PGLite E2E swaps its env-only helper for the shared hermetic withoutAnthropicKey (env + config file) so it can't flip to a live LLM call on a dev machine with a config-file key. Co-authored-by: Sinabina <sinabina@Sinabinas-MacBook-Pro-4.local> Co-authored-by: brettdavies <brettdavies@users.noreply.github.com> Co-authored-by: Claude Fable 5 <noreply@anthropic.com> |
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26d2f8abfc |
fix(calibration,takes,cli): calibration CLI routing, source-scoped takes reads, BigInt-safe outputs (takeover of #2452) (#2892)
Rebase-port of #2452 (spinsirr:fix/calibration-profile-scope-and-cli) onto current master after tonight's merges made the fork branch conflict. - cli: add 'calibration' to CLI_ONLY so dispatch reaches its existing handler instead of falling through to "Unknown command" (#2035); honor --source / GBRAIN_SOURCE in the calibration CLI. - takes: route takes_list / takes_search / takes_scorecard / takes_calibration through sourceScopeOpts(ctx) (federated array > scalar > nothing) and scope engine reads via the take's page.source_id — JOIN filter for list/search, EXISTS for scorecard/curve — on both engines (#2200-class). - bigint: shared takeHitRowToHit coercion in searchTakes / searchTakesVector (both engines) + bigintToStringReplacer on the cli.ts output normalizer and the `gbrain call` exit, so int8/BIGSERIAL columns no longer crash JSON.stringify (#2450); calibration profile id BIGSERIAL → string. - calibration: default model ids route through TIER_DEFAULTS (provider-prefixed) instead of bare model strings; admin calibration chart endpoints fixed (takes has no page_slug column; month-precision since_date; Date generated_at; bigint id in drill-down). The think/gather source-scope slice of the original PR was dropped: it already landed on master via #2739. Co-authored-by: Sinabina <sinabina@Sinabinas-MacBook-Pro-4.local> Co-authored-by: spinsirr <ID+spinsirr@users.noreply.github.com> Co-authored-by: Claude Fable 5 <noreply@anthropic.com> |
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+5
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86962b242b |
fix(gateway): consolidate tool-loop resume + provider fixes (fix-wave A) (#2820)
Collector branch superseding the gateway tool-loop duplicate cluster and adjacent provider fixes. Re-implemented from the best of each PR (deduped by content, not file-overlap); every fix carries test coverage. Gateway tool-loop resume (supersedes #1934 #2062 #2065 #2112 #2274 #2487 #2336 #2257 #2499 #2491, test #2063): - toolLoop now persists the tool-result user turn per round (onToolResultTurn), so a resumed subagent job reloads a balanced transcript instead of dangling assistant tool-calls that non-Anthropic providers reject with AI_MissingToolResultsError. - runSubagentViaGateway reconciles an already-corrupted transcript on resume: it heals every dangling assistant tool-call turn (not just the tail) from the settled subagent_tool_executions rows, re-dispatching idempotent-pending tools and throwing on non-idempotent, mirroring the legacy Anthropic path. Terminal early-return for a transcript that already reached end_turn. - repairToolPairing() is a last-resort normalization at the chat() boundary (from #2336): back-fills error stubs for any assistant tool-call still unanswered (partial turns, provider-duplicated/dropped IDs on local models, length-truncated batches). No-op on balanced input. - toModelMessages is Date-safe (Postgres timestamptz -> ISO via a JSON round trip at the SDK boundary, never a ::jsonb cast; degrades bigint/circular to a string instead of throwing) and drops non-string text blocks reasoning models emit that AI SDK v6 rejects (#2488). Adjacent provider fixes: - Model-aware default max output tokens: thinking-by-default Claude 5 models get headroom (gateway 32000, think 16000) while everything else stays 4096/4000, so DeepSeek/OpenAI subagents don't exceed provider caps (#2614 #2806). - DeepSeek: promote reasoning_content into content when content is empty, via a fail-open recipe fetch shim (#2617). - OpenRouter: map openrouter_api_key (config + env) into OPENROUTER_API_KEY through buildGatewayConfig; register agent.use_gateway_loop, zeroentropy and openrouter keys in KNOWN_CONFIG_KEYS so `config set` accepts them (#2572, config key from #2112). Preserves JSONB (no JSON.stringify into ::jsonb), engine parity, source isolation, and trust-boundary invariants. Verified with the gbrain-pr-test-env consumer matrix (clawlancer/Postgres, gstack + hivemindos/PGLite) baseline-FAIL -> candidate-PASS on the same repro, plus bun run verify (31/31) and 439 targeted unit + e2e tests. Co-authored-by: Sinabina <sinabina@Sinabinas-MacBook-Pro-4.local> Co-authored-by: thomaskong119 <thomaskong119@hotmail.com> Co-authored-by: maxpetrusenkoagent <max.petrusenko.agent@gmail.com> Co-authored-by: brettdavies <brettdavies@users.noreply.github.com> Co-authored-by: ivandebot <187176982+ivandebot@users.noreply.github.com> Co-authored-by: Rafael Reis <rafael.reis@contabilizei.com.br> Co-authored-by: fbal23 <fbal.public@gmail.com> Co-authored-by: javieraldape <javieraldape@users.noreply.github.com> Co-authored-by: David Carolan <david@joyrestart.com> Co-authored-by: Masashi-Ono0611 <masashi.ono.0611@gmail.com> Co-authored-by: spiky02plateau <155588579+spiky02plateau@users.noreply.github.com> Co-authored-by: psam-717 <mphilannorbah@gmail.com> Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> |
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vinsewandGitHub
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d0447a597b |
fix(files): normalize bigint sizes before JSON serialization (#472)
Postgres returns BIGINT file sizes as native BigInt values. Returning those values directly from file_list makes JSON serialization fail, and using them in CLI arithmetic can also throw. Convert size_bytes to Number at the operation boundary and in the CLI display path. File sizes remain exact well beyond any practical attachment size. Add a unit regression that exercises a native BigInt row and proves the operation result is JSON-serializable, plus a real-Postgres E2E assertion for the file_list response. |
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Time AttakcandGitHub
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010847c020 |
fix(think): enforce source scope across gather (#2200) (#2739)
Carry the caller's scalar or federated source scope through every think gather stream: hybrid page retrieval, takes keyword/vector retrieval, and graph traversal. Adds source predicates to the takes retrieval methods in both engines. Part of #2200 (the think slice; #2200 stays open as the tracking issue for the remaining by-slug read ops). |
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Time AttakcandGitHub
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8e84c5b4a1 |
fix(facts): parse escaped pipes in facts fence round-trips (#2726) (#2738)
parseRowCells now splits on unescaped pipes only and decodes escaped pipes while preserving ordinary backslashes and empty cells, so facts whose text contains literal | survive the fence->DB reconcile instead of being silently deleted. Fixes #2726. |
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Time AttakcandGitHub
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42ab0956a4 |
fix(migrate): preserve sources and scope resume targets (#2677) (#2736)
migrate --to now copies the complete source catalog before pages (fixes the pages_source_id_fkey failure on multi-source brains), and resume manifests carry an opaque target identity so a checkpoint from one target is discarded for a different target. Fixes #2677. |
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dde1132a29 |
v0.42.55.0 fix(security): dotfile/skills/slug confinement + DCR consent default + schema-lint migration (#418 #419 #245 #1353 #1647 #171 #1385) (#2399)
* fix(security): confine routing dotfiles, skills dir, slugs, and transcription exec Shared src/core/path-confine.ts consolidates the realpath-containment idiom (moved from sources-ops.ts) and adds isTrustedDotfile + isWriteTargetContained. - .gbrain-source (source-resolver) and .gbrain-mount (brain-resolver) walk-up dotfiles are now lstat trust-gated: a symlink, foreign-owned, or world-writable file is refused on multi-user hosts (#418), fail-closed on stat error. - resolveWorkspaceSkillsDir + every skills-dir tier (env, cwd_walk_up, repo_root, cwd_skills, install_path) route through realpath containment so a symlinked workspace/skills can't escape the declared workspace (#419). - resolveSourceId/resolveBrainId realpath both sides of the registered local_path / mount prefix match so a symlinked cwd can't misattribute source/brain. - validateSlug rejects NUL/control, bidi/RTL overrides, backslashes, and URL-encoded path separators at the shared putPage/updateSlug chokepoint; write-through confirms the file path stays within the source tree. - transcribeLargeFile uses execFileSync arg-arrays + fs.rmSync (no shell), so a path with shell metacharacters is never parsed by a shell (#245). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(security): default dynamic-registration clients to authorization_code Self-registered DCR clients (the unauthenticated network registration path) previously defaulted to the client_credentials grant, which bypasses the /authorize consent screen. They now default to authorization_code; an explicit client_credentials request is rejected with invalid_client_metadata unless the operator opts in with the new --enable-dcr-insecure flag. A loud stderr WARNING prints at startup whenever DCR is enabled (#1353). Manual CLI/admin client registration is unchanged (operator-trusted). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(security): schema-lint hardening migration (search_path + view security_invoker) Migration v120 brings existing brains to the same posture as fresh installs: - ALTER VIEW page_links SET (security_invoker = on) on Postgres so the view honors the caller's RLS instead of the owner's (the view-through-RLS bypass). - ALTER FUNCTION ... SET search_path on the gbrain-owned trigger/event functions (both engines, IF EXISTS so engine-only functions are skipped; body untouched, so the load-bearing auto_enable_rls event trigger is unchanged). Closes #171. - Broaden the BYPASSRLS preflight in the historical RLS migration gates to honor superuser and inherited-role BYPASSRLS, so a superuser-connected fresh install no longer aborts (#1385). Fresh-install function definitions in schema.sql / pglite-schema.ts are born-correct (regenerated schema-embedded.ts). scripts/check-search-path.sh is a new CI guard (wired into verify) that fails if a trigger function in the schema base files is added without SET search_path. Postgres-only assertions live in the bootstrap E2E; the PGLite path is covered by test/migration-v120.test.ts. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * v0.42.55.0 fix(security): dotfile/skills/slug confinement, DCR consent default, schema-lint migration Bump VERSION + package.json to 0.42.55.0 and add the CHANGELOG entry for the security-hardening wave (#418 #419 #245 #1353 #1647 #171 #1385). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs(security): note the DCR consent default in SECURITY.md (#1353) The "disable client_credentials, only allow authorization_code" guidance is now the built-in DCR default; document the new --enable-dcr-insecure escape hatch. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs(todos): add takes_search + code_def to the federated by-slug P1 (#2200) The v0.42.55.0 eng-review codex pass flagged takes_search (holder-allowlist only) and code_def (brain-wide raw SQL over content_chunks) as remaining same-class surfaces. Noted on the existing #2200 P1 follow-up, with the caveat that the #2399 close-list deliberately keeps #1371/#2200 open until this lands. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(security): correct plpgsql alias collision in #1385 BYPASSRLS gate (real-PG) The broadened BYPASSRLS preflight aliased `pg_roles r`, but several RLS DO-blocks already declare `r record` for their backfill FOR loop, so plpgsql resolved `r.oid`/`r.rolbypassrls` to the unassigned record variable → "record \"r\" is not assigned yet" on real Postgres (PGLite tolerated it; the DATABASE_URL-gated e2e jobs are the backstop). Renamed the subquery alias to `pr` at all 10 migrate.ts sites; also broadened the schema.sql base RLS gate the same way (with the `pr` alias) for #1385 consistency on superuser fresh installs, and regenerated schema-embedded.ts. Also fixes a PRE-EXISTING engine-parity bug (confirmed failing on clean origin/master): the relationalFanout shape compared `canonical_chunk_id`, a serial id that diverges between a fresh PGLite engine and a shared Postgres DB (setupDB TRUNCATEs without RESTART IDENTITY). Compare its presence, not the exact value. Validated on real Postgres (pgvector/pg16): migration v120 applies, the v35 RLS backfill runs, and engine-parity + postgres-bootstrap + jsonb-parity are green. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> |
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814258dda6 |
v0.42.53.0 fix(sync,db): #2339 op_checkpoints jsonb double-encode + bug-class sweep + CI guard (#2375)
* fix(sync): op_checkpoints pin write double-encodes jsonb — every sync aborts (#2339) recordCompleted bound JSON.stringify(array) to a $3::jsonb param via postgres.js .unsafe(), double-encoding it into a jsonb string scalar that violates the v119 op_checkpoints_completed_keys_array CHECK — aborting every multi-source sync on real Postgres at the first checkpoint write. PGLite parses the string silently, which is why unit tests stayed green and it shipped. Cast through $3::text::jsonb so the text->jsonb cast parses a genuine array. Adds a DATABASE_URL-gated parity test + a dedicated Postgres CI job so the guard can never silently skip. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(db): sweep positional jsonb double-encode sites + AST CI guard (#2324) Every executeRaw/.unsafe site that bound JSON.stringify(x) to a bare positional jsonb cast double-encodes on real Postgres (same class as #2339). Sweep them all to the text::jsonb form across query-cache, sources-ops, llm-base, calibration-profile, impact-capture, subagent, receipt-write, traversal-cache, symbol-resolver, and the agent/sources commands. Adds scripts/check-jsonb-params.mjs (AST-lite scanner for the positional form the legacy template grep misses, incl. generic-typed calls), wired into check-jsonb-pattern.sh, with a self-test. PGLite's native db.query is not scanned — it parses text to jsonb natively, so the bug can't occur there. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(search,eval): alias-hop injected results carry page_id (contradiction-probe crash) applyAliasHop injected synthetic SearchResults without page_id (the `as SearchResult` cast hid the missing field), so listActiveTakesForPages bound undefined/NaN into ANY($1::int[]) and crashed the whole contradiction probe on real Postgres. Stamp page_id=page.id at the injection site and add a finite-id filter in generateIntraPagePairs as a defensive backstop (mirrors hybrid.ts:63). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs(engines): positional jsonb binding rule (text::jsonb vs the double-encode trap) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * v0.42.53.0 fix(sync,db): #2339 op_checkpoints jsonb double-encode + bug-class sweep + CI guard Bumps VERSION + package.json to 0.42.53.0, adds the CHANGELOG entry, and regenerates llms-full.txt. Ships the #2339 sync-abort hotfix, the repo-wide positional jsonb double-encode sweep, the alias-hop contradiction-probe crash fix, and the new positional-form CI guard. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs: post-ship sync — jsonb invariant now covers the positional form + new guard CLAUDE.md JSONB invariant + KEY_FILES (sql-query, check-jsonb-pattern, op-checkpoint) now describe the #2339 positional double-encode class, the $N::text::jsonb fix, and the new check-jsonb-params.mjs guard. Regenerates llms-full.txt. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> |
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bb2e88c42a |
v0.42.52.0 fix(reliability): autopilot dead-job storm + supervisor wedge + sync/status/minion reliability (#2194 #2227 #1994 #1737 #1738 #1950 #1984) (#2287)
* test(supervisor): pin LOCK_HELD fence-exit is never counted as a crash (#2227) A duplicate supervisor loses the queue-scoped DB singleton lock (#1849) and exits LOCK_HELD before spawning a worker or emitting 'started'. summarizeCrashes counts only worker_exited, so the fence path is structurally uncountable. Pin it so a future refactor that logs worker_exited on the fence path fails here instead of silently re-introducing the crash-budget breaker-trip loop. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(autopilot): per-source cycle binds FS phases to source.local_path, not global repo (#2194 #2227) A per-source autopilot-cycle inherited the global sync.repo_path as brainDir while stamping DB freshness for source_id — mixed scope. FS phases (sync/lint/extract) ran against the wrong tree, so the failure-cooldown and freshness gates would attribute work to the wrong source. Resolve the source's local_path in the handler (reuse the archive-recheck SELECT) and bind brainDir to it; a pure-DB source gets null (FS phases skip) instead of falling through to the global checkout. Legacy no-source dispatch keeps the global repoPath. Prerequisite for the cooldown/split commits (codex outside-voice #8). Resolves TODOS:634. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(supervisor): detect a live supervisor via the DB lock under split $HOME (#2227) jobs supervisor status + doctor read the HOME-derived pidfile, so a supervisor started under a different $HOME (keeper=/root vs ops=/data) read as 'not running' while healthy — the false signal that drives an operator to spawn a duplicate. Both surfaces now fall back to the queue-scoped DB singleton lock (#1849), the HOME-independent authority, when the pidfile shows nothing. New isLockHolderLive keys on lock freshness (ttl + heartbeat steal-grace), never process.kill, so PID reuse can't false-positive (pid-liveness-alone-pid-reuse). Status surfaces the holder host/pid + recorded concurrency/max-rss from the latest started event. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(supervisor): degraded retry instead of permanent give-up on crash storm (#1994 #2227) max_crashes_exceeded gave up forever, so a transient DB-pooler blip that tripped the soft budget wedged the queue until a human restart (#2227's breaker-trips tail). Crossing the soft budget now enters degraded mode: keep respawning with capped exponential backoff (60s cap — a paced retry, not a hot loop) and emit a loud crash_budget_degraded health_warn. The existing stable-run reset clears the count once a respawn survives >5min, so a recovered DB self-heals. Permanent give-up fires only at a much-higher hard ceiling (maxCrashes × 10), tunable/disablable via GBRAIN_SUPERVISOR_HARD_STOP_CRASHES (0 = never). Resolves TODOS:92. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * feat(autopilot): clamp fan-out to worker concurrency + doctor warning (#2194) Fan-out resolved to 4 (Postgres) regardless of worker --concurrency, so surplus cycles queued behind the worker and raced the stalled-sweeper. Two fixes for the same mismatch: - resolveEffectiveFanoutMax clamps to max(1, concurrency-1) (reserve a slot), gated on a LIVE DB-lock holder so a stale started-audit row can't shrink throughput (codex #9/D5); no live holder → unknown → unclamped base. Escape hatch autopilot.fanout_clamp_to_concurrency. - doctor's autopilot_fanout_concurrency check warns when fan-out exceeds effective slots — the misconfig was silent before. Advisory (started-event concurrency), wired into both doctor surfaces. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * feat(autopilot): per-source failure cooldown — break the dead-job storm (#2194) Only SUCCESS gated dispatch, so a source whose cycle kept failing/timing-out re-fanned-out every 5-min tick forever (200+ dead jobs/24h). Now a failed source backs off with bounded exponential cooldown (10→120min). Read at DISPATCH from minion_jobs dead/failed rows (timeouts/RSS-kills dead-letter via SQL and never run handler code, so a write-only hook would miss them) AND re-checked at CLAIM time in the handler (codex #5: already-queued/retrying jobs). A success clears it (codex #7); null-source rows excluded (codex #6); engine-parity via executeRaw. Disable with autopilot.failure_cooldown_min=0. Fail-open if config/history reads error. Surfaced via fanout_cooldown_skipped + the fanout summary. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * feat(autopilot): split the cycle — per-source phases + one global-maintenance job (#2194 #2227) N per-source cycles each ran the brain-wide global phases (embed-all/orphans/ purge/…) concurrently, thrashing the same rows and taking the worker 4→10GB in <60s → RSS-kill → orphaned stalls. Split them: per-source jobs now run only source-scoped (+ mixed) phases and stamp last_source_cycle_at; a new autopilot-global-maintenance job runs the global phases ONCE per window (idempotency_key + maxWaiting:1 = structural single-flight) and stamps autopilot.last_global_at. This is the codex-endorsed design that replaced the rejected skip-and-stamp-fresh approach (codex #1/#2): no freshness poisoning, no starvation — global work always runs as its own job, never marked done when it wasn't. PHASE_SCOPE is now a runtime partition (GLOBAL ∪ NON_GLOBAL == ALL). last_full_cycle_at still written for doctor/legacy (no longer a global gate). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(doctor): guard nullable engine in supervisor DB-lock fallback (#2227) Follow-up to the supervisor-visibility commit: doctor's engine binding is BrainEngine | null, so the inspectLock fallback must guard on a non-null engine (tsc TS2345). No behavior change — a null engine simply skips the DB-lock probe and falls back to the pidfile reading, as before. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(doctor): categorize autopilot_fanout_concurrency check as ops (#2194) Follow-up to the fan-out/concurrency commit: the doctor-categories drift guard requires every check name in doctor.ts to belong to exactly one category set. Add the new autopilot_fanout_concurrency check to OPS_CHECK_NAMES (infrastructure liveness, alongside wedged_queue/supervisor). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs: update KEY_FILES for the autopilot cycle split + supervisor degraded-retry (#2194 #2227) Post-ship document-release: refresh the KEY_FILES current-state entries that drifted — cycle.ts (GLOBAL/NON_GLOBAL phase split + last_source_cycle_at / autopilot.last_global_at), jobs.ts (per-source local_path brainDir, claim-time cooldown, autopilot-global-maintenance handler), supervisor.ts + child-worker (degraded retry instead of permanent give-up; hard ceiling), db-lock.ts (isLockHolderLive), handler-timeouts (new handler). Regenerated llms bundle. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(minions): handleTimeouts counts the timed-out run as a spent attempt (#1737) The per-job timeout_at dead-letter (handleTimeouts) set status='dead' without incrementing attempts_made, unlike the wall-clock and stall dead-letter siblings. It is the FIRST killer to fire for the long-lane handlers (subagent / embed-backfill / autopilot-cycle) because timeout_ms is stamped at submit, so a timed-out long job reported `attempts: 0/N (started: N)`. Mirror the siblings with attempts_made + 1 (terminal, no retry). Safe against double-count: the worker sweep runs handleStalled -> handleTimeouts -> handleWallClockTimeouts sequentially and awaited, each guarded on status='active', so the first to dead-letter excludes the row from the rest. Regression assertions added (test/minions.test.ts + e2e/minions-resilience.test.ts) so the increment can't be silently dropped. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(agent): recognize trailing switches in `agent run`, keep prompts freeform (#1738) parseRunFlags() broke flag parsing at the first positional token, so any flag after the prompt (`gbrain agent run "do X" --detach`) was swallowed into the prompt string and silently ignored. Now the no-value switches --detach/--follow/ --no-follow are hoisted when they trail the prompt, while everything else stays verbatim: an unknown --word is treated as prompt text (no "unknown flag" throw), a --switch mid-prompt is preserved, and `--` suppresses hoisting entirely for a literal escape. Value-flags now reject a missing or flag-shaped value (and --max-turns/--timeout-ms a non-number) instead of capturing undefined/NaN. Contract change: a prompt that starts with or trails an unguarded --word no longer errors; a literal trailing --detach needs `--`. Help text updated; tests revised + extended (test/agent-cli.test.ts). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(sync): honest live-sync status + progress-aware stall-abort (#1950) Finishes the #2255 honest-freshness story for two gaps it left. (a) `gbrain sources status` printed "idle" while a sync proc held the per-source lock (the reported bug). New shared liveSyncStatus() helper in db-lock.ts reads the SAME live-lock signal `gbrain doctor` uses; runStatus now shows "running" (BACKFILL column + a sync_running field in --json) and suppresses the misleading "never synced" warning while a sync is live. One helper, so the surfaces can't drift (doctor/status retrofit tracked as a follow-up). (b) A sync wedged-but-alive kept refreshing its lock heartbeat (it fires on its own timer) and hadn't hit the wall-clock deadline, so only a manual pkill freed it. New in-band stall watchdog keys off FORWARD IMPORT PROGRESS (progress.tick), not the heartbeat: if no file completes for GBRAIN_SYNC_STALL_ABORT_SECONDS (default 900s), it aborts via a controller composed into opts.signal, so the drain returns partial() (last_commit unchanged, next run resumes from the checkpoint) and withRefreshingLock releases the lock. Limits, documented in code: a single file slower than the window trips it; a fully starved event loop won't fire the timer (the wall-clock hard deadline is that backstop). Tests: liveSyncStatus (live/expired/none/per-source) in db-lock-inspect; the resolveStallAbortSeconds env matrix in sync-hard-deadline. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * feat(status): version field + per-section --deadline-ms budget (#1984) `gbrain status` had no version in its JSON envelope and could hang on a slow connection with no way to get a partial answer. Two additions: - version: the StatusReport JSON now carries the local gbrain CLI version so a poller can pin behavior to a build. Thin-client also surfaces remote_version (the brain server's version), and the get_status_snapshot MCP op reports its version for that parity. - --deadline-ms=N / --fast: a shared wall-clock budget. Each section is raced against the REMAINING budget via Promise.race (NOT process-watchdog, which SIGKILLs and can't return partial output), so one slow/hung section can't strand the snapshot — it's marked stale and the rest still return. The envelope gains partial:true + stale_sections[]; exit code stays 0 (a snapshot was produced). Invalid --deadline-ms → exit 2. Tests: parseDeadlineFlag + withSectionDeadline (hermetic), the usage-error exit, version presence in the PGLite envelope, and the op's version key. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(sync): report stall_timeout distinctly + document in-flight limit (#1950) Pre-landing review (codex + adversarial): the stall watchdog aborted opts.signal but the per-iteration abort checks returned partial('timeout'), collapsing a wedge-reap into a user --timeout/SIGINT so JSON consumers couldn't tell them apart. Add a 'stall_timeout' reason (set via a stallAborted flag) on the three import-loop abort sites; deletes/renames-phase and checkpoint sites stay 'timeout'. Sharpen the watchdog comment: the abort is observed BETWEEN files, so a hang inside a single importFile is not interrupted until it returns (TODO: thread a cancellation signal through importFile). * fix(agent): `--` escape suppresses trailing-switch hoisting anywhere (#1738) Pre-landing review: the leading-flag loop breaks at the first positional, so the `escaped` flag only fired for a leading `--`. A `--` placed after a positional left trailing-switch hoisting active, so `agent run note -- body --detach` silently detached and dropped the `--` as junk. Suppress hoisting whenever a literal `--` appears in the prompt. Regression test added. * fix(status): deadline-ms usage-error + scoped stale_sections + cancel losing remote call (#1984) Pre-landing review (codex): (1) bare `--deadline-ms` with no value silently fell through to no-budget/--fast instead of a usage error; (2) thin-client timeout reported both sync+cycle stale even under `--section sync`, naming a section the caller excluded (local path was already correct); (3) the section race abandoned the remote promise locally but didn't cancel the in-flight MCP call — pass the budget as timeoutMs so the losing side actually cancels. Regression test added. * v0.42.52.0 fix(reliability): autopilot dead-job storm + supervisor wedge + sync/status/minion reliability (#2194 #2227 #1994 #1737 #1738 #1950 #1984) Bundles the already-reviewed autopilot/supervisor stabilization (#2194 #2227 #1994: cycle split, per-source failure cooldown, fan-out clamp, degraded supervisor retry, DB-lock live-supervisor detection) with four operational fixes: minion timeout attempt-accounting (#1737), agent-run trailing-flag parsing (#1738), honest live-sync sources status + progress-aware stall watchdog (#1950), and status version + --deadline-ms partial result (#1984). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs: document GBRAIN_SYNC_STALL_ABORT_SECONDS env knob (#1950) Post-ship doc sync (/document-release): add the sync stall watchdog env var to the CLAUDE.md sync-tuning table (Five → Six knobs) + regenerate the llms bundle. * test: quarantine #2249 fanout tests as *.serial (R1 env-isolation) (#2194) The cherry-picked autopilot-fanout-clamp + doctor-autopilot-fanout-concurrency tests mutate process.env.GBRAIN_AUDIT_DIR in beforeEach/afterEach, which the check:test-isolation R1 lint flags (parallel shards load multiple files per process). Rename to *.serial.test.ts (sanctioned quarantine — they run under --max-concurrency=1) instead of restructuring the reviewed test bodies. No logic change; both files stay green (9 tests). Fixes the failing verify CI check. --------- Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> |
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c023a6041d |
v0.42.46.0 fix(engine): federated read scope reaches by-slug reads (#2200) (#2239)
* fix(engine): federated sourceIds[] scope on by-slug secondary reads (#2200) getTags/getLinks/getBacklinks/getTimeline (both engines) + TimelineOpts now accept a federated `sourceIds[]` read grant, precedence over scalar sourceId, filtering `source_id = ANY($::text[])` — mirroring getPage from v0.42.37.0. - getTags: `page_id = (subquery)` -> `IN (subquery)` + DISTINCT so a slug present in >1 granted source unions tags instead of throwing on a multi-row subquery. - getLinks/getBacklinks: federated branch scopes ALL THREE page endpoints (from, to, AND the authoring origin) so a cross-source link can't disclose a foreign slug. Scalar/unscoped branches unchanged (trusted internal callers keep the cross-source view). - getTimeline: Postgres 8-branch cartesian tree collapsed to one fragment-composed query; PGLite adds the sourceIds branch to its dynamic WHERE. * fix(ops): route by-slug reads through the federated source scope (#2200) get_page resolves tags against the concrete page's source; get_tags/get_links/ get_backlinks/get_timeline route through sourceScopeOpts(ctx) (replacing the copy-pasted scalar `ctx.sourceId ? {sourceId} : {}`). New linkReadScopeOpts promotes an UNTRUSTED remote scalar scope to sourceIds[] so legacy/pre-federated tokens also get all-endpoint link scoping; trusted local CLI keeps cross-source. * test: federated read scope on by-slug reads + engine parity (#2200) Per-op federated reads, isolation (out-of-grant -> empty), cross-source decoy guard, far-endpoint + origin leak guards (F1), same-slug union (D3A), empty-array contract, scalar-remote promotion (D1), getTimeline date-window after the Postgres fragment refactor (D5A), and engine-parity arms for all four methods. * chore: bump version and changelog (v0.42.46.0) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs(key-files): document federated by-slug read scope + linkReadScopeOpts (#2200) The #2200 fix routed get_page tags + get_tags/get_links/get_backlinks/ get_timeline through the federated source scope and added sourceIds[] to the engine read methods + TimelineOpts. Bring KEY_FILES.md to current state: the operations.ts entry's sourceScopeOpts read-op list now includes the by-slug reads and documents the linkReadScopeOpts helper (three-endpoint link scoping + untrusted-remote scalar promotion); the engine.ts entry notes the by-slug read methods + TimelineOpts carry the same sourceIds[] federated axis. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> |
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a81f7e05e8 |
v0.42.43.0 feat(context): push-based context (#2095) + teardown-exit hardening (#2084) (#2175)
* fix(cli): exit deliberately after bounded teardown instead of riding the 10s backstop (#2084)
Root cause: bounded teardown (endPoolBounded, #2015) RESOLVES, but lingering
sockets — embedding-provider fetch keep-alive, PgBouncer txn-mode sockets the
bound raced past — keep Bun's event loop alive, so every `gbrain query` paid
a flat 10s tax exiting via the hard-deadline force-exit banner.
Three changes, one contract:
- flushStdoutThenExit (cli-force-exit.ts): when main() resolves and the
command is not a daemon, exit deliberately — after stdout AND stderr drain
(writableLength===0, 'drain'-event + poll loop, 2s unref'd guard for a
blocked pipe). Incident #1959 (force-exit truncating piped stdout) is the
regression class; pinned by a 256KB real-pipe subprocess test.
- drainThenDisconnect (cli.ts): ONE owner-disconnect helper at all 8 sites
(op-dispatch, CLI_ONLY fall-through, search dashboard, doctor remediation
x3, ze-switch, dream, read-only timeout path). Drains the background-work
registry, then disconnect (best-effort), bounded by the 10s unref'd
hard-deadline — which is now armed around the TEARDOWN window only, not
before the op handler (the old placement would have force-killed any op
slower than 10s). Closes the filed TODOS P3 drain-hoist: six sites
previously skipped the drain entirely and had no hang timer at all.
- Inner process.exit sweep: mid-handler exits in engine-owning/output-bearing
paths (status, friction, claw-test, smoke-test, eval cross-modal /
takes-quality replay / conversation-parser / whoknows-thin, status-thin)
become process.exitCode + return so they flow through the drains and the
flush-exit. Pre-engine usage/parse/refusal exits stay as-is.
BrainRegistry.disconnectAll deliberately unchanged: zero production callers
in src/, per-engine disconnects already bounded, and the kernel reclaims
sockets on exit (src/core/timeout.ts doctrine).
DAEMON_COMMANDS gains 'watch' ahead of the #2095 push transport.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* test(e2e): PgBouncer transaction-mode pooler in CI + teardown e2e (#2084)
Three consecutive waves (#1972 → #2015 → #2084) fixed pooler-teardown bugs
verified only against one production deployment — CI had no transaction-mode
pooler and could never see the class. Now it can:
- docker-compose.ci.yml: `pgbouncer` service (transaction pooling) fronting
postgres-1, mirroring the production split-pool topology (direct :5432 +
pooled :6543). AUTH_TYPE=plain (pg16 SCRAM verifiers need the plaintext
password in the userlist) + IGNORE_STARTUP_PARAMETERS for the
statement_timeout/idle_in_transaction_session_timeout startup params
gbrain's client sets (the Supabase pooler whitelists the same).
- test/e2e/pgbouncer-teardown.test.ts: schema + fixture via the DIRECT url
into a dedicated `gbrain_pgbouncer` database (never races shard TRUNCATEs),
then spawns the real CLI against the POOLED url and asserts: exit 0,
stdout intact (the #1959 truncation class), and NO
"did not return within 10000ms — force-exiting" banner (pre-#2084 it
printed on 100% of query-shaped ops on this topology). Class bound, not
exact timing. Skips gracefully without GBRAIN_PGBOUNCER_URL.
- scripts/ci-local.sh: threads GBRAIN_PGBOUNCER_URL +
GBRAIN_PGBOUNCER_DIRECT_URL into all three e2e phases.
Verified live: both tests green against pgbouncer 1.25.2 in transaction mode.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* feat(schema): context_volunteer_events table (v116) — push-context feedback log (#2095)
One row per page the brain volunteers (op / reflex / watch channels).
"Used" is DERIVED, never written: pages.last_retrieved_at > volunteered_at
(the existing bumpLastRetrievedAt write-back is the open/cite signal), so
there is no second tracking path. session_id/turn are nullable
caller-supplied attribution; rationale is a deterministic template string,
never raw conversation text.
- Migration v116 (idempotent) + mirrors in src/schema.sql +
src/core/pglite-schema.ts + regenerated schema-embedded.ts (regen also
folds in pre-existing comment-only drift from the v114 links edits).
- src/core/context/volunteer-events.ts: insertVolunteerEvents (ONE
multi-row parameterized INSERT — never per-row awaited round-trips) +
purgeStaleVolunteerEvents (90-day GC, returns 0 on pre-v116 brains).
- Dream cycle purge phase prunes stale events alongside op_checkpoints /
brainstorm checkpoints / batch-retry audit files.
- RLS on Postgres comes from the v35 auto_rls_on_create_table event
trigger (the same mechanism that covered v110 page_aliases and v115
op_checkpoint_paths); the volunteer Postgres e2e pins it.
- No ::jsonb anywhere; no bootstrap probe needed (nothing references the
table pre-creation; writers guard with try/catch).
Tests: v116 shape + columns + indexes + live insert/purge round-trip on
PGLite (test/migrate.test.ts, 161 pass); schema-bootstrap-coverage green.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* feat(context): multi-turn window extraction + confidence-scored volunteer core (#2095)
- entity-salience.ts: extractCandidatesFromWindow(turns) — runs the existing
per-turn extractor across the last N turns (oldest→newest), merges by the
normalizeAlias form with occurrence/newest-turn/user-mention metadata, and
orders by salience (recency > frequency > user-role) so the MAX_CANDIDATES
cap drops stale assistant chatter, not the entity the user just named.
Closes the filed assistant-introduced-entities recall TODO; true pronoun
coreference (never-named antecedents) stays out of scope.
- retrieval-reflex.ts: ReflexPointer gains source_id + arm + confidence +
matchedNorm. ARM_CONFIDENCE (alias 0.9 / title 0.8 / slug-suffix 0.6)
lives next to the arm definitions so identity and score can't drift.
Arm-2 provenance is classified in JS (codex D8 — the combined OR can't
report which predicate matched). Federated sourceIds[] scope (alias arm
loops per source; arm 2 uses source_id = ANY — no engine-interface
change). Suppression gains 'slug-only' mode (codex D7, REQUIRED for
windowing): the legacy title-whole-word rule would suppress every entity
merely MENTIONED in a prior window turn, breaking the feature by
construction — slugs only enter context when a pointer/page was actually
surfaced. Default stays 'slug-and-title' for the window=1 legacy path.
- volunteer.ts (new): parseWindow (lenient user:/assistant: prefixes, CRLF,
unprefixed → one user turn), volunteerContext (zero-LLM: extract →
resolve → +0.05 multi-turn/newest-turn boost → min_confidence 0.7 gate →
cap 3/5; deterministic rationale strings, never raw conversation text),
and volunteerUsageStats (per-arm/channel precision from the
last_retrieved_at join, labeled approximate — 5-min throttle false
negatives, unrelated-read false positives; codex D9).
Tests: 35 green across volunteer-context (window parsing, pronoun follow-up
via assistant-introduced entity, confidence gating, slug-only suppression,
takes-fence privacy, multi-source scope, caps, stats join math) +
retrieval-reflex back-compat + resolve-ipc.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* feat(ops): volunteer_context op — CLI (stdin) + MCP, drained event sink (#2095)
New read-scope op on the contract surface (CLI `gbrain volunteer-context`
with stdin → window, MCP tool for free): takes a rolling conversation
window, returns confidence-gated page pointers with rationales + synopses.
`window` is optional-unless-stats (validated in the handler, codex D9);
`stats: true` returns the volunteered-vs-used precision summary, labeled
APPROXIMATE (the 5-min last-retrieved throttle and unrelated reads both
bias the join). Source scope threads through sourceScopeOpts — federated
grants narrow the volunteer to the granted sources.
Event logging is fire-and-forget through a new `volunteer-events`
background-work sink (volunteer-events.ts, mirrors last-retrieved: tracked
dangling promise set + bounded drain + snapshot-drop on timeout so a
long-lived process never accumulates ghosts). ONE batched INSERT per call,
drained on every exit path by the commit-1 drain hoist; failure never
fails the op (pinned by an injected failing-engine test).
cli formatResult renders both shapes (pointer lines with confidence/arm/
rationale; the stats summary with per-arm precision).
Tests: op contract surface, window-required validation, sink round-trip
with session_id/turn attribution, failing-engine fail-open, federated
grant scoping, stats mode (26 green on PGLite) + a real-Postgres e2e
proving the op + sink + stats join AND that context_volunteer_events has
RLS enabled (keeps the auto-RLS event-trigger mechanism honest for v116).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* feat(context): reflex consumes the rolling window + ambient-channel logging (#2095)
The default-on retrieval reflex now extracts entities from the last N turns
(retrieval_reflex_window_turns, default 4; env
GBRAIN_RETRIEVAL_REFLEX_WINDOW_TURNS; window=1 reproduces the legacy
current-turn-only behavior exactly). assemble() passes the recent
user/assistant turns (hard cap 12); the reflex slices to the configured
window. Assistant-introduced entities and "what did she invest in?"
follow-ups whose antecedent was NAMED in the window now surface pointers —
the issue's "zero agent-initiated queries" success criterion on the
ambient path.
Under windowing, suppression switches to slug-only (codex D7): the legacy
title-whole-word rule would suppress every entity merely MENTIONED in a
prior window turn, breaking the feature by construction. Slugs only enter
prior context when a pointer/page was actually surfaced, so
already-surfaced pages still suppress. The suppression mode flows through
all three resolver rungs (host opts, serve IPC request, direct Postgres).
Ambient-channel feedback (codex D11): the server-side resolver paths
(serve IPC + direct Postgres) log volunteered pointers with
channel: 'reflex' through the drained volunteer-events sink, so
`gbrain volunteer-context --stats` measures the default-on path where most
volunteering happens. Host-injected resolvers (no gbrain engine) can't
log — documented gap. Precision gates, 1.5s ceiling, fail-open, and the
pointer cap are unchanged.
Tests: prev-assistant-turn entity fires; window=1 legacy parity; slug-only
vs already-surfaced suppression; throwing resolver stays fail-open
(16 green).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* feat(cli): gbrain watch — push transport over stdin (#2095)
The issue's headline: the brain volunteers pages as the conversation flows,
instead of waiting to be asked. `some-transcript-feed | gbrain watch` reads
turns line-by-line ('user:'/'assistant:' prefixes set the role; unprefixed
lines are user turns), keeps a rolling window (--window-turns, default 4),
and streams confidence-gated pointers with rationales to stdout (--json for
JSONL). Session dedupe rides the core's slug-only suppression — a slug is
volunteered at most once per session. Events log on channel 'watch' with
session_id + turn through the drained sink.
Lifecycle: watch BLOCKS in the stdin iteration (like `jobs work`) — an
interactive TTY stays alive until Ctrl-C/Ctrl-D, piped input ends at EOF —
so it is deliberately NOT in DAEMON_COMMANDS (reverts the commit-1
placeholder): when main() resolves the work is over, the CLI_ONLY finally
drains volunteer events via drainThenDisconnect, and the entrypoint
flush-exit ends the process. Keeping it in the daemon set would have made
the piped EOF path hang on lingering sockets — the exact #2084 class.
SIGINT closes the stream and flows through the same drain path instead of
killing mid-write. Per-turn resolution failures are fail-open (the stream
never dies on a transient DB error).
Full wiring (eng-review D12): CLI_ONLY + CLI_ONLY_SELF_HELP (WATCH_HELP) +
THIN_CLIENT_REFUSED_COMMANDS (thin clients use the volunteer_context MCP
op) + main --help entry.
Tests: 18 green — help, per-turn volunteering + clean EOF return, rolling
window via assistant-introduced entity, session dedupe, --json shape with
turn attribution, channel-watch event rows, --min-confidence gate, CRLF/
blank tolerance, daemon-gate semantics. Live smoke: piped `gbrain watch`
on a fresh PGLite brain exits 0 at EOF with no force-exit banner.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* docs: KEY_FILES + push-context guide + TODOS for the #2084/#2095 wave
- docs/architecture/KEY_FILES.md (current-state): context entries gain the
window extractor, arm provenance/confidence, suppression modes, volunteer
+ volunteer-events modules; background-work entry now lists FIVE sinks and
the drainThenDisconnect owner-disconnect contract; new entries for
src/core/cli-force-exit.ts (the exit contract) and src/commands/watch.ts.
- docs/guides/push-context.md (new): the three channels (reflex/op/watch),
the confidence model, CLI usage, config keys, and the approximate-stats
caveat. Linked from CLAUDE.md's reference map.
- CLAUDE.md: ops line mentions volunteer_context + the guide link;
bun run build:llms regenerated in the same commit (freshness test green).
- TODOS.md: #2095 deferrals filed (SSE push channel, policy skill + doctor
check, structured messages[] param); the #1981 entity-detection TODO
narrowed (window extraction covered assistant-introduced entities +
named-antecedent follow-ups); the drain-hoist P3 marked DONE by the
#2084 wave.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* test(e2e): truncate context_volunteer_events in setupDB (#2095)
The new feedback-log table wasn't in ALL_TABLES, so volunteered-event rows
persisted across e2e runs on a reused database and poisoned count/stats
assertions in volunteer-context-postgres on the second run. No FK to pages
(slug join), so position before pages is for hygiene only.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* fix(cli): own the exit verdict — never trust ambient process.exitCode (#2084)
Caught by the full unit suite: `gbrain apply-migrations` on PGLite started
exiting 99. Root cause: PGLite's Emscripten runtime writes the WASM
backend's proc_exit status into process.exitCode (initdb at create-time,
the postmaster at close-time — `exitCode=status` in pglite's dist), and
the writes land ASYNCHRONOUSLY, outside any snapshot/restore window around
create/close (a guarded attempt verified this). The pre-#2084 success path
never read process.exitCode, so the pollution was invisible; the new
deliberate flush-exit propagated it faithfully.
Fix: gbrain records its own verdict. setCliExitCode(n)/getCliExitCode() in
cli-force-exit.ts — every gbrain-owned exit-code assignment routes through
the setter (still mirrored to process.exitCode for outside readers), and
both exit paths (entrypoint flushStdoutThenExit + the drainThenDisconnect
hard-deadline backstop) read the getter. Swept all assignment sites:
cli.ts (op error, friction, claw-test, smoke-test, eval runners, status,
import errors) + reindex/transcripts/brainstorm/frontmatter/autopilot.
Also updates the v0.42.20 structural pins to the drainThenDisconnect shape
(ordering invariant asserted INSIDE the helper + >=8 helper call sites,
superseding the two-inline-pairs assertion).
Verified: apply-migrations spawn test green; `init --migrate-only` exits 0;
an errored op still exits 1.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* test: re-pin the teardown-arming invariant at its post-#2084 home
Master's v0.42.41.0 triage wave and the #2084 wave fixed the same
pre-armed-timer bug independently; the merge keeps #2084's shape (arming
inside the shared drainThenDisconnect helper, covering all 8 exit paths).
The structural pin now asserts the same invariant — no pre-try arming;
gated, unref'd, before-drain, cleared — at the helper.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* test: coverage for ambient reflex-channel logging + watch window/cap flags
Ship coverage audit (85%, gate PASS) named five gaps; the two substantive
cheap ones close here: the codex-D11 logChannel='reflex' path now has a
behavioral pin (events land on channel 'reflex' through the drained sink;
no logChannel → no events), and gbrain watch's --window-turns / --max-pages
flags are exercised (turn-1 attribution under window=1; cap to one page).
Remaining flagged-not-blocking: the wallclock-timeout branch (untestable
without >10s real-clock flake — same rationale as the arming pin),
formatResult's volunteer case (module-private), and the cycle purge wiring.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* test: close the remaining plan-audit gaps — formatResult rendering + watch SIGINT
formatResult exported for tests (same import-safety contract as cliAliases);
test/cli-format-volunteer.test.ts pins the pointer lines, empty-gate message,
and approximate stats summary. test/watch-command.test.ts gains a real
subprocess SIGINT test: piped stdin that never reaches EOF, SIGINT mid-stream,
assert exit 0 with no force-exit banner — the drain-then-exit lifecycle under
the actual signal, not just the shared exit path.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* fix: doctor's FAIL verdict was zeroed by the owned exit — sweep stragglers + class pin
The merged-state suite caught it: doctor --fast --json reported FAIL but
exited 0. Master's v0.42.41.0 brought raw `process.exitCode =` writes
(doctor.ts hasFail ternary, extract.ts) that the #2084 verdict-owning exit
silently zeroes — getCliExitCode() deliberately never reads ambient
process.exitCode (the PGLite-Emscripten pollution defense), so any setter
that bypasses setCliExitCode reports success on failure.
Swept both sites and added the structural class pin: a test greps src/ for
raw `process.exitCode =` outside cli-force-exit.ts, so the next merge that
introduces one fails loudly instead of lying about exit codes.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* chore: bump version and changelog (v0.42.43.0)
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* test: quarantine the watch SIGINT subprocess test to the serial lane
The parallel unit shards flake on concurrent CLI subprocess spawns (failed
at 7ms in-suite, green solo) — same isolation rationale as
apply-migrations-pglite-spawn.serial.test.ts and #2141's R3 quarantine.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* docs: update project documentation for v0.42.43.0
Post-ship doc verification against the release diff (#2095 push-based
context + #2084 superset hardening), with a cross-model doc review:
- push-context.md: version tag corrected to v0.42.43.0; per-call knobs
now cover prior_context/days and watch's flag surface accurately;
feedback-log writes described as best-effort; synopsis fence-strip
described as unconditional.
- CLAUDE.md: stale operation count (~47 -> ~90); volunteer_context
release reference corrected to v0.42.43.0.
- KEY_FILES.md: ci-local entry rewritten to current topology (4-shard
parallel default, four Postgres services, transaction-mode PgBouncer
+ GBRAIN_PGBOUNCER_URL/_DIRECT_URL exports); stale E2E file counts
dropped from the selector entry.
- TESTING.md: inventory entries for the new #2084 structural pins
(cli-exit-verdict-pin, cli-pipe-truncation), the push-context test
suite (volunteer-context, watch-command, watch-sigint.serial,
cli-format-volunteer), migrate v117 coverage, and the two new E2E
files (pgbouncer-teardown env gating, volunteer-context-postgres RLS
pin); check:all row corrected (not a superset of verify).
- AGENTS.md + RELEASING.md: ci:local descriptions updated to the
sharded + pooler topology.
- CHANGELOG (wording only, entry preserved): "retrieved" instead of
"opened" for the used-signal, pooler scoped to the local CI gate,
feedback log labeled best-effort.
- llms-config.ts: index the new push-context guide; bundles
regenerated (build:llms) and freshness test green.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* docs(test): correct the v116 reference — the table shipped as migration v117
* fix: pre-landing review hardening — federated alias parallelism, trust-boundary clamps, shared protocol helpers (#2095)
Five specialist reviewers (testing/maintainability/security/performance/
data-migration) on the reconciled diff; every finding applied:
Performance: the alias arm now resolves all granted sources CONCURRENTLY
(a federated caller paid M sequential RTTs per turn — ~355ms at 5 sources
cross-region, inside the reflex's 1.5s budget); watch's session dedupe is
O(1) Set membership instead of a monotonically growing priorContext string
(O(T²) over a long-lived session); getWindowTurns iterates from the tail
(per-turn cost no longer grows with session length); the resolver's
provenance maps fold into the existing candidate pass.
Security: volunteer_context clamps caller-supplied attribution at the trust
boundary — session_id capped at 256 chars (a read-scoped token could bank
~1MiB TEXT per request, retained 90 days), turn logged only when a safe
integer (a non-integer threw inside the batched INSERT and silently dropped
the whole batch). The privacy comments now state precisely what rationale
may contain (the matched entity's surface form — which by construction
resolved to an existing alias/title/slug — never free conversation text).
Maintainability: TURN_PREFIX_RE + formatVolunteeredPage exported from
volunteer.ts and shared by watch/cli (the two surfaces can no longer
drift); volunteerEventRowsFrom is the single VolunteerEventRow assembly
site for all three channels; watch's window default now honors the same
retrieval_reflex_window_turns config knob the reflex reads; the stale
pre-v116 comments swept to pre-v117.
Testing: the two flake-class CRITICALs fixed (pipe test asserts the
backstop banner instead of a cold-CI-hostile 9s wall bound; the SIGINT test
waits on watch's new machine-readable ready line instead of a fixed 15s
sleep — 2.5s and deterministic now); new coverage for the sink's timeout
branch + ghost-reference drop, watch per-turn fail-open, untrusted knob
clamps (min_confidence/max_pages/days), window-cap ordering (newest user
mention survives), serve-IPC suppression passthrough + channel=reflex
logging, windowTurnCount edge semantics, and structural pins for the sink
registration + cycle purge wiring. The exit-verdict pin's grep is now
operator/whitespace-tolerant.
Deferred with TODOs: resolver index shapes for the per-turn query;
batched first-prune after a long dream-cycle gap.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* fix(context): red-team hardening — pre-cap dedupe, delivery-side reflex logging, window clamp
Four red-team findings on the #2095 push-context surface:
- RT1 starvation: watch's session-dedupe Set filtered AFTER volunteerContext's
cap, so a recurring already-pushed entity burned cap slots every turn and
starved fresh pages behind it. VolunteerOpts.excludeSlugs now skips inside
the pointer loop BEFORE the confidence gate and the cap.
- RT3 honest stats: reflex-channel event logging moved from inside the
resolver to the DELIVERY point — serve's resolve-IPC onDelivered hook fires
only after the response write succeeds, and buildReflexAddition logs only
after the per-turn timeout admits the block. A block the client's 250ms
budget abandoned was never injected and no longer counts as volunteered.
(logChannel resolver opt removed; logDeliveredReflexPointers is the seam.)
- RT5 unbounded window: --window-turns is clamped to [1, 64] so a config typo
can't reintroduce the re-scan-everything-per-turn cost class.
- RT2/RT4 documented + filed: PGLite watch connection monopoly (WATCH_HELP,
push-context guide, TODO to route watch via serve IPC); host-resolver
suppression contract at ResolveEntitiesFn (TODO for a capability gate).
Tests: starvation guard (watch + volunteerContext unit), window clamp floor +
ceiling, delivery-side logging (helper writes channel=reflex through the
drained sink; bare resolver writes nothing; empty list no-op), IPC wiring test
rewired to onDelivered. KEY_FILES.md + push-context.md updated; build:llms run.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* fix(context): env-plane window knob works config-less; harden two gateway-state-leak victims
Three CI-only check failures, two root causes:
1. windowTurnCount ignored GBRAIN_RETRIEVAL_REFLEX_WINDOW_TURNS when
loadConfig() returned null (no config file AND no DATABASE_URL — a clean
CI shard with no brain). loadConfig drops its env→config mapping in that
case, so the documented escape hatch silently died and the window fell
back to 4 → windowed extraction widened when the test set window=1 →
prior-turn entity leaked. Fixed: read the env var directly in
windowTurnCount, mirroring reflexEnabled's direct process.env read. This
is a real product bug, not just a test artifact — any config-less host
using the env hatch was affected. Regression test pins it.
2. sync-cost-preview + doctor-federation-health failed only IN-SHARD: a
sibling test configured a non-legacy (ZeroEntropy 1280-d / $0.05) gateway
and never reset it. The legacy-embedding preload only restores the
OpenAI/1536 default when the gateway slot is EMPTY, so a non-empty foreign
config survives into the next file — and a file's beforeAll runs BEFORE
the preload's restoring beforeEach, so federation-health built a
vector(1280) column and its 1536-d fixture hit CheckExpectedDim. My new
test files reshuffled the deterministic file→shard assignment, exposing
this latent ordering bug. Hardened both victims to establish the gateway
state they assert (sync-cost-preview resets to the unconfigured fallback;
federation-health pins legacy 1536 before initSchema) so they're
order-independent. Verified against a simulated leaker run before them.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* test(context): use withEnv() in the window env-hatch test (test-isolation guard)
The regression test added in
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v0.42.42.0 fix(cli): bounded teardown + explicit exit — kill the 10s force-exit tax on txn-mode poolers (#2084) (#2141)
* feat(core): finishCliTeardown + flushThenExit — bounded teardown, owned exit verdict (#2084) cli-force-exit.ts becomes the single owner of one-shot CLI exit + teardown: - finishCliTeardown: bounded sink drain -> bounded disconnect under a backstop whose deadline is COMPUTED from the bounds it guards (floor 10s; GBRAIN_TEARDOWN_DEADLINE_MS env override). Arms at teardown start, never before the op handler. - flushThenExit: stdio write-fence (unref'd guard, EPIPE-safe) + REF'D aliveness grace for non-TTY stdio — Bun only delivers queued pipe writes while the process is alive (no flush API reaches the native queue). - setCliExitVerdict/currentExitCode: the exit verdict lives in a gbrain-owned channel, never read back from process.exitCode (PGLite's Emscripten runtime scribbles its own status there mid-run). - background-work.ts exports backgroundWorkSinkCount() for the deadline formula. Unit tests + a spawned-Bun harness proving byte-complete piped output. * fix(cli): route all nine disconnect sites through finishCliTeardown; one exit seam (#2084) Deletes the pre-handler 10s force-exit timer (it measured handler + teardown combined: PgBouncer txn-mode deployments paid a flat 10s banner tax on every query, and any >10s op was killed mid-run with exit 0 and truncated output). Sweeps op-dispatch, CLI_ONLY fall-through, search dashboard, read-only timeout path, dream, doctor x3 (fixing a pre-existing pool leak when DB checks throw), and ze-switch. The ONE process exit lives in main().then/catch via flushThenExit(currentExitCode()), gated by shouldForceExitAfterMain(). Exit-code writers (op-dispatch catch, reindex, transcripts, brainstorm, autopilot, frontmatter) now set the verdict through setCliExitVerdict. * fix(pglite): contain Emscripten's process.exitCode writes at PGlite.create (#2084) PGLite's WASM runtime writes its own status into process.exitCode (99 at create; in-memory brains run initdb whose status lands on a later tick; the exit status at close) — on PGLite every error exit was silently clobbered. preservingProcessExitCode wraps create() to keep the global tidy; db.close() stays unwrapped (its 0-write is baseline behavior test runners depend on). The CLI verdict itself is immune: it lives in the owned channel. * test: e2e + structural pins for the #2084 teardown contract E2E: failed op exits 1; every swept command spawned (brain-copy isolation for mutators, no-network); slow-handler regression via the deadline env knob; piped --json parses complete; teardown banner absent on every happy path; daemon survival untouched. Structural: no bare awaited engine disconnects in cli.ts; DISCONNECT_HARD_DEADLINE_MS gone; >=9 helper call sites; verdict channel + create-wrap pins. * test: fix R1 env-isolation violations in retrieval-reflex tests Pre-existing on master: both files mutated GBRAIN_RETRIEVAL_REFLEX directly, failing scripts/check-test-isolation.sh (bun run verify). Converted to the canonical withEnv() pattern; the reflex describe's beforeEach also never restored the flag, leaking it across the shard. * docs: KEY_FILES entries for the teardown contract; close + file TODOS (#2084) KEY_FILES.md: current-state entry for cli-force-exit.ts (helper + central exit seam pair, verdict channel, cli.ts-scoped claim); background-work.ts and pglite-engine.ts entries updated. TODOS.md: the drain-before-owner-disconnect P3 (filed from #1972) is done by this wave; files the trigger-gated GBRAIN_COMMAND_DEADLINE_MS follow-up (eng-review D2/D14). * fix: pre-landing review fixes (#2084) Review army (testing/maintainability/security/performance, 0 critical): - drain defense-in-depth: a throwing drain warns and still disconnects (cannot escape a caller's finally or skip the engine teardown) - behavioral tests for preservingProcessExitCode (connect pins 0; create-throw restores the pre-call verdict) - D9 widening test (live-registry sink count feeds the deadline formula), env 0/negative boundary cases, verdict mirror-write assertion - stale comments: header diagram backstop line, structural-test 'both lifecycle calls' contradiction, KEY_FILES 10s-force-exit clauses, e2e D11 falsification story corrected - named the formula's pool-end literals * fix: adversarial-review hardening — daemon-safe command resolution, flush knob, ref'd backstop (#2084) Cross-model adversarial review (Claude subagent + Codex, both P1'd it): - shouldForceExitAfterMain now resolves the command through parseGlobalFlags — the old first-non-dash heuristic read `gbrain --timeout 30s serve` as command "30s" and the new exit seam would have killed the daemon ~250ms after boot with exit 0 (unit-pinned) - GBRAIN_FLUSH_GRACE_MS env override for the non-TTY aliveness grace (batch consumers piping large payloads to slow readers can raise it; agent loops can lower it) - backstop timer is now REF'D: a hung teardown on an otherwise-empty event loop previously exited naturally — skipping the flush and surfacing PGLite's scribbled process.exitCode - flushThenExit: real process.exit latched once per process - doctor-site comment corrected; in-command process.exit teardown-bypass class (pre-existing) filed as a P2 TODO * chore: bump version and changelog (v0.42.42.0) Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * test: move #2084 exitCode-containment lifecycle tests to the serial quarantine (R3) * docs: update project documentation for v0.42.42.0 - docs/TESTING.md: replace the stale 4-file serial-quarantine enumeration with a current-state description (the quarantine is glob-discovered, now several dozen files incl. the #2084 exitCode-containment suite); add unit inventory entries for test/cli-finish-teardown.test.ts and test/flush-then-exit-harness.test.ts. - docs/architecture/KEY_FILES.md: rephrase the pglite-engine exitCode containment note to current-state wording (clears the check-key-files-current-state prose-history warning). llms bundles regenerated (byte-identical: both docs are link-only). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * docs: apply cross-model doc-review findings for v0.42.42.0 Codex review of docs-vs-shipped-code found 9 gaps; all verified against the code before fixing: - CHANGELOG.md (0.42.42.0 entry, precision narrowing only — no entries touched): "every CLI exit path" -> "every cli.ts disconnect site"; "on every path" -> "on every routed exit path"; dream/doctor/ze-switch claim scoped to dispatcher teardown (command-internal process.exit sites are tracked in TODOS as the open P2). - docs/architecture/KEY_FILES.md: the teardown backstop is REF'D, not unref'd (matches the F3 adversarial-review decision in the code). - src/core/cli-force-exit.ts: header diagram comment had the same stale unref'd claim + `process.exitCode ?? 0`; now matches the implementation (ref'd timer, `currentExitCode()`). Comment-only change. - docs/TESTING.md: verify is the 30-check parallel battery via run-verify-parallel.sh (was described as 4 checks); CI is 10 weighted LPT shards + dedicated verify/serial/slow jobs (was "4-way FNV on shard 1"); test:serial runs one bun process per file (not --max-concurrency=1); dead "cap: 10" line rewritten as debt guidance; inventory entries added for test/cli-should-force-exit.test.ts and test/e2e/pglite-cli-exit.serial.test.ts. bun run verify green (30/30); #2084 test files green; llms bundles regenerated (byte-identical — reference docs are link-only). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix: route v0.42.41.0's raw exitCode writers through the verdict channel; reconcile merged structural pins (#2084) CI fallout from merging the v0.42.41.0 triage wave into the #2084 exit-seam design — both waves fixed the same timer-placement bug independently: - doctor.ts + extract.ts set failure exit codes via raw `process.exitCode =` writes (v0.42.41.0's process.exit -> exitCode conversion); the #2084 exit seam reads only the gbrain-owned verdict channel, so doctor FAILs exited 0 (Tier 1 RLS e2e + half-migrated-Minions tests). Converted to setCliExitVerdict, same as the wallclock-124 site in the merge commit. - cli-force-exit-teardown-arming.test.ts pinned v0.42.41.0's inline finally-armed timer, which the merge replaced with finishCliTeardown; rewritten to pin the merged invariant (no pre-try arming in cli.ts; the backstop arms inside the helper before the drain). - eval-capture drain timing bound 1s -> 2s: flaked at 1023ms under CI shard load after the new test files shifted LPT shard packing (13x budget slack still proves bounded-not-hung). --------- Co-authored-by: Claude Fable 5 <noreply@anthropic.com> |
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ecd6ae8772 |
v0.42.40.0 fix(extract,ingest): well-form lone UTF-16 surrogates before jsonb (#2011) (#2031)
* fix(extract,ingest): well-form lone UTF-16 surrogates before jsonb (#2011) excerpt() in link-extraction.ts sliced the link-context window by raw UTF-16 index, so a boundary landing inside a non-BMP char (emoji, math, CJK) left an unpaired surrogate half in `context`. Serialized to JSONB for the jsonb_to_recordset batch insert, Postgres rejects it at the ::jsonb cast and aborts the whole batch — wedging `extract --stale` because the staleness bookmark only advances on a clean finish. - text-safe.ts: new ensureWellFormed() (Bun isWellFormed/toWellFormed) — one shared surrogate-cleaning primitive. - link-extraction.ts: excerpt() well-forms the slice (root-cause fix). - batch-rows.ts: new sanitizeForJsonb() = ensureWellFormed(stripNul(s)) applied to every free-text body field (link context; timeline summary/detail/source; take claim/source). Identity/security fields stay un-sanitized and fail closed. - postgres-engine.ts + pglite-engine.ts: scalar addLink + addTimelineEntry use sanitizeForJsonb too, matching the batch path on both engines. - brainstorm/orchestrator.ts: consolidate hand-rolled sanitizeUnicode onto ensureWellFormed (also fixes consecutive-lone-surrogate mishandling). Tests: ensureWellFormed unit cases (incl. consecutive lone surrogates), an excerpt window-split regression, PGLite + Postgres-e2e surrogate cases across all free-text fields and scalar paths, and fail-closed identity-field tests proving sanitization was NOT extended to slugs/holders. * v0.42.39.0 chore: bump version and changelog (#2011) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs: update project documentation for v0.42.39.0 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * v0.42.40.0 chore: re-slot release version (was 0.42.39.0) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test: fix env-mutation isolation violations in retrieval-reflex tests check:test-isolation (rule R1) flags direct process.env mutation in non-serial test files — bun's parallel runner loads multiple files into one process, so a leaked GBRAIN_RETRIEVAL_REFLEX flips reflex behavior in unrelated tests. Both files landed via the #2019 merge; convert the beforeEach/afterEach env juggling to the canonical withEnv() wrapper, which restores the prior value via try/finally even on throw. Fixes the failing `verify` CI check on #2031 (and the `test-status` aggregate that inherits it). All 30 verify checks green locally. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> |
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099d9a8f55 |
v0.42.34.0 feat(search): typed-edge relational retrieval — relationship questions get relationship answers (#1959)
* feat(search): deterministic relational-query parser
Pure, ReDoS-bounded parser that detects relationship queries ("who invested
in X", "who at X works on Y", "who introduced me to X", "what connects A and
B") and maps them to typed edges. Schema-pack-extensible vocab with subset
validation against the link types ingest produces, so query-side and
ingest-side relation vocabularies can't drift. No-match / pronoun-seed /
adjacency guards keep it precision-first (a candidate only; the arm fires
only when a real seed also resolves).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* feat(engine): relationalFanout typed-edge fan-out (both engines)
Generalizes traversePaths to a SEED ARRAY, aggregating to ranked NODES
(shortest hop, edge-richness count, via-link-types, shortest connecting
path, canonical chunk id) instead of edges. Within-source traversal (never
crosses a source boundary even across a federated scope), link_source=
'mentions' excluded by default, deleted_at filtered at seed + every neighbor
+ every node, bounded depth (<=3) + candidate cap. Adds RelationalFanoutRow
/ RelationalFanoutOpts + the relational SearchResult/SearchOpts fields to
types.
Lands in lockstep in postgres + pglite engines, pinned by a DATABASE_URL-
gated parity block in engine-parity.test.ts; a PGLite unit test exercises
the SQL (typed-edge filter, mentions exclusion, deleted_at, canonical chunk,
multi-seed connects, determinism) in default CI.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* feat(search): relational recall arm + federation key hardening
Wires edge-derived candidates into bare hybridSearch as a FOURTH RRF arm
(relational-recall.ts): parse the original query -> scope-aware,
confidence-gated seed resolution (drops fallback_slugify; never traverses
from a guess) -> relationalFanout -> batch-hydrate, reinforcing each page's
REAL canonical chunk (page-level key for chunkless entity pages) ->
--explain attribution + fail-open audit row. Text-only (no-op in image
mode); pure no-op for non-relational queries; rides every downstream stage
(cosine, post-fusion boosts, dedup, reranker, autocut, token budget).
Mode wiring: relationalRetrieval + relational_retrieval_depth knobs
(conservative off; balanced/tokenmax on; depth 2), per-call thread-through
in both bare + cached paths, KNOBS_HASH_VERSION 9->10 (rel=/reld=), config
keys, modes-dashboard descriptions, and a `relational` param on the query op.
Federation hardening (structural, engine-wide): the RRF/dedup key now
carries source_id via a shared rrfKey() (fixes a latent cross-source
collapse where same-slug pages in different sources merged), and the query
cache scopes by a canonical source-set key (cacheScopeKey) so a federated
read can't be served a single-source row.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* feat(eval): relational benchmark + recall@k harness metrics
NamedThingBench harness gains recall@k / recall@10 (the relational headline
metric) on QuestionResult + FamilyReport, plus typed seed/linkTypes/kind on
NamedThingQuestion so the graph-relationship family is machine-checkable.
Adds the relational benchmark corpus (test/fixtures/retrieval-quality/
relational/): a small entity graph whose answers are LEXICALLY UNRECOVERABLE
— every page body is generic and never names the entity it relates to, so
only the typed edge connects query to answer. corpus.ts is the canonical
source for both the seed loader and the 38-question gold set; relational.jsonl
is generated from it (a drift test pins them equal).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* feat(eval): relational A/B proof + arm fires on all retrieval paths
Fixes the integration bug the eval caught: the relational arm was only
injected on the main RRF path, so it silently did nothing whenever vector
was unavailable — no embedding provider configured (the default in many
deployments) OR embed failure. The arm is now built once and fused via RRF
on ALL THREE hybridSearch return paths (no-embedding-provider, embed-failed
keyword fallback, main path). Without this it would have been dead in
exactly the setups that most need it.
Adds `gbrain eval retrieval-quality --ab-relational`: runs the gold set
twice (arm off vs on) in a fixed mode and reports the graph-relationship
recall@10 lift + Hit@3 + latency add. The CI A/B test pins the headline
result — recall@10 jumps from <25% (lexically unrecoverable) to >75% with
the arm on — and a non-relational query returns identical results arm-on vs
off (the no-op / no-regression gate).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* chore: bump version and changelog (v0.42.34.0)
Relational retrieval feature: typed-edge recall arm + federation key
hardening. Also updates the KNOBS_HASH_VERSION 9→10 assertions across the
remaining search test files (the bump invalidates relational-off cache rows).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* docs: document typed-edge relational retrieval (v0.42.34.0)
CLAUDE.md Search Mode: add relationalRetrieval to the knob table, the
knobs_hash v=9→10 note, and a relational-retrieval summary. RETRIEVAL.md:
add the relational recall arm to the pipeline diagram. Regenerate llms
bundles (build:llms).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* fix(test): size relational fixtures to the actual embedding-column dim
CI shard runs with the ZeroEntropy gateway default (1280-d), but the
relational test fixtures hardcoded 1536-d embeddings, so chunk inserts were
rejected with "expected 1280 dimensions, not 1536" (CheckExpectedDim) — the
`test (6)` shard + `test-status` failures. The column width tracks the
configured gateway default and can shift with shard order, so fixtures now
probe `content_chunks.embedding`'s actual `atttypmod` after initSchema and
size embeddings to it (the pglite-engine.test.ts pattern), via a shared
`probeEmbeddingDim` helper. Verified passing at a forced 1280-d column.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---------
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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5a06af5a57 |
v0.42.32.0 fix(sync): coerce non-string frontmatter titles + bounded auto-skip failure ledger (#1939) (#1956)
* fix(import): coerce non-string frontmatter title/slug/type (#1939) YAML `title: 2024-06-01` parses to a Date and `title: 1458` to a number; the old `(frontmatter.X as string)` cast was a compile-time lie, so downstream `.toLowerCase()` threw and (via the importer failure gate) could wedge sync indefinitely. parseMarkdown now coerces via coerceFrontmatterString (Date -> UTC ISO date, deterministic), and the pure assessContentSanity self-protects against a non-string title. * feat(sync): bounded auto-skip failure ledger; poison file can't wedge indexing (#1939) New src/core/sync-failure-ledger.ts owns the failure store + a crash-safe, multi-source, concurrent bounded auto-skip valve. A file that fails N consecutive syncs (GBRAIN_SYNC_AUTOSKIP_AFTER, default 3) auto-skips so it can't freeze all indexing forever, while fresh failures still fail-closed and a `<head>` history-rewrite sentinel hard-blocks even with --skip-failed. - (source_id, path) keying — failures never merge across sources - success clears a path so attempts are truly consecutive - advance-before-ack ordering (a crash can't mark a file skipped while wedged) - shared applySyncFailureGate used by BOTH the incremental and full-sync gates - legacy-row normalization + duplicate collapse on load - cross-process lock + atomic temp-rename, age-based stale-lock break sync.ts re-exports the ledger for existing callers; import.ts records source-scoped and defers the bookmark to the gate under managedBookmark. * fix(doctor): sync_failures severity via one shared decision on both surfaces (#1939) Local buildChecks and remote doctorReportRemote now both route through decideSyncFailureSeverity, so a stuck bookmark escalates WARN -> FAIL consistently (oldest-open age > fail cadence, or large unresolved count), auto-skipped pages stay visible (WARN, not hidden), and the acknowledged/acknowledged_at field-split that caused drift is gone. The remote surface stays subprocess-free (file read + Date.parse only). * chore(test): add trailing newline to e5-lease-cap-ab baseline fixture * fix(sync): address adversarial review findings on the failure ledger (#1939) - #1: a parse-failed file that is later deleted/renamed-away no longer leaves a permanent open ledger row. Removed paths (filtered.deleted, renamed-from, and the "gone from disk" forward-delete skip branch) are treated as resolved so the ledger self-heals instead of aging doctor to a stuck FAIL. - #3: decideSyncFailureSeverity escalates to FAIL on OPEN (blocking) failures only — auto_skipped rows already advanced the bookmark, so they stay WARN-visible regardless of count, matching the state-machine contract. * chore: bump version and changelog (v0.42.30.0) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs: document sync-failure ledger + auto-skip valve for v0.42.30.0 KEY_FILES.md: new src/core/sync-failure-ledger.ts entry (bounded auto-skip state machine, decideGateAction/decideSyncFailureSeverity/applySyncFailureGate, GBRAIN_SYNC_AUTOSKIP_AFTER); update sync.ts (failure store moved to ledger, re-exported), doctor.ts (sync_failures severity via shared rule on both surfaces), markdown.ts (coerceFrontmatterString), import.ts (managedBookmark). live-sync.md: poison-file auto-skip tricky-spot. Regenerated llms-full.txt. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * chore: re-bump to v0.42.31.0 (queue collision on 0.42.30.0) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * chore: re-bump to v0.42.32.0 (queue collision) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> |
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f401d7407e |
v0.42.31.0 feat(links): open link_source provenance + link-add/link-rm/link-sources (#1941) (#1957)
* feat(links): relax link_source CHECK to kebab-case provenance + migration v114 Open link_source from a closed allowlist to a kebab-case format gate (^[a-z][a-z0-9]*(-[a-z0-9]+)*$, char_length<=64) so external derivers stamp their own provenance (e.g. citation-graph) without a per-deriver migration. Migration v114: Postgres NOT VALID + VALIDATE (lock-friendly, transaction:false); PGLite plain DROP+ADD. Updates the schema.sql + engine provenance contract comments. (#1941) * feat(links): expose link provenance on link ops + link-add/link-rm/link-sources add_link/remove_link now accept --link-source/--link-type; add_link guards the reconciliation-managed built-ins (markdown/frontmatter/mentions/ wikilink-resolved) and defaults omitted provenance to 'manual' (was the misleading engine default 'markdown'). New cliHints.aliases mechanism with a startup collision guard registers link-add/link-rm; printOpHelp shows the invoked alias name. New list_link_sources read op + listLinkSources engine method (both engines, {sourceId?,sourceIds?}, deterministic order) powers `gbrain link-sources`, added to the minion read allowlist. (#1941) * test(links): kebab provenance, op guard, link-sources, aliases + parity Covers the v114 regex/length boundaries, upgrade-path constraint swap on existing data, the managed-built-in op guard + manual default, remove_link type/source filters, list_link_sources scoping (scalar + federated) and PG/PGLite parity, and alias resolution/collision/help. Fixes the prior 'inferred'-rejection assertion (now valid kebab) in the mentions test. (#1941) * chore: bump version and changelog (v0.42.31.0) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs: update KEY_FILES for v0.42.31.0 link provenance surface KEY_FILES.md current-state updates for #1941: link_source now an open kebab-case provenance (migration v114), the add_link/remove_link guard + defaults, list_link_sources + listLinkSources, and cliHints.aliases. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(minions): supervisor queue-singleton keying + pidfile cleanup (follow-up #1849) Two correctness bugs in the v0.42.29.0 supervisor-singleton work, caught by adversarial review: - supervisorLockId mixed a config-derived DB identity into the key, but the lock row already lives inside the target database. Two supervisors on the same physical DB via different-but-equivalent URLs (pooler vs direct port, host alias, trailing params) computed different ids and BOTH acquired the "singleton" lock. Key on the queue alone; the database half of the mutex is physical. Removes the now-dead currentDbIdentity() from worker-registry. - The pidfile-cleanup process.on('exit') listener was installed AFTER the DB-lock acquire, so the LOCK_HELD early-exit stranded the pidfile this process had just created. Install the listener first. Regression test pins the listener-before-lock ordering; updates the lockId test to the queue-only invariant; KEY_FILES updated to current state. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> |
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f7f8512b14 |
v0.42.28.0 fix(engine): batch inserts use jsonb_to_recordset, not text[] array literals (#1861) (#1927)
* fix(engine): batch inserts use jsonb_to_recordset, not text[] array literals (#1861) addLinksBatch/addTimelineEntriesBatch/addTakesBatch passed free text through unnest(${arr}::text[]); postgres.js serialized it to a Postgres text[] literal that array_in rejected ("malformed array literal") on calendar/Zoom context, aborting the whole `extract links --stale` sweep. Bind the batch as one JSONB doc via jsonb_to_recordset(($1::jsonb)->'rows') through the audited executeRawJsonb contract instead. Shared row builders (src/core/batch-rows.ts) keep both engines byte-identical; NUL is stripped only from free-text body fields (context/summary/detail/claim), while identity/security fields (slugs/source_ids/holder/kind/dates) still reject NUL. addTakesBatch is now batchRetry-wrapped ('addTakesBatch' audit site) and its BrainEngine signature takes BatchOpts. Scalar addLink context is NUL-stripped too. Regression tests on both engines: PGLite always-on poison/NUL/parity suite + DATABASE_URL-gated Postgres lane (the engine that actually crashed). * test: make "no Anthropic key" tests hermetic via withoutAnthropicKey hasAnthropicKey() reads both ANTHROPIC_API_KEY and ~/.gbrain config; tests that only deleted the env var fired a real LLM call on configured machines (warning flipped NO_ANTHROPIC_API_KEY -> LLM_OUTPUT_NOT_JSON). New test/helpers/no-anthropic-key.ts neutralizes both sources (env + GBRAIN_HOME temp dir) for the duration of the call. Refactors the five no-key tests in think-pipeline + takes-mcp-allowlist to use it, including two that previously passed only by luck of the live LLM output. * chore: docs + version bump (v0.42.28.0) KEY_FILES.md/RETRIEVAL.md describe the jsonb_to_recordset batch path; TODOS.md files the #1861 follow-ups (element-isolation, remaining ::text[] sites, shared SQL-string hoist, batch-insert edge-case tests). CHANGELOG + VERSION + package.json to 0.42.28.0. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs: sync TESTING.md batch-insert references for v0.42.28.0 The #1861 fix migrated links/timeline/takes batch inserts from unnest(::text[]) to jsonb_to_recordset. Update the stale "postgres-js unnest() binding" note and add the two new poison-regression test files (test/links-timeline-jsonb-poison.test.ts PGLite half, test/e2e/jsonb-batch-poison-postgres.test.ts Postgres lane) to the inventory. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(sql-query): reject top-level array jsonb params in executeRawJsonb (#1861 P2a) The "no top-level array" rule was only a comment. A bare JS array bound to a $N::jsonb position can serialize as a Postgres array literal (not jsonb) through postgres.js, silently re-entering the "malformed array literal" class #1861 just escaped. executeRawJsonb now throws a clear error steering callers to the { rows: [...] } object wrapper. Verified breaks zero call sites (all pass objects or null). Codex adversarial P2a; batch-size enforcement (P2b) filed as a TODO. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> |
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f11d56cfca |
v0.42.23.0 feat(jobs): --nice scheduling-priority flag for jobs work/supervisor (#1815) (#1820)
* feat(jobs): niceness core, worker registry, shared supervisor-pid reader OS scheduling-priority primitives for issue #1815: - niceness.ts: parseNiceValue (whole-string), applyNiceness (re-reads effective in success AND failure paths), getEffectiveNiceness, formatNice. - worker-registry.ts: live workers self-register pid + requested/effective nice under gbrainPath('workers'); readWorkers prunes ESRCH (keeps EPERM) with a pid-reuse start-time guard. - supervisor-pid.ts: readSupervisorPid extracted from the copy-pasted PID-file + liveness block. * feat(jobs): --nice flag for jobs work/supervisor + doctor niceness check Wires the --nice <n> flag (and GBRAIN_NICE env) through the CLI (issue #1815): - jobs work: applies niceness + registers the worker; cleanup on finally and process.on('exit'). - jobs supervisor: applies in the foreground-start path only (after the --detach fork), passes the apply result into MinionSupervisor. - supervisor.ts: nice opts, extracted testable buildWorkerArgs (appends --nice), emits niceness on started/worker_spawned audit events. - jobs stats / supervisor status: surface effective worker + supervisor nice. - doctor: separate supervisor_niceness check (warns on requested != effective) so it can't clobber the supervisor crash-check precedence; registered in doctor-categories. * test(jobs): cover niceness, worker registry, supervisor-pid, build args Unit tests for issue #1815: parseNiceValue rejects 3.5/10abc that parseInt would accept; applyNiceness re-reads effective on EPERM; registry ESRCH/EPERM + pid-reuse guard + brain-isolated path; readSupervisorPid states; parseNiceFlag flag>env precedence; buildWorkerArgs --nice propagation. * chore: bump version and changelog (v0.42.23.0) --nice flag for jobs work/supervisor (issue #1815). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs: document --nice flag for jobs work/supervisor (v0.42.23.0) - minions-deployment.md: niceness tuning section (full concurrency, low priority). - KEY_FILES.md: entries for niceness.ts, worker-registry.ts, supervisor-pid.ts; supervisor.ts entry notes buildWorkerArgs + nice opts. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test(e2e): add enrich_thin to dream cycle EXPECTED_PHASES The enrich_thin cycle phase (src/core/cycle.ts ALL_PHASES, between conversation_facts_backfill and skillopt) shipped without updating the e2e phase-order expectation, so dream-cycle-phase-order-pglite failed on master. Sync the expected list to the real ALL_PHASES order. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test(e2e): align sync-lock-recovery with the shipped --break-lock --all contract v0.41.13.0 intentionally dropped the "--break-lock + --all is refused" guard so cron can self-heal every source in one call (sync.ts runBreakLock iterates sources under --all). The e2e test still asserted the old exit-1 refusal and failed on master. Assert the current contract: the combination is accepted and takes the iterate / no-active-sources path (exit 0, no refusal message). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test(e2e): de-flake ingestion-roundtrip chokidar first-drop race The native fsevents watcher occasionally missed a freshly written file, timing out the 15s waitFor (~1/3 on master under load). Three fixes: - inject a polling chokidar watcher via the source's _watchFactory seam (usePolling, 20ms interval) so detection never depends on fsevents timing; - drop deterministic fixtures BEFORE start so the initial scan (ignoreInitial:false) emits them, keeping live-watch coverage only where it's robust; - poll for the dedup hit instead of a fixed 600ms sleep. 15/15 green under stress. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test(e2e): make hermetic-PGLite serve tests actually hermetic connect-bearer and serve-stdio-roundtrip init a PGLite brain and spawn serve, but passed {...process.env} through — leaking an ambient DATABASE_URL / GBRAIN_DATABASE_URL into the subprocess, which then came up on Postgres and failed the `engine: pglite` assertion. Strip both DB vars from the spawned env so the tests are deterministic whether or not the shell/CI has a DB URL set. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test(e2e): type the hermetic-PGLite env so tsc passes The DATABASE_URL/GBRAIN_DATABASE_URL strip used `delete` on a narrowly-typed env literal (tsc-only failure; bun test doesn't typecheck). Annotate connect-bearer's env as Record<string,string|undefined> and build serve-stdio's as a concrete Record<string,string> (StdioClientTransport.env rejects undefined). Runtime behavior unchanged (7/7 + 3/3 green). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test: quarantine worker-registry to *.serial (R1 env-mutation isolation) worker-registry.test.ts sets process.env.GBRAIN_HOME per-test so gbrainPath resolves to a temp dir, then lazy-imports the module — a process-global mutation the parallel isolation lint (rule R1) forbids. Rename to worker-registry.serial.test.ts: it runs in the serial pass (own bun process, max-concurrency=1) where env mutation is safe, and the lint skips *.serial files. No logic change (6/6 green); fixes the failing `verify` CI job. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> |
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f3ade6c0c3 |
v0.42.21.0 fix(postgres): module-singleton ownership — canonical landing for the dream-cycle "connect() has not been called" class (#1404/#1471/#1619) (#1805)
* fix(postgres): module-singleton ownership — borrower disconnect no longer nulls the cycle's connection (#1404/#1471/#1619) gbrain dream on Postgres failed every DB phase with "No database connection: connect() has not been called": a short-lived borrower probe engine (lint/doctor config-lift, no poolSize) called db.disconnect() in its own disconnect(), nulling the shared module singleton the long-lived cycle owner was still using. The module `sql` is only ever nulled by db.disconnect() (postgres.js auto-reconnects its own pool), so the failure was always a borrower-disconnect, never an idle-pooler drop. Fix: db.connect() returns whether THIS call created the singleton (atomic — no await between the null-check and the sql=postgres() assignment), PostgresEngine stores it as _ownsModuleSingleton, and disconnect() only calls db.disconnect() when it owns the connection. Borrowers no-op. Hardening: db.disconnect() snapshots +nulls sql before awaiting end(); reconnect() shares one in-flight _reconnectPromise. Tests: new postgres-engine-singleton-ownership.test.ts; expanded DB-gated e2e matrix (owner/borrower, creation-not-role, symmetric CLI-exit, owner-reconnect- with-live-borrower); module-style getter asymmetry; #1570 shared-recovery regression updated to assert the fixed contract. Co-Authored-By: nullhex-io <noreply@github.com> Co-Authored-By: joelwp <noreply@github.com> Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * chore: bump version and changelog (v0.42.15.0) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: nullhex-io <noreply@github.com> Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> |
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ec5fed2921 |
v0.42.20.0 fix: reliability wave — PGLite capture lock-pin + Postgres reconnect race + search embed-hang (#1762 #1745 #1775) (#1810)
* fix(core): drain fire-and-forget sinks before disconnect via a background-work registry (#1762) New src/core/background-work.ts registry (Map<name,drainer>, ordered drain, awaited abort). facts-queue (order 0, abort=shutdown), last-retrieved (1), and eval-capture (3, now self-tracked) register as sinks. Both CLI exit paths (op-dispatch finally + handleCliOnly finally) drain the registry before engine.disconnect() so a PGLite db.close() can't race in-flight work into the re-pump busy-loop that pinned the single-writer lock. Op-dispatch error path converts process.exit(1) to exitCode+return so the finally still drains. * fix(ai): bound every outbound AI call so a stalled provider can't hang (#1762/#1775) withDefaultTimeout composes a per-touchpoint default deadline (chat 300s, embed/multimodal 60s) with any caller signal via AbortSignal.any. Applied at the SDK call layer (chat generateText, expand generateObject, OCR, per-sub-batch embed) — covers native-anthropic + retries — plus per-request multimodal fetch. embedQuery forwards abortSignal. Env: GBRAIN_AI_{CHAT,EMBED,MULTIMODAL}_TIMEOUT_MS. * fix(postgres): module-mode reconnect preserves the shared singleton (#1745) reconnect() branches on connection style. Module-singleton engines re-establish idempotently via db.connect() (no-op when alive) + refresh the ConnectionManager read pool, never db.disconnect() — so a transient blip no longer nulls the shared sql out from under concurrent ops (which threw 'connect() has not been called'). Fail-loud on real connect failure. Instance pools keep teardown+recreate. * fix(search): bound the query-time embed so a stall falls back to keyword (#1775) search/query default to cheap-hybrid (embeds the query); a stalled provider made the embed never settle, so the keyword fallback never engaged and the command force-exited with no output. One shared QueryEmbedDeadline (6s, floored 2s per embed) covers both the cache-lookup and inner embeds via embedQueryBounded (abortSignal + Promise.race) → existing keyword fallback engages. Also registers the search-cache background-work drainer (now bounded). Env: GBRAIN_QUERY_EMBED_TIMEOUT_MS. * test+chore: reliability wave tests + v0.42.11.0 (#1762 #1745 #1775) New: background-work registry unit, query-embed deadline unit, eval-capture drain unit, postgres reconnect E2E (#1745), gbrain capture exit-clean case in the PGLite serial test. Updated fix-wave-structural assertions to the registry shape. VERSION/package.json/CHANGELOG -> 0.42.11.0; TODOS retrofit marked done. Incorporates + hardens PR #1763 (drain-before-disconnect + embed fetch timeout); the residual hung-Haiku hole is closed by the facts shutdown() abort belt. Co-Authored-By: ElliotDrel <noreply@github.com> Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs: document background-work registry + v0.42.11.0 reliability wave in CLAUDE.md (regen llms) * chore: bump release version 0.42.11.0 -> 0.42.20.0 Rename the reliability-wave release version per request. Trio (VERSION / package.json / CHANGELOG) reconciled; in-code version-tag comments and test fixtures updated; llms regenerated. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: ElliotDrel <noreply@github.com> Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> |
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488f89e0dc |
v0.42.15.0 fix: decouple CLI primary output from process.stdout.isTTY (#1784) (#1806)
* feat(eval): cycle-default — single source of truth for TTY/non-TTY cycle count (#1784) * fix(jobs): decouple 'jobs watch' format (--json) from loop (--follow); non-TTY prints one human snapshot (#1784) * fix(reindex): human cost-refusal unless --json; spend guardrail unchanged (#1784) * fix(eval): annotate non-interactive cycle/budget defaults; runner core TTY-agnostic (#1784) * chore: bump version and changelog (v0.42.15.0) Decouple CLI primary output from process.stdout.isTTY (#1784): human by default, JSON only with --json; jobs watch non-TTY one-shots; eval banners annotate non-interactive defaults; reindex-code refusal is human unless --json. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs: CLAUDE.md Key Files notes for v0.42.15.0 isTTY-output decoupling (#1784) Annotate jobs.ts (jobs watch format/loop split + resolveWatchMode + the new cycle-default.ts), reindex-code.ts (human cost-refusal), and eval-cross-modal.ts (cycle/budget banner annotations). Regenerate llms-full.txt. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> |
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1036f8f752 |
v0.42.14.0 fix(zero-config): code-* readiness signal + init embedding-key validation + lock self-heal (#1780) (#1804)
* feat(code-intel): readiness signal on code-def/refs/callers/callees (#1780 Gap 1) New src/core/code-graph-readiness.ts: resolveCodeReadiness() returns a typed status (not_built | indexing | ready | unknown) + ready boolean so callers can tell "graph not built / still indexing" apart from "genuinely no match" when count===0. EXISTS-based (cheap), chunk-grain, resolver-version-matching pending predicate, fail-open. Wired into the 4 CLI envelopes (+ human hint) and the 4 MCP op handlers. def/refs are 2-state brain-wide; callers/callees 3-state scoped. * feat(db-lock): automatic same-host dead-pid cycle-lock takeover (#1780 Gap 3) tryAcquireDbLock now reclaims a held, not-TTL-expired lock when the same-host holder is provably dead (process.kill ESRCH) past a 60s grace, via guarded DELETE + one normal-upsert retry returning the normal handle. New shared injectable classifyHolderLiveness/isHolderDeadLocally (EPERM treated as ALIVE — never steals a live lock). runBreakLock's safe path consumes the shared predicate, fixing its prior EPERM-as-dead bug. Cross-host stays TTL-only. * feat(init): validate the embedding key at gbrain init (#1780 Gap 2) New src/core/init-embed-check.ts: config-only diagnoseEmbedding (missing key, all providers) + best-effort 1-token live test-embed (invalid/expired key, 5s timeout, never blocks). Loud warning to stderr, init still exits 0; skipped by --no-embedding / --skip-embed-check / GBRAIN_INIT_SKIP_EMBED_CHECK=1. Builds the effective env (process.env + file-plane keys + --key) via buildGatewayConfig, extracted to src/core/ai/build-gateway-config.ts (cli.ts re-exports) so the check sees the same keys + provider base URLs as runtime. embedding_check added to --json. * chore: bump version and changelog (v0.42.14.0) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs: document the #1780 zero-config gaps for v0.42.14.0 CLAUDE.md Key Files: add src/core/code-graph-readiness.ts, init-embed-check.ts, ai/build-gateway-config.ts, and the db-lock auto-takeover + code-* readiness field behaviors. Regenerate llms-full.txt. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> |
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bea2d3e6c9 |
v0.42.13.0 fix(search): archive/ content findable by default, demoted not hard-excluded (#1777) (#1797)
* fix(search): archive/ findable by default — demote not hard-exclude (#1777) Move archive/ out of DEFAULT_HARD_EXCLUDES into a 0.5 source-boost demote so archived historical content is findable by default, ranked below curated content. Add a hidden_by_search_policy doctor check so the surviving exclude policy (test/, attachments/, .raw/) is auditable. Bump KNOBS_HASH_VERSION 8->9 so the policy change invalidates archive-excluded query_cache rows. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * chore: bump version and changelog (v0.42.13.0) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs: correct search-exclude.test.ts annotation for archive demote (#1777) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> |
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a57d98b813 |
v0.42.12.0 feat: self-upgrading gbrain — invocation-riding update check + opt-in auto-upgrade (#1798)
* feat(self-upgrade): decision/cache/snooze foundation + atomic binary self-update Pure decideSelfUpgrade (invocation + autopilot channels), atomic untrusted cache + escalating snooze + shared marker grammar (forged-marker rejection), semver helpers, and real darwin-arm64/linux-x64 binary self-update (download -> fsync -> smoke -> atomic rename; failure leaves old binary intact). Tests incl. real-HTTP-server swap E2E. * feat(self-upgrade): check-update cache/markers, self-upgrade command, CLI heartbeat hook check-update gains gstack-style cache/snooze/markers + refreshUpdateCache + exported fetchLatestRelease. New 'gbrain self-upgrade' command. cli.ts emits the update marker on every invocation (cache-read-only hot path, detached single-flight refresh, skip-set + recursion guard + NODE_ENV=test gate). * feat(self-upgrade): autopilot silent channel, doctor check, runPostUpgrade setup, config + identity marker autopilot opt-in silent channel (auto+quiet+idle, swap-only+breadcrumb+exit-relaunch) + installSystemd Restart=always + migrateSystemdUnitToRestartAlways. doctor self_upgrade_health. runPostUpgrade applySelfUpgradeSetup (one-time consent + systemd rewrite). init defaults mode=notify. config self_upgrade plane + KNOWN_CONFIG_KEYS. get_brain_identity carries update marker. * docs(self-upgrade): gbrain-upgrade agent skill, RESOLVER/manifest, auto-update doc reversal, HEARTBEAT New skills/gbrain-upgrade agent flow (mirror gstack-upgrade) wired into RESOLVER + manifest. upgrades-auto-update.md reversed to document opt-in auto + conservative gates. HEARTBEAT self-upgrade --check-only line. llms-full regenerated. * chore: bump version and changelog (v0.42.12.0) Self-upgrading gbrain: invocation-riding update marker + opt-in autopilot silent channel + real atomic binary self-update. Mirrors gstack's mechanism. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(self-upgrade): write just-upgraded-from breadcrumb + clear stale cache after upgrade Codex ship-review P3: the CLI startup hook reads just-upgraded-from to print the one-time JUST_UPGRADED confirmation, but nothing wrote it — dead path. runUpgrade now writes the breadcrumb (covers full + --swap-only) and clears the update-check cache + snooze so a now-applied 'upgrade available' marker stops nudging. * feat(self-upgrade): surface what's-new in notify + wire agent integration (AGENTS.md, HEARTBEAT) + e2e - self-upgrade --check-only --json now includes changelog_diff + release_url (export fetchChangelog); the gbrain-upgrade skill shows 3-5 what's-new bullets before the 4-option prompt instead of just version numbers. - setup injects a self-upgrade marker protocol into AGENTS.md so interactive agents (Claude Code, Codex) act on the UPGRADE_AVAILABLE stderr marker — the piece that makes notify actually fire for them. - HEARTBEAT daily beat routes through the gbrain-upgrade skill (OpenClaw/Hermes cron cadence); auto-mode daemons ride the autopilot tick. - e2e: real subprocess invocation proves the marker fires (notify emits; off/snooze/up-to-date silent; JUST_UPGRADED fires+clears; --quiet suppresses). Serial test: --check-only surfaces the changelog. --------- Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> |
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d4211f4176 |
v0.42.11.0 feat(skillopt): held-out eval gate, honest receipts, ENFORCE + ablation opts (#1759)
* feat(skillopt): wire held-out gate, honest receipts, ENFORCE + ablation opts Wire the F11 held-out gate into the orchestrator at checkpoint acceptance (runHeldOutGate was dead code); parse + thread --held-out through CLI, batch, fleet, background job, and the run_skillopt MCP op. Populate the real receipt.baseline_sel_score (was hardcoded 0) and add a final-test eval (test_score + baseline_test_score) via a shared scoreSkillOnTasks primitive. Fix the --no-mutate proposed.md write (was a stub) and enforce maxRuntimeMin. D16 ENFORCE in core mutation policy (assertBundledMutationHeldOut): mutating a bundled skill in place requires a non-empty (>=5), benchmark-disjoint held-out set or hard-refuses. Add three eval-internal ablation opts (reflectMode, disableValidationGate, optimizerMode='one-shot-rewrite') recorded in the receipt + audit; ROLLOUT_SUCCESS_THRESHOLD named constant. Security: run_skillopt MCP op validates skill_name (kebab-only) and confines caller-supplied benchmark/held-out paths to the skills dir for remote callers. * test(skillopt): held-out gate, ENFORCE, one-shot rewrite, runtime + receipt honesty New test/skillopt/rollout.test.ts (rollout had zero coverage). Held-out ENFORCE unit cases + one-shot-rewrite fence handling (whole-response unwrap, embedded-fence preserved, error path). E2E: F11 held-out BLOCKS/ALLOWS, bundled no-mutate write, reflectMode/disableValidationGate/optimizerMode, maxRuntimeMin abort, receipt baseline/test-score honesty, held-out/benchmark disjointness, D2 no-DB-pollution. * chore: bump version and changelog (v0.42.9.0) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs: document skillopt held-out gate + bundled mutation requirement for v0.42.9.0 Wire --held-out into the skill-optimizer SKILL.md, guide flags/safety tables, and the tutorial's bundled-skill step: mutating a bundled skill in place now requires --allow-mutate-bundled AND --held-out (>=5 benchmark-disjoint tasks) or it hard-refuses. Add the --held-out flag row + F11 held-out gate to the guide; update the receipt contract to the honest baseline/test-score fields. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(gateway): AI SDK v6 toolLoop compat — multi-turn tool calls work again The ai@6.x bump tightened ModelMessage + tool-schema validation, which silently broke every multi-turn tool loop. Both `gbrain skillopt` rollouts and production background `subagent` jobs route through `chat()`/`toolLoop` and crashed the moment the model called a tool ("messages do not match the ModelMessage[] schema" / "schema is not a function"). Surfaced end-to-end by the SkillOpt real-LLM eval. Three fixes: - chat(): wrap tool defs with the SDK's `jsonSchema()` helper instead of a bare `{jsonSchema}` object (v6 asSchema() treated the bare object as a thunk and threw). - chat(): new exported pure `toModelMessages()` converts gbrain's provider-neutral ChatMessage[] into v6 ModelMessage[] — tool results ride a dedicated `role:'tool'` message with structured `{type,value}` output; null output preserved as json null. Load-bearing for the production subagent path, not just skillopt. - rollout.ts: replace the inline params→schema mapper (dropped `items` on array params) with the shared `paramDefToSchema` single source of truth. Pinned by test/gateway-model-messages.test.ts (8 cases). Folds into the open v0.42.9.0 PR (#1759) — these complete the eval-readiness wave by making skillopt actually run against a live model. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(skillopt): budget no-pricing for Haiku silently scored every rollout 0 Surfaced by the SkillOpt real-LLM eval (Track B). Two coupled bugs that made a budget-capped Haiku run report a vacuous "0/N" measurement in ~2ms with zero LLM calls — indistinguishable from a real deficient-skill score: 1. Claude Haiku 4.5's canonical dateless id (`claude-haiku-4-5`) was missing from anthropic-pricing.ts (only the dated `-20251001` was present). With `--max-cost` set, BudgetTracker.reserve() threw no_pricing on the FIRST chat() of every rollout. Added the dateless entry (sonnet already had its dateless form). 2. runValidationGate swallowed that BUDGET_EXHAUSTED error — runWithLimit settled it as {ok:false}, which the gate turned into median:0. A pricing/cap crash became a fake score. The gate now scans settled results for isMustAbortError() and re-throws so the caller aborts loudly; ordinary (non-abort) rollout errors still fail-open to 0 (judge-hiccup posture kept). Pinned by test/skillopt/validate-gate-abort.test.ts (3 cases). Folds into the open v0.42.9.0 PR (#1759). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(ci): llms-full.txt over size budget — drop what-schemas-unlock from full bundle The toolLoop + budget bug-fix annotations grew CLAUDE.md, pushing llms-full.txt to 756KB over the 750KB FULL_SIZE_BUDGET (the `build-llms > size budget` test failed, failing the `test` CI job). CLAUDE.md stays inlined by design (it's the point of the one-fetch bundle), so per the budget comment's own guidance ("ship with includeInFull=false exclusions") this excludes docs/what-schemas-unlock.md (15.4KB value-explainer, not load-bearing operational reference) from llms-full.txt; it stays linked in llms.txt. Bundle now 740KB with ~9KB headroom. No budget bump — 750KB is near the ~190k-token-context fit ceiling. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * chore(ci): re-admit policy docs into ci-cache-hash before doc relocation docs/**/*.md is deny-listed from the CI cache hash (test-irrelevant). The CLAUDE.md restructure moves test/release POLICY into docs/TESTING.md + docs/RELEASING.md, which DO carry contracts the test suite reads. Without re-admitting them, a policy-only edit would produce the same cache hash and skip the test shard that runs the build-llms + doc-history guards (false-pass). Adds an ALLOW_PATTERNS re-admit step after the deny, scoped to the named policy docs (not a blanket docs un-deny). Lands FIRST, before any doc moves. Pinned by 3 new cases in test/scripts/ci-cache-hash.test.ts: TESTING.md + RELEASING.md edits MUST change the hash; docs/guide.md still must not. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * refactor(docs): relocate Key files / thin-client / Testing out of CLAUDE.md (verbatim) CLAUDE.md had grown to 592KB / ~147k tokens auto-loaded every session (~77% of the llms-full.txt single-fetch bundle). The per-file index was append-only by mandate. This is the exact thin-dispatcher-vs-fat-blob anti-pattern gbrain exists to fix, so CLAUDE.md becomes a thin orientation + resolver that points at on-demand docs. This commit is the VERBATIM move (content-preserving — the next commit compresses): - docs/architecture/KEY_FILES.md <- ## Key files + the calibration key-files cluster + Schema Cathedral v3 impl detail - docs/architecture/thin-client.md <- ## Thin-client routing - docs/TESTING.md <- ## Testing - ## Commands DROPPED (18 'added in vX.Y' history blocks; current surface is gbrain 0.41.38.0 -- personal knowledge brain USAGE gbrain <command> [options] SETUP init [--pglite|--supabase|--url] Create brain (PGLite default, no server) migrate --to <supabase|pglite> Transfer brain between engines upgrade Self-update check-update [--json] Check for new versions doctor [--json] [--fast] Health check (resolver, skills, pgvector, RLS, embeddings) integrations [subcommand] Manage integration recipes (senses + reflexes) PAGES get <slug> Read a page put <slug> [< file.md] Write/update a page delete <slug> Delete a page list [--type T] [--tag T] [-n N] List pages SEARCH search <query> Keyword search (tsvector) query <question> [--no-expand] Hybrid search (RRF + expansion) ask <question> [--no-expand] Alias for query IMPORT/EXPORT import <dir> [--no-embed] Import markdown directory sync [--repo <path>] [flags] Git-to-brain incremental sync sync --watch [--interval N] Continuous sync (loops until stopped) sync --install-cron Install persistent sync daemon export [--dir ./out/] Export to markdown export --restore-only [--repo <p>] Restore missing supabase-only files [--type T] [--slug-prefix S] With optional filters FILES files list [slug] List stored files files upload <file> --page <slug> Upload file to storage files upload-raw <file> --page <s> Smart upload (size routing + .redirect.yaml) files signed-url <path> Generate signed URL (1-hour) files sync <dir> Bulk upload directory files verify Verify all uploads EMBEDDINGS embed [<slug>|--all|--stale] Generate/refresh embeddings LINKS link <from> <to> [--type T] Create typed link unlink <from> <to> Remove link backlinks <slug> Incoming links graph <slug> [--depth N] Traverse link graph (returns nodes) graph-query <slug> [--type T] Edge-based traversal with type/direction filters [--depth N] [--direction in|out|both] TAGS tags <slug> List tags tag <slug> <tag> Add tag untag <slug> <tag> Remove tag TIMELINE timeline [<slug>] View timeline timeline-add <slug> <date> <text> Add timeline entry TOOLS extract <links|timeline|all> Extract links/timeline (idempotent) [--source fs|db] fs (default) walks .md files; db iterates engine pages [--dir <brain>] brain dir for fs source [--type T] [--since DATE] filters (db source) [--dry-run] [--json] publish <page.md> [--password] Shareable HTML (strips private data, optional AES-256) check-backlinks <check|fix> [dir] Find/fix missing back-links across brain lint <dir|file> [--fix] Catch LLM artifacts, placeholder dates, bad frontmatter orphans [--json] [--count] Find pages with no inbound wikilinks salience [--days N] [--kind P] v0.29: pages ranked by emotional + activity salience anomalies [--since D] [--sigma N] v0.29: cohort-based statistical anomalies (tag, type) transcripts recent [--days N] v0.29: recent raw .txt transcripts (local-only) dream [--dry-run] [--json] Run the overnight maintenance cycle once (cron-friendly). See also: autopilot --install (continuous daemon). check-resolvable [--json] [--fix] Validate skill tree (reachability/MECE/DRY) report --type <name> --content ... Save timestamped report to brain/reports/ BRAIN (capture / ideate / explore — v0.37/v0.38) capture [content] [--file PATH] Single entrypoint for getting content into the brain [--stdin] [--slug s] [--type t] Inline content / file / stdin; writes to inbox/ by default [--source ID] [--quiet|--json] Multi-source brains: route to a non-default source brainstorm <question> [--json] Bisociation idea generator (hybrid search + far-set + judge) [--save|--no-save] [--limit N] lsd <question> [--json] Lateral Synaptic Drift: inverted-judge brainstorm [--save|--no-save] [--limit N] rewarding far-from-obvious + axiomatic inversions SOURCES (multi-repo / multi-brain) sources list Show registered sources sources add <id> --path <p> Register a source (id = short name, e.g. 'wiki') sources remove <id> Remove a source + its pages sync --all Sync all sources with a local_path sync --source <id> Sync one specific source repos ... DEPRECATED alias for 'sources' (v0.19.0) CODE INDEXING (v0.19.0 / v0.20.0 Cathedral II) code-def <symbol> [--lang l] Find the definition of a symbol across code pages code-refs <symbol> [--lang l] Find all references to a symbol (JSON-first) code-callers <symbol> Who calls this symbol? (v0.20.0 A1) code-callees <symbol> What does this symbol call? (v0.20.0 A1) query <q> --lang <l> Filter hybrid search to one language (v0.20.0) query <q> --symbol-kind <k> Filter to symbol type (function|class|method|...) (v0.20.0) reconcile-links [--dry-run] Batch-recompute doc↔impl edges (v0.20.0) reindex-code [--source id] [--yes] Explicit code-page reindex (v0.20.0) sync --strategy code Sync code files into the brain JOBS (Minions) jobs submit <name> [--params JSON] Submit background job [--follow] [--dry-run] jobs list [--status S] [--limit N] List jobs jobs get <id> Job details + history jobs cancel <id> Cancel job jobs retry <id> Re-queue failed/dead job jobs prune [--older-than 30d] Clean old jobs jobs stats Job health dashboard jobs work [--queue Q] Start worker daemon (Postgres only) ADMIN stats Brain statistics health Brain health dashboard history <slug> Page version history revert <slug> <version-id> Revert to version features [--json] [--auto-fix] Scan usage + recommend unused features autopilot [--repo] [--interval N] Self-maintaining brain daemon config [show|get|set] <key> [val] Brain config storage status [--repo <path>] Storage tier status and health [--json] (git-tracked vs supabase-only) serve MCP server (stdio) serve --http [--port N] HTTP MCP server with OAuth 2.1 --token-ttl N Access token TTL in seconds (default: 3600) --enable-dcr Enable Dynamic Client Registration --public-url URL Public issuer URL (required behind proxy/tunnel) call <tool> '<json>' Raw tool invocation version Version info --tools-json Tool discovery (JSON) Run gbrain <command> --help for command-specific help. + the per-command KEY_FILES entries; content stays in git) CLAUDE.md gains: a Reference map (resolver), a Maintaining section (the anti-disease rule), and a Cross-cutting invariants subsection under Architecture so the must-never-violate rules (trust fail-closed, sourceScopeOpts isolation, JSONB trap, engine parity, contract-first, migrations, multi-source) still auto-load after the index moved out. Result: CLAUDE.md 592KB -> 61KB; llms-full.txt 740KB -> 210KB (new docs link-only until compressed). build-llms drift + budget test green; verify 29/29 green. The pre-move content is recoverable at git show <this^>:CLAUDE.md. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * refactor(docs): compress relocated docs to current-state + add recurrence guard Compresses the verbatim-relocated reference docs from append-only release-history to current-state-only (the disease cure), then makes recurrence structurally impossible via a CI guard. Compression (fan-out subagents + adversarial verify, audited mechanically): - KEY_FILES.md 453KB -> 356KB; TESTING.md 42KB -> 38KB; thin-client.md already clean. - 393/393 entries preserved; every src/test/scripts path from the verbatim original survives (mechanical comm-check); zero bolded **v0. markers remain. - Conservative ratio (~22%) because the content is invariant-dense — correctness over brevity. Dropped: **vX.Y.Z (#NNN):** clauses, codex/review tags, contributor credits, PR-numbers-as-ids, pre-fix/then/was-now history deltas. Kept: every exported symbol, invariant, and Pinned-by reference. Verbatim original recoverable at git show <relocation-commit>:docs/architecture/KEY_FILES.md. Recurrence guard (scripts/check-key-files-current-state.sh, wired into verify + check:all): - HARD: bans the bolded **v0.<digit> marker in the reference docs (scoped — plain 'as of pgvector 0.7' prose is fine, no false positives). - HARD: CLAUDE.md size cap (90KB; currently 61KB) — the structural backstop. - Pinned by test/scripts/check-key-files-current-state.test.ts (7 cases). Content contracts (test/build-llms.test.ts, +5 cases per codex outside-voice): CLAUDE.md keeps inline ship IRON RULES (version format, document-release, never-hand-roll); AGENTS.md keeps its boot order; llms indexes the new docs; KEY_FILES stays link-only (not inlined). Privacy: scrubbed the relocated 'wintermute/chat/' source-boost examples + the literal harvest-lint regex to generic placeholders (legitimate in allowlisted CLAUDE.md; genericized for the new public docs per the privacy rule). Reverts the |
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f09f9177a9 |
v0.42.10.0 feat(extract): opt-in global-basename wikilink resolution (closes #972) (#1388)
* v0.40.8.2 fix(extract): opt-in global-basename wikilink resolution (#972) Bare wikilinks like [[struktura]] that point at pages in another folder were silently dropped from the graph. The issue reporter saw 71 wikilinks in Obsidian render to 12 in gbrain (~83% lost). Symptoms downstream: `gbrain graph` returns thin neighborhoods, `gbrain backlinks` undercounts. This release adds an opt-in mode that resolves bare wikilinks by basename match, covers all three resolver surfaces (FS-source extract, DB-source extract, put_page auto-link), and emits one edge per match — no silent winner on ambiguity. `gbrain doctor` surfaces a paste-ready enable hint when ≥5 bare wikilinks would resolve under the new mode. Enable with: gbrain config set link_resolution.global_basename true gbrain extract links Default stays off. Existing brains see zero behavior change on upgrade. Closes #972. Adapts PR #1233 from @rayers (regex shape + slug-tail index) into a multi-match, opt-in form with FS-source coverage that the original PR explicitly skipped. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * docs: document opt-in global-basename wikilink resolution (#972) The #972 feature shipped with no user-facing docs — only CHANGELOG + CLAUDE.md. Anyone migrating an Obsidian/Notion vault with bare [[name]] wikilinks couldn't discover the link_resolution.global_basename flag unless gbrain doctor happened to surface its hint. - README "Self-wiring knowledge graph": one sentence on the opt-in mode for Obsidian-style cross-folder bare wikilinks + the doctor pre-check, linking to the install step. - INSTALL_FOR_AGENTS Step 4.5 (Wire the Knowledge Graph): a dedicated agent- facing subsection — when bare [[name]] links need it, the enable command, re-running extract, the doctor opportunity hint, and the multi-match behavior. - Regenerated llms-full.txt. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(#972): resolve aliased wikilinks by target slug, not display text Codex outside-voice [P1]: `[[struktura|the project]]` resolved the basename "the project" (the alias) instead of `struktura` (the target), because extractPageLinks called resolveBasenameMatches(ref.name) and the doctor check keyed basenameIndex.get(e.name). ref.name is the display alias (match[2]); ref.slug is the wikilink target (match[1]). - extractPageLinks resolves ref.slug; context excerpt locates ref.slug. - doctor link_resolution_opportunity keys e.slug so its estimate matches what extraction actually resolves. - Test: aliased wikilink calls resolveBasenameMatches with the target, never the display text. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(#972): reconcile wikilink-resolved edges in put_page auto-link Codex outside-voice [P1]: put_page's reconcilableOut filter excluded link_source='wikilink-resolved', so a basename edge written by auto-link survived after the bare wikilink was deleted from the page OR the link_resolution.global_basename flag was turned off (the stale-removal loop only iterates reconcilableOut). Add 'wikilink-resolved' to the reconcilable set; manual edges still untouched. Test: write page with [[struktura]] (flag on) → edge lands; re-put without the wikilink → edge reconciled away. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(#972): source-scope basename resolution (no cross-source edges) Codex outside-voice [P1]: makeResolver.resolveBasenameMatches called engine.getAllSlugs() unscoped, so a bare [[name]] could resolve to a same-tail page in a DIFFERENT source and create a cross-source edge. The engine exposes getAllSlugs({sourceId}) precisely to prevent this. #972 is "global basename across folders," not "cross-source federation" — the canonical gbrain multi-source bug class. - makeResolver gains opts.sourceId; ensureBasenameIndex passes it to getAllSlugs (unscoped only when sourceId omitted — back-compat). - runAutoLink (put_page) passes opts.sourceId; extractLinksFromDB passes sourceIdFilter. FS extract is already single-source (walks one dir). - Tests: scoped index returns only the source's slugs (no cross-source); unscoped call stays brain-wide. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(#972): FS-source basename edges carry link_source='wikilink-resolved' The FS extract path is the issue's default repro (gbrain extract links with no --source db). ExtractedLink had no link_source field, so FS basename edges landed with the engine default ('markdown') instead of the 'wikilink-resolved' provenance the DB / put_page paths set and the docs promise. The e2e FS test only asserted link_type, so it was blind to this. - ExtractedLink gains link_source?; extractLinksFromFile sets it to 'wikilink-resolved' on basename edges (undefined for ordinary markdown). - Carries through the addLinksBatch snapshots automatically (LinkBatchInput already has link_source); single-row addLink fallback now passes it too. - e2e FS repro asserts link_source === 'wikilink-resolved'. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * refactor(#972): one shared basename matcher across resolver/FS/doctor Codex outside-voice [P2] DRY: three surfaces each hand-rolled a basename matcher with divergent key sets — the doctor omitted the slugified key, so its link_resolution_opportunity estimate undercounted what extraction resolves, and the resolver returned matches in unsorted getAllSlugs bucket order. New shared exports in link-extraction.ts: buildBasenameIndex(slugs) + queryBasenameIndex(index, name) (keys raw/lower/slugified tail; stable sort shorter-first then lexical) + normalizeBasename. - makeResolver.resolveBasenameMatches → queryBasenameIndex (now stable-sorted). - extract.ts resolveBasenameMatchesFromSlugs → delegates to the shared pair. - doctor link_resolution_opportunity → shared builder/query (slugified key added; estimate now matches extraction). - Test: doctor counts a slugified-only match ([[Fast Weigh]] → companies/fast-weigh). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(#972): P2 cluster — masking, code-fence, self-link, dedup decision Codex outside-voice P2 findings: - P2a markdown-label masking: a wikilink inside a markdown-link label ([see [[acme]]](companies/acme.md)) spawned a stray generic basename ref. Pass-1 can't match the nested brackets, so a new MARKDOWN_LABEL_WIKILINK_RE masks those spans out of pass 2c. Inner [[acme]] is now inert. - P2b FS code-fence: the FS path (extractMarkdownLinks on raw content) didn't strip code blocks like the DB path. extractLinksFromFile now scans stripCodeBlocks(content) so [[name]] inside a fence creates no FS edge. - P2c self-link guard: a basename [[own-tail]] on its own page resolved back to itself. Dropped in both extractPageLinks and the FS path. - P2d dedup: documented the decision to KEEP qualified + bare edges to the same target as separate rows (distinct provenance/audit trail). - P2e: skipFrontmatter unresolved-contract tests added. Tests: P2a inert-label, P2c self-link drop, P2b code-fence, P2e unresolved. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * perf(#972): bound the doctor link_resolution_opportunity scan The check did listAllPageRefs() + a getPage() per page under a 60s budget. On a large brain (the eng-review concern) it hit the budget every non-fast doctor run and returned a perpetual partial, adding ~60s. Now batch-loads the 1000 most-recent pages in ONE query (ORDER BY id DESC LIMIT SAMPLE_LIMIT) and scans in memory, with the 60s cap kept as a backstop. Mirrors the v0.40.9 sampling convention. The estimate message names the bound when the brain exceeds the sample ("scanned the 1000 most-recent of N pages"). Test: source-grep pins the bounded query + the absence of the per-page getPage walk. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs(#972): reconcile stale version/migration references to v112 / 0.42.6.0 Merge churn left intermediate refs: schema.sql + schema-embedded.ts said "migration v93", CLAUDE.md said "v0.41.32.0 / Migration v109", CHANGELOG said "Migration v93". Reconciled all to migration v112 / shipping 0.42.6.0. The CLAUDE.md annotation is also refreshed to describe the final behavior (shared matcher, source-scoping, alias-by-target, stale-edge reconciliation, bounded doctor scan) and credit @rayers + @ukd1. Regenerated schema-embedded + llms. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(#972): register doctor check category + bump llms budget to 800KB Two full-suite gate failures from the re-sync: - doctor-categories drift guard: the new `link_resolution_opportunity` check wasn't in any category set. Added to BRAIN_CHECK_NAMES (alongside graph_coverage / orphan_ratio — it's a graph-quality signal). - build-llms size budget: the #972 Key Files annotation (landing with master's #1696/#1699 waves) pushed llms-full.txt past 750KB. Bumped FULL_SIZE_BUDGET 750KB→800KB, the established "budget tracks CLAUDE.md's legitimate per-feature growth" pattern (600→700→750→800 across releases). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com> Co-authored-by: Garry Tan <garrytan@gmail.com> |
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0bfe0d0c7e |
v0.42.8.0 feat: content-quality gate on sync — quarantine junk + flag boilerplate (#1699) (#1756)
* feat: content-quality gate on sync — quarantine junk + flag boilerplate (#1699) Three-tier disposition at the importFromContent narrow waist: - High-confidence junk (Cloudflare/CAPTCHA interstitial patterns + operator literals) -> quarantine (hidden from search, zero chunks) or reject. - Fuzzy markup-heavy (prose-vs-markup ratio, warn-tier window, code-exempt) -> content_flag marker, stays searchable, agent warned. - Oversize -> existing embed_skip soft-block + content_flag:oversized warning. Agent-warning channel: SearchResult.content_flag (stamped in hybridSearch + the keyword-only search op) and a top-level content_flag on get_page. New quarantine.ts markers, gbrain quarantine CLI (list/clear/scan), doctor quarantined_pages + flagged_pages checks (engine.executeRaw, works on PGLite), sources-audit disposition awareness, markup-heavy lint rule, config keys. Security: gate-owned markers stripped from untrusted (remote MCP) frontmatter so a write-scoped client can't hide pages or inject the warning channel. Markers excluded from content_hash so flagged pages don't re-embed every sync. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * chore: bump version and changelog (v0.42.8.0) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs: document content-quality gate (quarantine + content_flag) for v0.42.8.0 Add CLAUDE.md Key Files + Commands entries for the #1699 content-quality gate: src/core/quarantine.ts, gbrain quarantine CLI (list/clear/scan), the agent-warning channel (SearchResult.content_flag + get_page), doctor quarantined_pages/flagged_pages checks, the markup-heavy lint rule, sources-audit disposition awareness, and the three new content_sanity config keys. Regenerate llms-full.txt from CLAUDE.md. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> |
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ca68a551db |
v0.42.7.0 feat(extract): link/timeline extraction freshness watermark — gbrain extract --stale + doctor lag check (#1696) (#1755)
* feat(extract): link/timeline extraction freshness watermark (#1696) Closes the "imported != curated" gap: plain `gbrain sync` only extracts CHANGED pages, so a brain with autopilot off accumulated a links table that was ~99.7% untyped `mentions` with nothing surfacing it. Adds a per-page freshness watermark (pages.links_extracted_at, migration v112) and three things built on it: - `gbrain extract --stale [--source-id] [--catch-up] [--dry-run] [--json]`: incremental DB-source link+timeline sweep over pages whose extraction is stale (never extracted, edited since, or extractor version bumped). Small byte-bounded batches, non-swallowing flush, stamp-after-flush so a crash re-extracts idempotently. Stamps with the row's READ updated_at (not now()) so a concurrent edit during the sweep stays stale instead of being lost. - `links_extraction_lag` doctor check (local + remote): warn-only by default (>20%), hard-fail only via GBRAIN_EXTRACTION_LAG_FAIL_PCT. Vacuous-skip <100 pages; pre-v112 brains graceful-skip. - `gbrain sync --no-extract` flag + end-of-sync nudge (fires on synced|first_sync|up_to_date so the initial import surfaces its backlog). Three new BrainEngine methods (countStalePagesForExtraction / listStalePagesForExtraction / markPagesExtractedBatch) with Postgres<->PGLite parity + bootstrap probes. Schema parity: schema.sql + regenerated pglite-schema.ts + schema-embedded.ts + bootstrap-coverage test. Migration v112 (composite (source_id, links_extracted_at) index, no backfill so the real backlog surfaces on first doctor run). * test(audit): hermetic GBRAIN_AUDIT_DIR override for prune ENOENT case The "no-op when audit dir does not exist (ENOENT)" case called pruneOldBatchRetryAuditFiles without a GBRAIN_AUDIT_DIR override, so it read the developer's real ~/.gbrain/audit and flaked (kept>0) on any machine with prior gbrain audit history. Point it at a guaranteed-nonexistent temp path so it tests the real missing-dir branch hermetically — matching the file header's "never touches ~/.gbrain/audit" contract. Pre-existing flake (introduced by v0.41.19.0 #1537), unrelated to #1696. * chore: bump version and changelog (v0.42.2.0) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs: CLAUDE.md key-files entry for the #1696 extract-stale wave + regen llms-full --------- Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> |
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662a6e27d4 |
v0.42.6.0 feat(enrich): gbrain enrich --thin — brain-internal grounded synthesis for stub pages (#1700) (#1757)
* feat(engine): listEnrichCandidates source-aware candidate selection (#1700) One SQL query per engine: thin-filter + per-page source-correct inbound-link count (to_page_id = p.id, mentions excluded) + enriched_at recency guard + whitelisted ORDER BY (ENRICH_ORDER_SQL) + LIMIT, returning a lightweight projection (no page bodies). EnrichCandidate/EnrichCandidatesOpts types. pg + pglite parity, pinned by engine-parity.test.ts. * feat(enrich): gbrain enrich --thin brain-internal grounded synthesis (#1700) Develops stub pages at scale by consolidating scattered brain knowledge (search + backlinks + facts + raw_data) into one grounded gateway.chat call per page. Resumable (op-checkpoint), budget-capped (best-effort under --workers), per-page advisory lock, put_page write-through. CLI + thin-client refuse + Minion handler. Includes codex-review fixes: sanitizeContext neutralizes the <context> envelope delimiters (P1 injection escape); background fan-out idempotency key carries the run fingerprint (P1); post-hoc budget-overage flag via new BudgetTracker.cap getter (P1); checkpoint flush on budget exhaustion (P2). Accepts the documented best-effort in-flight-cancel limitation (D5) with an explicit code note. * feat(cycle): enrich_thin opt-in autopilot phase (#1700) Default-OFF trickle around runEnrichCore: develops a few thin pages per source per tick so the brain compounds over time. Per-source cap enforced as min(per-source, brain-wide remaining) with brain-wide total + walltime caps (P2 fix: per-source max_cost_usd was parsed but never enforced). Wired into CyclePhase / ALL_PHASES / PHASE_SCOPE / NEEDS_LOCK + dispatch. * chore: bump version and changelog (v0.42.6.0) gbrain enrich --thin batch enrichment (#1700) + codex-review fixes. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> |
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766604dea0 |
v0.42.5.0 fix(minions): RSS watchdog opacity + pooler-reap self-heal + silent lens backlog + cycle lint DB-disconnect (#1678) (#1735)
* fix(minions): self-identifying RSS watchdog + cgroup-aware default + pooler-reap self-heal (#1678) Problem 1: distinct WORKER_EXIT_RSS_WATCHDOG exit code + cause-keyed supervisor breaker (bypasses the stable-run reset that hid the 400x/24h loop) + rss_watchdog audit bucket + 80% soft-warn; cgroup-aware resolveDefaultMaxRssMb replaces the flat 2048 default at every spawn site. Problem 2: CONNECTION_ENDED classified retryable; postgres-engine sql getter throws a retryable error on a reaped instance pool instead of the misleading module-singleton fallthrough; promoteDelayed reconnect-retry; claim recovers on the next poll tick (no double-claim); lock-renewal tick reconnect-once dep. * feat(cycle): surface silent extract_atoms backlog + bounded --drain + fix lint clobbering the shared DB connection (#1678) Problem 3: extract_atoms_backlog doctor check + pack_gated skip marker + shared countExtractAtomsBacklog; `gbrain dream --phase extract_atoms --drain [--window N]` single-hold bounded drain (same cycleLockIdFor, rediscover each batch, reports remaining, exits non-zero while work remains). Also fixes a real production bug found via E2E: the cycle lint phase's resolveLintContentSanity created + disconnected a module-style engine that nulled the shared db singleton mid-cycle, breaking every later phase with "connect() has not been called". Lint now reuses the caller's live engine (cycle + Minion handlers thread it; standalone CLI keeps the create-own path). * chore: bump version and changelog (v0.41.39.0) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(#1678): pre-landing review — route transaction/withReservedConnection through the sql getter + drain treats failed count as incomplete Codex adversarial review findings: - #2: transaction(), withReservedConnection(), and one other site bypassed the v0.42.2.0 sql-getter self-heal via `this._sql || db.getConnection()`, so a reaped instance pool fell through to the module singleton there. Route all three through `this.sql` so they throw the retryable instance-pool error and recover consistently (MinionQueue.transaction hits this). - #4: `gbrain dream --drain` treated a null backlog count (query failure) as success via `remaining ?? 0`; now null exits EXIT_DRAIN_INCOMPLETE so automation never believes an unverified backlog drained. - #1 (claim orphan) + #3 (PGLite drain lock) documented as follow-ups in TODOS. * docs: document v0.42.2.0 #1678 modules + behavior in CLAUDE.md Adds Key Files entries for worker-exit-codes.ts, rss-default.ts, and extract-atoms-drain.ts, plus v0.42.2.0 annotations on worker.ts, child-worker-supervisor.ts, lock-renewal-tick.ts, and dream.ts. Regenerated llms-full.txt to match (test/build-llms.test.ts gate). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * chore: re-version v0.42.2.0 → v0.42.5.0 across VERSION/package.json/CHANGELOG/docs/comments Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> |
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7b0d99adb0 |
v0.42.2.0 feat: gbrain connect — one-command Claude Code onboarding from a bearer token (#1683)
* fix: gbrain auth create dropped the name on the bare (no-flag) form Extract parseAuthCreateArgs; only exclude the --takes-holders value from the positional search when the flag is present (rest[takesIdx+1] resolved to rest[0] when takesIdx === -1, silently dropping the name). Add regression test. * feat: gbrain connect — one-command Claude Code onboarding from a bearer token New connect command prints a paste-ready claude-mcp-add block (or --install wires it + smoke-tests the token via a raw-bearer get_brain_identity probe). Direct HTTP MCP, literal-token default, URL normalization, token header-injection guard, --json redaction, execFileSync (no shell). Wired into CLI_ONLY + CLI_ONLY_SELF_HELP + handleCliOnly. 58 unit + 3 PGLite-E2E cases; e2e-test-map updated. * docs: lead CLAUDE_CODE.md with gbrain connect (remote fast path) + README one-liner Regenerate llms-full.txt for the README change. * refactor: pre-landing review fixes for gbrain connect - DRY: single DEFAULT_PROBE_TIMEOUT_MS + shared isAuthErrorMessage predicate - reuse promptLine (shared stdin lifecycle) for the --install confirm - harden redactToken with a Bearer <value> scrub (defense in depth) - +8 tests: orchestrator guard paths, deterministic timeout, invalid --timeout-ms, Bearer-redaction * fix: adversarial-review hardening for gbrain connect - probe: Promise.race the call against a real timer so a stalled connect()/SSE handshake (signal alone doesn't cover it) can't hang --install indefinitely - probe: close transport even if client.connect() throws - parseArgs: reject a missing/flag-shaped value (e.g. --token --install) - block link-local / cloud-metadata hosts (169.254/fe80:/fd00:ec2::254) — keeps localhost + RFC1918 LAN brains working - non-interactive --install now requires --yes - clearer message when --force removed then add failed +8 tests covering each * fix: codex-review P2s for gbrain connect - POSIX single-quote the rendered claude-mcp-add command so a token with shell metacharacters ($(), backticks) can't trigger command substitution on paste - detect IPv4-mapped IPv6 metadata addresses (::ffff:169.254.x.x / ::ffff:a9fe:*) so they don't bypass the link-local guard +3 tests * chore: bump version and changelog (v0.42.2.0) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs: document gbrain connect + connect-probe in CLAUDE.md Key files (v0.42.2.0) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * feat: gbrain connect — add codex and perplexity agents --agent codex emits 'codex mcp add ... --bearer-token-env-var GBRAIN_REMOTE_TOKEN' (token read from the env var at runtime, never in Codex config; --install runs it). --agent perplexity prints the URL + token for the Settings → Connectors GUI (no --install). Generalized the command file: AGENT_SPECS table, buildCodexMcpAddArgv, cmdString(binary,argv), binary-generic ConnectDeps (hasBinary/runBinary/env), agent-aware buildConnectBlock/buildJson. +25 tests. * docs: codex + perplexity connect paths (new CODEX.md, README, CHANGELOG, CLAUDE.md) Regenerate llms-full.txt for the CLAUDE.md/README edits. * test: real-CLI E2E for connect — drive actual claude + codex against a live server Adds claude-code + codex cases to connect-bearer.test.ts that run the real 'claude mcp add' / 'codex mcp add' through 'gbrain connect --install' against a live 'gbrain serve --http' (sandboxed HOME/CODEX_HOME), then assert via 'claude mcp get' / 'codex mcp get' that the server registered (and codex's token stays out of config). Skips when the binary is absent. Perplexity is GUI-only so it's print-asserted. Regen llms for the CLAUDE.md note. * docs: perplexity OAuth + serve --bind/--public-url footgun (per Perplexity feedback) PERPLEXITY.md now documents the host-side HTTP setup (gbrain serve --http --bind 0.0.0.0 --public-url, the v0.34 ECONNREFUSED footgun) and the OAuth 2.1 client_credentials path (gbrain auth register-client) alongside the legacy bearer token. The 'connect --agent perplexity' output points at the same bind/public-url requirement + PERPLEXITY.md. * feat: gbrain connect --oauth — client-credentials path for perplexity/generic OAuth is the correct path for a third-party cloud connector (Perplexity): instead of a long-lived full-access bearer token, the connector gets Issuer URL + Client ID + Client Secret and mints short-lived scoped tokens. --oauth --register mints a least-privilege client on the host (shells gbrain auth register-client); --oauth --client-id/--client-secret uses an existing one. Rejected for claude-code/codex (bearer) and with --install. Issuer derived from the mcp-url. New E2E proves the full chain: register → connect --oauth → OAuth discovery → /token client_credentials mint → get_brain_identity tool call against a live server. Docs: PERPLEXITY.md leads with OAuth; README + CLAUDE.md updated; +18 unit cases. * docs: add gbrain connect to INSTALL.md MCP section + link CODEX.md The remote-client onboarding command was documented in README/CLAUDE_CODE/CODEX/ PERPLEXITY but missing from INSTALL.md §3 (the natural 'how do I connect a client' home). Add the one-command connect how-to (claude-code/codex/perplexity) and the missing docs/mcp/CODEX.md link. * fix: connect LEARN_INSTRUCTION names put_page, not CLI-only capture The self-orientation block told a connected agent that `capture` is an available MCP tool. It isn't — `capture` is a CLI-only convenience command; the MCP write tool is `put_page`. An agent that followed the instruction hit "unknown tool". Drop capture; put_page was already in the list. Adds a regression block to connect.test.ts. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * feat: serve --http surfaces skill-publishing status (banner + nudge) When mcp.publish_skills is OFF, connected agents can search/write but can't call list_skills/get_skill, so the host's skill catalog is invisible to them. The startup banner now shows a Skills: line, and a stderr nudge fires when off with the paste-ready fix. Pure skillPublishStatus() helper, unit-tested. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test: prove the local stdio MCP funnel end-to-end Spawns real `gbrain serve` (stdio) against a freshly init --pglite brain and drives the official MCP SDK client through initialize -> tools/list -> tools/call (get_brain_identity + search). Pins the advertised core-tool set against what the server actually exposes (asserts capture is NOT advertised). This funnel had zero e2e coverage before. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test: make batch-retry-audit ENOENT case hermetic The 'no-op when audit dir does not exist' case called pruneOldBatchRetryAuditFiles(30) without a GBRAIN_AUDIT_DIR override, so it read the real ~/.gbrain/audit and flaked (kept:1) on any dev machine with a batch-retry-*.jsonl on disk. Point it at a guaranteed-missing temp subdir, matching this file's own hermetic-header contract. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs: two-funnel coding-agent onboarding (Claude Code / Codex) New tutorial docs/tutorials/connect-coding-agent.md: Path A (connect to an existing brain) + Path B (start from nothing, local stdio), the brain-first protocol to paste into CLAUDE.md/AGENTS.md, and the four translatable habits. README gains a 'Quick start: Claude Code or Codex' fork separating lightweight retrieval from the full autonomous install. INSTALL.md shows the one-command wire-up at the standalone CLI section. mcp/CLAUDE_CODE + CODEX cross-link the tutorial + note publish_skills + capture-is-CLI-only. Tutorial promoted to Shipped in the tutorials index. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * chore: changelog + regenerated llms (v0.42.2.0) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs: CLAUDE.md Key Files annotation for two-funnel onboarding wave Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> |
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eefe8b5741 |
v0.42.1.0 feat: gbrain skillopt — self-evolving skills (closes #1481) (#1563)
* feat(skillopt): foundation modules — types, lr-schedule, benchmark, score, audit, lock
* feat(skillopt): edit primitives — apply-edits (D5+D9), rejected-buffer LRU, version-store (D8 history-intent-first)
* feat(skillopt): rollout (D2 gateway.toolLoop + D13 read-only allowlist), reflect (D7 two calls), validate-gate (D12 median+epsilon, D4 parallel), preflight (D3), bundled-skill-gate (D16)
* feat(skillopt): orchestrator (D6 slow-update, D10 ASCII diagrams, D11 caching), checkpoint, bootstrap (D15 sentinel), CLI dispatch + help
* feat(skillopt): cycle phase (F1 dream-loop wiring), PROTECTED_JOB_NAMES + MCP op (F6 admin scope + allowlist) + Minion handler (F7 --background)
* feat(skillopt): full cathedral — --all batch (F4), --target-models fleet (F5), write-capture (F10), held-out scaffold (F11), adversarial suite 41 cases (F2), E2E PGLite (F3), meta-skill bundle (T7), reflect+judge evals (F8+F9), docs (T10)
* chore: bump version to v0.42.0.0 (MINOR — significant new feature)
* fix(skillopt): wire trajectories from forward gate to reflect + fix parseEditsResponse parser misuse
Two related v0.42.0.0 bugs that conspired to make `runSkillOpt` structurally
unable to accept any candidate edit. Either alone would have killed self-evolution;
together they made the loop a no-op for every input.
**Bug 1 (orchestrator gap):** `runOptimizationLoop` in orchestrator.ts called
`runReflect({successes: [], failures: []})` with hardcoded empty arrays. The
forward gate's `scoredRollouts` were computed then voided. `runReflect`
short-circuits both modes when their batches are empty, so the optimizer was
never asked to propose an edit. Every step hit the no_edits_applied branch.
Fix: add `scoredRollouts: ScoredRollout[]` to `GateResult` and
`runsPerTask?: number` to `ValidateGateOpts`. Forward pass uses
`runsPerTask: 1`; orchestrator partitions returned rollouts by `score >= 0.5`
and threads real successes + failures into `runReflect`.
**Bug 2 (parser misuse):** `parseEditsResponse` in reflect.ts routed every
optimizer response through `parseJudgeJson` first. `parseJudgeJson` looks for
a `score` key (it's a judge-output parser, not an edits parser) and returns
null for any JSON without one — including the well-formed `{"edits": [...]}`
the optimizer is contractually required to emit. The function then early-
returned `[]` and the actual `tryExtractEdits` path on the next line was
unreachable dead code.
Fix: drop the wrong-typed guard. `parseEditsResponse` now calls
`tryExtractEdits` directly. Export it so `reflect.test.ts` can pin the
contract independently of the chat transport.
**Why this slipped through 152 prior skillopt tests:** zero unit coverage
of `parseEditsResponse` or `runReflect`. The existing E2E `all-reject` case
asserted no_improvement (which was true for the wrong reason — empty edits,
not gate rejection). Both bugs were structurally invisible to the existing
test surface.
**New coverage:**
- `test/skillopt/reflect.test.ts` (15 cases):
- 8 `parseEditsResponse` cases including the IRON-RULE regression pin
for the v0.42.0.1 fix (`{"edits": [...]}` JSON must survive the parser).
- 7 `runReflect` D7 contract cases: both modes fire, empty-batch skips,
additive token usage, one-mode-throws-other-still-works, rejected-buffer
flows into anti-bias prompt.
- Documents the trailing-comma limitation as an explicit out-of-scope pin
(so a future tightening of `tryExtractEdits` lights this test up
intentionally).
- `test/e2e/skillopt-loop.serial.test.ts` (7 cases):
- HAPPY PATH: stubbed `gateway.chat` acts as both target agent (emits
sections based on skill content) and optimizer (proposes a real
add-Citations edit). Drives `runSkillOpt` end-to-end against PGLite.
Asserts outcome=accepted, SKILL.md mutated with new section,
frontmatter preserved (D5), history has one committed row,
best.md mirrors disk, delta > epsilon, receipt fields populated.
- 5 broken cases (each isolates a distinct orchestrator-visible failure):
1. Below-baseline regression: optimizer proposes a destructive edit;
gate rejects with reason=below_baseline; SKILL.md unchanged;
rejected-buffer captures the bad edit for anti-bias context.
2. Malformed reflect JSON: orchestrator degrades gracefully to
no_improvement without crashing.
3. Anchor-not-found: applyEditBatch rejects all; sel gate skipped;
rejected-buffer captures with reason=apply_failed.
4. Budget exhausted mid-step: outcome=aborted, no pending rows survive.
5. Converged-skill re-run: starting from already-perfect skill →
no_improvement (no thrash on a well-tuned starting point).
- IDEMPOTENT RE-RUN: drive runSkillOpt twice in sequence. Run 1 accepts.
Run 2 sees improved baseline, no failures, returns no_improvement.
SKILL.md byte-identical to post-run-1; history still has exactly 1
committed row. Proves stability at the fixed point.
All hermetic (no DATABASE_URL, no API keys). PGLite in-memory engine,
tempdir SKILL.md + benchmark, stubbed gateway.chat via
`__setChatTransportForTests`. `.serial.test.ts` because the stub installs
module state and the loop walks shared disk state across epochs.
Test counts after fix: 174 skillopt-surface tests pass (149 pre-existing
unit + 15 new reflect unit + 3 existing E2E + 7 new E2E). Typecheck clean.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
* fix(cycle): align ALL_PHASES skillopt position with actual dispatch order
v0.42.0.0 added skillopt to ALL_PHASES right after `patterns` (line 127), but
the dispatch block in runCycle (line ~1912) actually runs skillopt between
`conversation_facts_backfill` and `embed`. The two were inconsistent, and the
serial test `report.phases.map(p => p.phase)).toEqual(ALL_PHASES)` was failing
on master because of it.
A second pre-existing failure: the two phase-count assertions in
`test/core/cycle.serial.test.ts` still said `toBe(20)` even though
ALL_PHASES grew to 21 when skillopt was added. The author bumped the array
but forgot the test.
Two fixes, one commit:
1. Move `'skillopt'` in ALL_PHASES from after `patterns` to between
`conversation_facts_backfill` and `embed`, matching where runCycle
actually dispatches it. Runtime behavior is unchanged — only the
declaration order moves. Updated the surrounding comment to call out
the position invariant and reference the test that pins it.
2. Update both `toBe(20)` assertions in cycle.serial.test.ts to `toBe(21)`
with a v0.42.0.0 history line in the running comments.
Why declaration follows runtime (not the other way around): the comment
intent ("Runs AFTER patterns — graph-fresh") is still satisfied because
"after the entire main graph-mutating cluster" is strictly fresher than
"right after patterns". No design intent is lost.
Test result: cycle.serial.test.ts is now 28/28 (was 27/28 on master + my
prior commit). Skillopt suite still 174/174.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
* fix(ci): bump PHASE_SCOPE assertion to 21 + fix skill-optimizer Anti-Patterns case
Two CI failures pre-existing on this branch since the v0.42.0.0 skillopt
cathedral landed; master is green because skillopt didn't exist there yet.
1. test/phase-scope-coverage.test.ts asserted ALL_PHASES.length === 20.
skillopt is the 21st phase. Bumped to 21 with v0.42.0.0 history line
in the comment chain. Sibling fix to the cycle.serial.test.ts bump
in commit
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146a8f1eed |
v0.41.31.0 feat(embed): delta-aware sync --all cost gate + real stale-embedding semantics (#1632)
* fix(cost): embedding cost preview uses configured model rate, not hardcoded OpenAI
The sync --all cost gate computed spend from a hardcoded
EMBEDDING_COST_PER_1K_TOKENS = 0.00013 (OpenAI text-embedding-3-large)
and labeled the preview with the back-compat EMBEDDING_MODEL constant,
regardless of the actually-configured embedding model. A brain running a
cheaper model (e.g. zeroentropyai:zembed-1 @ $0.05/Mtok) saw a preview
that named the wrong provider and over-stated spend ~2.6x ($337 vs $130
on a 2.6B-token corpus).
estimateEmbeddingCostUsd now resolves the live model via the gateway and
prices it through embedding-pricing.ts (the existing per-provider:model
table), falling back to the OpenAI rate only when the gateway is
unconfigured (unit-test context) or the model is unknown. sync.ts surfaces
the real model name in the preview message and JSON.
Regression test pins model-aware pricing: openai 3-large vs zembed-1 must
produce materially different previews; collapsing both to the OpenAI number
fails the assertion.
* fix(cost): sync --all gate is informational when embed is deferred; delta-aware inline gate
Under federated_v2 (default), sync --all DEFERS embedding to per-source
embed-backfill jobs that already cap spend at $25/source/24h. The v0.20
cost gate predated that cap and fired ConfirmationRequired + exit 2 on
EVERY non-TTY sync --all without --yes, regardless of cost — blocking
nightly crons over already-synced corpora and forcing permanent --yes.
The gate is now mode-aware:
- Deferred embed (v2 default): print an FYI deferred notice (cap-aware,
"not charged by this sync") + the stale-chunk backlog estimate, and
NEVER exit 2. The backfill cap is the real money gate.
- Inline embed (v2 off, or --serial without --no-embed): keep the
blocking gate, but estimate the actual delta — full-tree ceiling for
changed sources (unchanged sources contribute 0 via the same git +
chunker_version "do work?" gate doctor/sync use) + stale backlog — and
block only when it exceeds the new configurable floor
sync.cost_gate_min_usd (default $0.50).
New pure helpers in embedding.ts (willEmbedSynchronously, shouldBlockSync)
keep the decision logic hermetically testable. New engine method
sumStaleChunkChars (both engines) prices the embedding backlog via
estimateCostFromChars. estimateSyncAllCost's per-source walk extracted to
estimateSourceTreeTokens (reused by the inline estimator).
Regressions pinned: R-1 deferred non-TTY never exit 2 (headline), R-2
inline above-floor still exit 2 (protection), plus the willEmbedSynchronously
/ shouldBlockSync matrix and sumStaleChunkChars engine + scope + embed_skip
coverage.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* feat(embed): real stale semantics — re-embed on model/dims swap (migration v108)
Pre-v0.41.30 "stale" meant only `embedding IS NULL`, so swapping the
embedding model or dimensions left the whole corpus silently embedded under
the OLD model — `embed --stale` ignored it and search quality quietly
degraded.
New `pages.embedding_signature` (TEXT, migration v108) stamps the embedding
provenance (`<provider:model>:<dims>`) whenever a page's chunks are embedded.
A later model/dims swap makes the stored signature differ from the current
one, which the embed paths now detect and re-embed.
GRANDFATHER (critical): the stale predicate is
`embedding IS NULL OR (embedding_signature IS NOT NULL AND <> $current)`
so a NULL signature is NEVER stale. After the migration every existing page
has NULL → none flagged → the next `embed --stale` does NOT re-embed the
whole corpus. Signatures are stamped going forward only.
Surface:
- countStaleChunks / sumStaleChunkChars gain an optional `signature` opt
that widens staleness (read-only; used by the dry-run preview + the
sync cost preview, which is now signature-aware).
- invalidateStaleSignatureEmbeddings(signature, sourceId?) NULLs the
embeddings of signature-mismatched pages so the EXISTING NULL-embedding
cursor (listStaleChunks, untouched) re-embeds them — keeps the keyset
pagination logic intact.
- setPageEmbeddingSignature stamps after a page's chunks land.
- Both embed loops wired: `gbrain embed --stale`/`--all` (embed.ts) and the
embed-backfill minion (embed-stale.ts) invalidate-then-stamp.
Migration v108 + bootstrap probe (both engines) + REQUIRED_BOOTSTRAP_COVERAGE
entry. Pinned by test/embedding-signature-stale.test.ts (R-4 grandfather,
mismatch detection, matching no-op, scoped invalidate, stamp) + the
bootstrap-coverage gate.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* feat(sync): surface embed-backfill job state in sources status + deferred notice
Under federated_v2, `sync --all` exits 0 and embedding lags behind in
embed-backfill jobs (subject to cooldown + the per-source 24h cap). Pre-fix
an operator had no signal those jobs were queued or lagging — the sync looked
"done" while embeddings trickled in later.
`gbrain sources status` now shows a BACKFILL column per source
(active(N)/queued(N)/idle) plus the last completion timestamp, read from
minion_jobs. The deferred-sync notice appends "N backfill job(s) queued" so a
cron operator sees work is enqueued, not lost. Both reads are best-effort —
a brain that never ran a worker (no minion_jobs table) reports idle/0 instead
of crashing the dashboard.
SyncStatusReportSource gains backfill_queued / backfill_active /
backfill_last_completed_at (additive; JSON envelope schema_version unchanged).
Pinned by a new case in test/e2e/sync-status-pglite.test.ts.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* test: add currentEmbeddingSignature to embedding.ts mocks + sync stale EXPECTED_PHASES
Commit 3 made embed.ts import currentEmbeddingSignature from embedding.ts.
Four tests mock.module the whole embedding.ts and omitted the new export, so
embed.ts (imported transitively) failed at load with "Export named
'currentEmbeddingSignature' not found". Add the export to each mock:
embed.serial.test.ts, e2e/cycle.test.ts, e2e/dream.test.ts,
e2e/dream-cycle-phase-order-pglite.test.ts.
Also sync the stale EXPECTED_PHASES in dream-cycle-phase-order-pglite.test.ts
to match cycle.ts ALL_PHASES — extract_atoms, synthesize_concepts, and
conversation_facts_backfill drifted in after the test was last touched
(v0.41.0.0) and were never added, so both phase-order assertions were failing
on the branch before this wave (confirmed against
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041d89babe |
v0.41.29.0 feat(conversation-parser): bold-name-no-time builtin + fix(orphans): source-scoped orphan_ratio (supersedes #1613) (#1620)
* feat(conversation-parser): add bold-name-no-time builtin (Circleback/Granola/Zoom, no timestamp) The 14th built-in pattern parses `**Speaker:** text` transcripts with NO per-line timestamp — the shape Circleback / Granola / Zoom emit. Every prior builtin required a time anchor, so this shape matched nothing: a production brain had 104 conversation pages + 3,423 eligible pages silently extracting zero facts. Messages anchor at T00:00:00Z of the frontmatter date (no fabricated wall-clock; line order preserves sequence), same convention as irc-classic. Hardening beyond the original community proposal: - regex `/^\*\*(?!\[)(.+?):\*\*\s*(.*)$/`: the colon-inside-bold (NOT declaration order) is what prevents shadowing bold-paren-time; the `(?!\[)` lookahead rejects telegram-bracket `**[18:37] Name:**` so disabling telegram-bracket yields an honest no_match instead of speaker="[18:37] Name". - new optional PatternEntry.score_full_body: `**Label:** text` is a common prose idiom, so a notes page with bold labels clustered in its first 10 lines scored 0.3 on the head pass (NOT < SCORING_HEAD_TRIGGER_THRESHOLD, so the full-body fallback never fired) and cleared the 0.05 floor. parse.ts now recomputes the winner's score over the full body before the floor, so such a page drops to its true low density and stays no_match. - scrubbed pre-existing real names from bold-paren-time test_positive samples (privacy rule). Fixtures use placeholder names only. Pinned by new bold-name-no-time + clustered-head no_match cases in parse.test.ts and the eval corpus. Co-Authored-By: garrytan-agents <noreply@github.com> Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix(orphans): scope orphan_ratio + find_orphans by source; fix total_linkable denominator `gbrain doctor --source <id>` and `gbrain orphans --source <id>` now scope the orphan scan to that source instead of reporting brain-wide. Three fixes: - findOrphanPages(opts?: { sourceId?, sourceIds? }) on both engines scopes the CANDIDATE set (scalar `= $1` or federated `= ANY($1::text[])`). Inbound links from ANY source still count, so a page in source X linked FROM source Y is reachable and NOT an orphan of X (the deliberate, less-surprising definition). - corrected the total_linkable denominator in findOrphans: it now enumerates all live pages (scoped) and subtracts every excluded-by-slug page, not just excluded orphans. The old `total - excludedOrphans` left excluded NON-orphan pages (templates/, scratch/) with inbound links in the denominator, inflating it and suppressing warnings. Changes orphan_ratio output for every brain, in the accurate direction. - the find_orphans MCP op threads sourceScopeOpts(ctx), closing a cross-source read leak where a source-bound OAuth client saw brain-wide orphans (v0.34.1 source-isolation class). doctor uses an explicit `--source` flag parse (NOT resolveSourceWithTier, which would scope bare invocations to a default), and under explicit --source reports the ratio with a low-scale caveat below 100 entity pages instead of a vacuous "ok". Thin-client doctor --source orphan_ratio deferred (TODOS.md). Pinned by test/orphans-source-scope.test.ts (PGLite: scoping, cross-source inbound, denominator, find_orphans op scope) + a Postgres↔PGLite parity case in test/e2e/engine-parity.test.ts (scalar + federated binding). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs: v0.41.29.0 — bold-name-no-time + orphan source scoping VERSION + package.json → 0.41.29.0; CHANGELOG entry; CLAUDE.md conversation-parser (13→14 patterns) + orphans source-scoping notes; regenerated llms bundles; TODOS for thin-client doctor --source + check-test-real-names widening. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: garrytan-agents <noreply@github.com> Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> |
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ffac8ce0f4 |
v0.41.27.0 fix: withRetry self-heals on null singleton + facts:absorb drain + disconnect audit (closes #1570) (#1608)
* merge master: rebump v0.41.25.0 → v0.41.27.0 (queue collision) Master shipped v0.41.25.0 (#1538 batched sync deletes) and v0.41.26.0 (#1571 dream --source fix) while this branch was in flight. Conflict resolution rebumps to the next available slot. - VERSION: 0.41.25.0 → 0.41.27.0 - package.json: synced - CHANGELOG.md: my v0.41.27.0 entry placed above master's v0.41.26.0 and v0.41.25.0; in-entry version references updated 0.41.25.0 → 0.41.27.0 and forward-references bumped to v0.41.28+. - TODOS.md: kept master's v0.41.20.x section + my v0.41.27.0+ follow-ups No source-file conflicts during the merge. * feat(diagnostics): db-disconnect audit + doctor surface (v0.41.27.0) Instruments every db.disconnect() and PostgresEngine.disconnect() call with a JSONL audit record so the next user-reported #1570 cycle gives us the offender's caller stack instead of the symptomatic "No database connection" error. Audit shape (~/.gbrain/audit/db-disconnect-YYYY-Www.jsonl): {ts, engine_kind, connection_style, caller_stack[], command, pid} - src/core/audit/db-disconnect-audit.ts (NEW): the audit writer, built on the v0.40.4.0 createAuditWriter cathedral. Captures a 6-frame stack via new Error().stack so the offender is readable without spending stderr noise. - src/core/db.ts: logDbDisconnect call at the top of disconnect() (best-effort; never blocks the real teardown). - src/core/postgres-engine.ts: same instrumentation in PostgresEngine.disconnect() — distinguishes 'module' vs 'instance' connection_style so we can tell legitimate worker-pool teardowns apart from the load-bearing module-singleton class. - src/commands/doctor.ts: extends batch_retry_health to surface 24h disconnect count + most-recent caller stack. Warns when the caller frame isn't a known CLI-exit frame (e.g. cli.ts's finally block at the end of an op-dispatch). This is the diagnostic that tells v0.41.28+ where to apply the real ownership fix. - test/db-disconnect-audit.test.ts: unit coverage for the audit writer + caller-stack capture + JSONL shape. - test/e2e/db-singleton-shared-recovery.test.ts: real-Postgres regression that exercises the singleton-null path end-to-end. Refs #1570 * feat(retry): self-heal on null singleton — closes #1570 symptom (v0.41.27.0) withRetry gains an opt-in reconnect callback that fires between the isRetryableConnError classification and the inter-attempt sleep. PostgresEngine.batchRetry injects this.reconnect() — race-safe via the existing _reconnecting guard, handles module and instance pools. Closes the production loss reported in #1570: dream cycles on Supabase no longer drop ~150 link rows per cycle when the singleton goes null mid-batch. The retry now rebuilds the connection between attempts so the second try has somewhere to write to. - src/core/retry.ts: WithRetryOpts gains `reconnect?: () => Promise<void>`. Awaited in the catch branch. onRetry is also now awaited (back-compat- safe: every existing in-tree caller is a sync arrow). Reconnect failures propagate as the real cause — replaces the symptomatic "No database connection" error with whatever the connect() throw was, so operators see the truth. - src/core/postgres-engine.ts:batchRetry — injects `reconnect: () => this.reconnect()`. Covers all 9 batch-retry call sites (addLinksBatch, addTimelineEntriesBatch, upsertChunks, plus the 6 caller-supplied auditSite labels in extract / sync / reindex). - test/core/retry-reconnect.test.ts: 8 hermetic cases pinning the contract — reconnect fires before sleep, only on retryable errors, back-compat when omitted, signal-aborted bypasses reconnect, onRetry is awaited, full success path end-to-end. The deeper bug (who's calling disconnect mid-cycle) is left unaddressed in this commit by design — the diagnostic instrumentation in the prior commit will tell us in the next production run. Refs #1570 * feat(facts): drainPending() + CLI await before disconnect (v0.41.27.0) Closes the silent 'No database connection' tail-end errors after gbrain capture / put_page: the facts:absorb fire-and-forget queue sometimes outlived the CLI process's connection lifetime, so absorb attempts after engine.disconnect() landed in stderr as the GBrainError shape. - src/core/facts/queue.ts: new drainPending({timeout: 1000}) method distinct from shutdown(). Stops accepting new enqueues, awaits in-flight settle, bounded by timeout, returns count of unfinished. Semantically different from shutdown() (which aborts in-flight) so the symptom — drop work that hasn't started yet but let in-flight work finish — matches what CLI exit actually needs. - src/cli.ts: op-dispatch finally block awaits the drain BEFORE engine.disconnect(). Bounded 1s. Opt-out env GBRAIN_NO_FACTS_DRAIN for callers that don't enqueue (keeps fast-exit paths fast). Mirrors the v0.41.8.0 awaitPendingLastRetrievedWrites pattern. - test/facts-queue-drain-pending.test.ts: 6 hermetic cases — empty drain returns immediately, single in-flight settles, timeout bounds wait, shutdown-after-drain is idempotent, post-drain enqueues are dropped, signal-aborted skips waiting. Refs #1570 * docs: update project documentation for v0.41.27.0 README.md: added troubleshooting entry for the v0.41.27.0 retry-reconnect + facts:absorb drain fix (closes #1570), pointing operators at `gbrain doctor --json` to find the offending disconnect caller. CLAUDE.md: extended `src/core/retry.ts` entry with the new optional `reconnect` callback (v0.41.27.0); added two new Key Files entries for `src/core/audit/db-disconnect-audit.ts` (the diagnostic half of the "instrument first, fix later" pivot) and `FactsQueue.drainPending`; extended `doctor.ts:checkBatchRetryHealth` entry with the in-place extension that surfaces 24h disconnect-call count. llms-full.txt: regenerated to absorb CLAUDE.md edits. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> * chore: rebump v0.41.27.0 → v0.41.28.0 (queue collision with #1573) Master shipped v0.41.27.0 (#1573 git-aware sync_freshness) claiming the same slot. Rebump to the next available version. - VERSION + package.json → 0.41.28.0 - CHANGELOG.md: my entry header + in-entry refs 0.41.27.0 → 0.41.28.0 - TODOS.md: my #1570 follow-up section header + body refs bumped * test: pin gateway in put-page-provenance + embedding-dim-check (CI shard fix) Both files failed on CI shards 1 and 8 under the cross-file gateway-state leak class (CLAUDE.md "Test-isolation lint and helpers"). The v0.41.28.0 merge reshuffled the weight-based shard bin-packing, landing a gateway-mutating sibling ahead of these two victims in the same `bun test` process. Mechanism: - put-page-provenance: put_page embeds via the gateway. A sibling left the gateway configured with OpenAI + the CI placeholder `sk-test` (captured at configureGateway time, survives the withEnv restore as cached gateway state). put_page's embed then fired against live OpenAI and 401'd. The bunfig legacy-embedding preload's beforeEach only re-applies legacy when the gateway was RESET — it does NOT correct a sibling that configured a different LIVE config. - embedding-dim-check: initSchema builds the content_chunks vector column at the gateway's configured dim. A sibling leaking ZE/1280 made the column 1280-d, so `expect(dims).toBe(1536)` failed. Fix (victim-side pinning, the escape hatch the preload documents): - Both: configure the gateway explicitly in beforeAll BEFORE initSchema (OpenAI/1536), resetGateway() in afterAll so neither leaks onward. - put-page-provenance also stubs the embed transport via __setEmbedTransportForTests so embed is deterministic and offline; a dummy OPENAI_API_KEY is supplied in the gateway env because instantiateEmbedding builds the OpenAI client (key check) BEFORE the stubbed transport is reached — the stub then intercepts the actual call so the key never leaves the process. Verified: CI shards 1 (1337 pass) + 8 (905 pass) green with OPENAI_API_KEY unset, plus adversarial sibling orderings (gateway.test / doctor-ze-checks preceding). Typecheck + check-test-isolation clean. --------- Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com> |
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ff32fcaa78 |
v0.41.25.0 perf(sync): batched deletes + global page-generation clock (supersedes #1538) (#1566)
* feat(engine): add deletePages + resolveSlugsByPaths to BrainEngine (v0.41.21.0 T1) Two new REQUIRED methods on the BrainEngine interface, implemented on both Postgres and PGLite engines. Closes the per-file N+1 query pattern that PR #1538 batched on Postgres only. deletePages(slugs: string[], opts: { sourceId: string }): Promise<string[]> — Single SQL round-trip: DELETE FROM pages WHERE slug = ANY($1::text[]) AND source_id = $2 RETURNING slug — Returns slugs ACTUALLY DELETED (D6, codex CDX-8) so callers can filter pagesAffected to exclude phantom slugs (paths in the deletion list but with no DB row). — Single-batch primitive: caller chunks input to DELETE_BATCH_SIZE. Throws if input exceeds the cap. — sourceId is REQUIRED at the type level (D5, codex CDX-10). Asymmetric with single-row deletePage which keeps the optional 'default' fallback for back-compat. v0.42+ TODO to tighten. resolveSlugsByPaths(paths, opts): Promise<Map<path, slug>> — Batch path → slug lookup. Single SQL round-trip: SELECT slug, source_path FROM pages WHERE source_path = ANY($1::text[]) AND source_id = $2 — Missing paths absent from the Map (caller falls back to path-derived slug, same contract as resolveSlugByPathOrSourcePath). — Empty input short-circuits to empty Map (no SQL). src/core/engine-constants.ts (NEW) — Single source of truth for DELETE_BATCH_SIZE = 500. — Both engines import; no engine-from-engine coupling. — Lives outside engine.ts (the interface module) to avoid circular imports. Also updates the deletePage JSDoc (CDX-11): drops the misleading "hard delete is admin-only" framing. `gbrain sync` hard-deletes on every run that sees a deleted file; not admin-only. Co-Authored-By: garrytan-agents <noreply@anthropic.com> Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * perf(sync): batched delete + rename + DRY refactor (v0.41.21.0 T2/T3/T4) Replaces the per-file delete loop (sync.ts:1241-1257) and per-file rename slug-resolve (sync.ts:1263-1295) with interleaved per-batch flows using engine.resolveSlugsByPaths + engine.deletePages. Also refactors resolveSlugByPathOrSourcePath (sync.ts:267) to delegate to the new batch helper when sourceId is set — one owner of the SQL + fallback semantics (D8). ROUND-TRIP COUNTS (73K-delete commit): pre-fix: 73,000 SELECTs + 73,000 DELETEs = 146,000 (~5 hours) post-fix: 146 SELECTs + 146 DELETEs = 292 (~2 minutes) Headline win: a single commit deleting 73K files no longer jams the sync pipeline for hours, no longer cascades staleness across every other source on the brain. Shape (T2 delete loop, per the plan's ASCII diagram): filtered.deleted (73K paths) │ ▼ slice into batches of DELETE_BATCH_SIZE (500) │ ▼ for each batch: abort-check ──► partial('timeout') │ ▼ engine.resolveSlugsByPaths(batch, {sourceId}) ◀── 1 SQL round-trip │ ▼ slugs = batch.map(path => map.get(path) ?? resolveSlugForPath(path)) ◀── pure-JS fallback │ for frontmatter- ▼ fallback slugs try { deleted = engine.deletePages(slugs, opts) ◀── 1 SQL round-trip pagesAffected.push(...deleted) ◀── D6 confirmed only } catch { // D7 decompose: per-slug deletePage, // unrecoverable failures → failedFiles } Per-batch try-catch (D7) decomposes batch DELETE failures to per-slug deletePage so a transient blip on batch 73 doesn't lose 500 deletes — it self-heals to one-at-a-time for that batch only. Unrecoverable per-slug failures land in failedFiles (matching the existing import-loop pattern at sync.ts:~1350). failedFiles declaration hoisted above the delete loop so both delete decompose and import loops feed the same sync-bookmark gate. T4 rename loop: pre-resolves all `from` slugs in batches via resolveSlugsByPaths BEFORE iterating. Per-file updateSlug + importFile calls stay (those are inherently per-file). The try/catch around updateSlug for slug-doesn't-exist preserves verbatim. T3 DRY refactor: resolveSlugByPathOrSourcePath delegates to resolveSlugsByPaths via a single-element array when sourceId is set. When sourceId is undefined (legacy unscoped callers), falls back to the original executeRaw shape — the batch engine surface requires sourceId per D5 (multi-source-bug-class defense). Atomicity coarsening (D3): each batch is one transaction. A mid-batch abort or connection failure rolls back up to DELETE_BATCH_SIZE - 1 successful deletes from the in-flight batch. Sync is idempotent so the next run picks them up via git diff regenerating the deletion list. Documented at the call site + in the deletePages JSDoc. Co-Authored-By: garrytan-agents <noreply@anthropic.com> Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * feat(schema): global page-generation clock + statement-level trigger (v0.41.21.0 T5) Migration v104: page_generation_clock_and_statement_trigger. The pre-v0.41.21.0 query-cache Layer 1 bookmark read MAX(generation) FROM pages to detect "writes happened since cache-store". Two bugs in that contract — independent of any sync work, surfaced by codex outside-voice on the /plan-eng-review pass: 1. The row-level bump_page_generation_trg (migration v91) sets NEW.generation = OLD.generation + 1 on UPDATE. Updating a NON-MAX page didn't advance MAX(generation). Cache silently served stale for any UPDATE-to-non-max page. (CDX-2) 2. The trigger is BEFORE INSERT OR UPDATE — DELETE doesn't fire it at all. Even an AFTER DELETE wouldn't move MAX (surviving rows are untouched). (CDX-1) Fix: single-row page_generation_clock counter, bumped per-statement (FOR EACH STATEMENT — per-row would turn a 73K-row batch DELETE into 73K UPDATEs on the same counter, recreating the bottleneck this PR fixes elsewhere — codex CDX-4). Layer 1 reads the clock value directly (T6, separate commit). Per-row pages.generation stays for Layer 2 (per-page snapshot via jsonb_each + LEFT JOIN pages) which doesn't care about MAX, only per-page advancement. Seeded with COALESCE(MAX(pages.generation), 0) so existing query_cache rows stored under the old MAX semantics aren't all instantly invalidated on upgrade. Their max_generation_at_store stamp compares cleanly against the seeded clock; future writes bump the clock and the bookmark fires correctly. CREATE TABLE page_generation_clock ( id INTEGER PRIMARY KEY CHECK (id = 1), value BIGINT NOT NULL DEFAULT 0 ); CREATE TRIGGER bump_page_generation_clock_trg AFTER INSERT OR UPDATE OR DELETE ON pages FOR EACH STATEMENT EXECUTE FUNCTION bump_page_generation_clock_fn(); Mirror in src/core/pglite-schema.ts so fresh PGLite installs get the table + trigger via SCHEMA_SQL replay. The forward-reference bootstrap probe doesn't need an entry: page_generation_clock is created directly by SCHEMA_SQL (no separate index or FK references it), so the schema-bootstrap-coverage gate is satisfied as-is. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * fix(cache): move Layer 1 to global clock + invalidate empty snapshots (v0.41.21.0 T6) Closes the silent stale-cache bug class that's been live in master since the bookmark feature shipped. Pre-fix, gbrain search would silently serve stale cached results in three independent scenarios: 1. UPDATE to a non-max-generation page (CDX-2) — the row-level trigger advanced per-page generation but didn't move MAX(generation), so the bookmark passed. 2. DELETE of any page (CDX-1) — the trigger didn't fire at all, and even an AFTER DELETE wouldn't move MAX. 3. Empty-result cache row + subsequent matching INSERT (CDX-6 / D20) — page_generations = '{}'::jsonb was "vacuously valid" via Layer 2, surviving any clock bump. Fix: buildPageGenerationsSnapshot (store path) — Replaces the SELECT MAX(generation) FROM pages reads at cache-write time with SELECT value FROM page_generation_clock WHERE id = 1. — Empty pageIds path: only need the clock value (D20 contract). — Combined non-empty path: per-page generation (Layer 2 substrate) + clock value, both folded in one round trip via UNION ALL. CACHE_GATE_WHERE_CLAUSE (lookup path) — Layer 1 reads page_generation_clock.value (single-row O(1) lookup, faster than the pre-fix MAX(generation) backward index scan). — Layer 2 stricter: requires page_generations <> '{}'::jsonb AND the per-page check (not OR with the vacuously-valid `= '{}'` shortcut). Empty snapshots can no longer survive a Layer 1 miss. validateCacheRowAgainstPages (pure validator) — Layer 2 returns false for empty snapshots when Layer 1 fails. — Documented contract change. Backward compat: pre-v0.40.3.0 cache rows have max_generation_at_store = 0 AND page_generations = '{}'::jsonb. On a populated brain, Layer 1 fails (clock > 0). Layer 2 is now stricter so legacy rows invalidate once on first post-upgrade lookup, then the cache fills back correctly. Acceptable one-time miss spike; post-upgrade cache is structurally sound. The clock seed (COALESCE(MAX(pages.generation), 0)) from migration v104 keeps NON-empty legacy rows passing Layer 1 until the next write — they don't all invalidate at once. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * test: cover v0.41.21.0 delete-batch + global clock + cache contract (T7+T8+T9) Tests for every behavior the v0.41.21.0 wave introduces or changes. New test files: test/sync-delete-batch.test.ts (PGLite hermetic) — engine.deletePages: empty input short-circuit, returns confirmed slugs (D6), multi-source isolation, cascade integrity (chunks + links cleared via FK), rejects oversized input. — engine.resolveSlugsByPaths: empty input, present + missing rows, D10 exotic-filename substrate (🌟.md / ทดสอบ.md / عربي.md), source isolation. — D13 pagesAffected filter: 100 deletable + 10 ghost paths → deletePages returns 100 (regression-pin: pre-fix would return all 110 via D6's pre-RETURNING shape). test/sync-delete-batch.slow.test.ts (.slow suffix keeps it out of the fast loop) — 10K-page batched delete completes in <5s on PGLite. Measured 277ms on dev hardware (18x under the gate); pins the headline perf promise. test/sync-rename-batch.test.ts (PGLite hermetic) — 500-rename batch slug-resolve in 1 round-trip (exactly at DELETE_BATCH_SIZE boundary). — Frontmatter-fallback rename: exotic source_paths resolve via the batch SELECT. — Mixed present + missing: partial Map (missing → caller falls back to path-derived). test/page-generation-counter.test.ts (PGLite hermetic) — Statement-level trigger fires once per INSERT statement (raw SQL — NOT putPage, which uses ON CONFLICT DO UPDATE and bumps by 2 in PG semantics). — Statement-level trigger fires once per UPDATE statement. — Headline contract: batch DELETE bumps clock by 1, NOT by row count (25-row batch → +1). — CDX-1 regression: DELETE of non-max page bumps clock. — CDX-2 regression: UPDATE of non-max page bumps clock (raw SQL). — D14 end-to-end: clock advances after batch DELETE → cache rows stamped at the prior clock value are now stale by Layer 1. — CDX-6/D20: empty-result cache + INSERT matching page → clock advances (Layer 1 fires). — Documents the PG quirk: putPage's INSERT...ON CONFLICT DO UPDATE bumps clock by 2 (both INSERT and UPDATE triggers fire). Test-helper update: test/helpers/reset-pglite.ts — Added page_generation_clock to PRESERVE_TABLES so the seeded single-row counter survives resetPgliteState between tests (same treatment as schema_version). Production never truncates. Existing test contract inversions (CDX-6 / D20 fix): test/query-cache-gate.test.ts — Pre-v0.41.21.0 "vacuously valid for legacy empty snapshot" assertion inverted: empty snapshot now invalidates when Layer 1 fires. Add positive CDX-6 regression test (empty-result + INSERT matching page). — SQL shape regression: page_generation_clock in Layer 1 (negative regression guard: MAX(generation) FROM pages MUST be gone). — Empty-snapshot reject guard: `qc.page_generations <> '{}'::jsonb` present; the old `qc.page_generations = '{}'::jsonb OR` shortcut MUST be gone. test/e2e/cache-gate-pglite.test.ts — Pre-v0.41.21.0 "legacy row serves vacuously" test inverted: legacy rows now invalidate on first clock advance post-upgrade. — CDX-1 regression: DELETE bumps clock → cached query for surviving pages invalidates. — CDX-2 regression: UPDATE-to-non-max-page bumps clock → cache invalidates. — CDX-11 comment fix: drop misleading "hard delete is admin-only" framing; gbrain sync hard-deletes on every run. Engine parity extension: test/e2e/engine-parity.test.ts — deletePages parity: same input set, both engines return same string[] of confirmed-deleted slugs (D6). — resolveSlugsByPaths parity: same Map on both engines. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * chore(release): v0.41.21.0 — batched sync deletes + global page-generation clock (T10) VERSION bump (0.41.18.0 → 0.41.21.0; master is at 0.41.20.0 so next free slot per the queue allocator). CHANGELOG entry with the ELI10 lead per CLAUDE.md voice rules. CLAUDE.md annotations on engine.ts, postgres-engine.ts, pglite-engine.ts, sync.ts, and query-cache-gate.ts plus a new entry for engine-constants.ts. llms-full.txt regenerated to match CLAUDE.md (per CLAUDE.md mandatory rule). Co-Authored-By: garrytan-agents <noreply@anthropic.com> Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * dx(test-runner): heartbeat shows real progress instead of 0p 0f Bun's default test reporter doesn't print per-test markers — only a single shard-end summary block when you pass it a file list. The existing heartbeat tried to count `^[[:space:]]+✓` lines as a live pass-count proxy, but bun never emits them in the multi-file mode this runner uses, so every mid-run heartbeat showed `0p 0f` for the entire 12-20 minute wallclock. Users (and agents polling the runner) couldn't distinguish "still bootstrapping" from "wedged" from "almost done." Fix: parse three complementary real-time signals instead. 1. Total files this shard was assigned — parsed from the `[unit-shard N/M] running X files` banner that run-unit-shard.sh echoes before invoking bun test. Available from second 1. 2. PGLite initSchema() count — proxy for "test files started so far." Each PGLite-using test file's beforeAll triggers one initSchema(), which logs `Schema version 1 → 106 (101 migration(s) pending)`. Undercounts because not every test file opens a PGLite engine (covers ~30-60% of files in practice), but it's the only real-time progress signal bun's default reporter leaves in the log. The output uses a `~` prefix to convey "approximate count." 3. Log size in KB — strictly monotonic liveness signal that works even when the PGLite count is still 0 (early-shard startup before the first initSchema fires). 4. Per-shard elapsed time — formatted as MmSSs. New mid-run heartbeat line: [heartbeat] [s1: ~62/190f 476KB 12m31s] [s2: ~63/190f 513KB 12m31s] ... When a shard finishes, the heartbeat upgrades to its final summary including pass/fail counts from bun's end-of-shard summary block: [heartbeat] [s1: done ✓ 2807p 0f] [s2: done ✓ 2784p 0f] ... Portability: BSD awk on macOS doesn't support `match($0, /re/, arr)` with the array sink — that's a gawk extension. The total-files parser uses sed instead so the runner stays portable to the default Mac toolchain. Helpers are pure functions and unit-testable in isolation: pass a log file path, get the parsed number. No mocking. No bun runtime required. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * chore(release): rebump v0.41.23.0 → v0.41.25.0 Per user request — skip v0.41.23.0 / v0.41.24.0 slots to land at v0.41.25.0. Master is at v0.41.22.1, no version-trio collision. Touches VERSION, package.json, CHANGELOG header, CLAUDE.md annotations, src/core/engine-constants.ts header, src/core/migrate.ts migration v106 comment, regenerated llms-full.txt + llms.txt. Migration version (v106) and CDX1-6 trigger semantics unchanged. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * fix(schema): reorder migration_impact_log AFTER minion_jobs (CI green) Pre-existing bug in master's SCHEMA_SQL ordering, surfaced by CI on this PR but lived silently on master since v0.41.18.0. migration_impact_log declares `job_id BIGINT REFERENCES minion_jobs(id)`, but its CREATE TABLE was at line 658 while minion_jobs's CREATE TABLE was at line 778. On any fresh-install initSchema() the FK target didn't exist yet: psql:/tmp/schema.sql:672: ERROR: relation "minion_jobs" does not exist postgres-js's `unsafe()` aborts the multi-statement batch on the first error response, so every CREATE TABLE after migration_impact_log (including minion_jobs itself) never ran. Every subsequent CLI subprocess that opened a connection then crashed with `relation "minion_jobs" does not exist` on its first query. Why master CI sometimes passed: the per-shard advisory lock + the test setup's `engine.initSchema()` second pass (which runs the migrations array) would eventually create minion_jobs via the v5 `minion_jobs_table` migration. From there migration_impact_log would land via migration v103 with its FK resolving correctly. But CLI subprocesses spawned by mechanical.test.ts's Parallel Import block open their OWN connections and run a fresh `engine.connect() → initSchema()` — that path runs SCHEMA_SQL FIRST and aborted at the same forward-reference error before the migrations array could repair. Fix: relocate the migration_impact_log CREATE TABLE + its two indexes to AFTER the minion_jobs CREATE TABLE block (lines ~865), keeping the rest of the schema layout intact. PGLite schema (pglite-schema.ts) already had the correct ordering — only Postgres SCHEMA_SQL needed the move. Verified: fresh-DB local repro that previously failed 31/34 tests with `relation minion_jobs does not exist` now passes 78/78 in test/e2e/mechanical.test.ts. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> --------- Co-authored-by: garrytan-agents <noreply@anthropic.com> |
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5d42f3295e |
v0.41.22.0 feat: type-unification cathedral — 94 types → 15 canonical (closes #1479) (#1542)
* Merge branch 'master' into garrytan/type-taxonomy-unification Resolve VERSION, package.json, CHANGELOG conflicts with v0.41.22.0 on top, preserving master's v0.41.19.0 entry below. * feat: v0.41.22.0 type-unification cathedral — collapse 94 types to 15 (closes #1479) Ships gbrain-base-v2 as the new install default (15 canonical types: 14 + note catch-all) and the unify-types PROTECTED Minion handler that runs the gbrain-base→v2 migration end-to-end on existing brains. What this delivers: - gbrain-base-v2.yaml standalone schema pack (no extends:) with 14 canonical page_types + 9 cluster mapping_rules + catch-all sentinel - 3 new schema-pack primitives: runRetypeCore (chunked UPDATE with legacy_type stamping), runPageToLinkCore (edge-shaped pages → link rows), runPageToAliasCore (concept-redirect → slug_aliases) - rewriteLinksBatch for N-pair atomic FK rewrite - Migration v104 slug_aliases table (forward-bootstrap probed on both engines for safe upgrade chain) - New engine method resolveSlugWithAlias(slug, sourceOrSources) on both Postgres + PGLite with multi-source ambiguity warning - inferTypeAndSubtypeFromPack overload + subtypes: + mapping_rules: + migration_from: schema-pack manifest extensions - findPackSuccessors version-range walker (1.x / 1.0.x / exact match) - expandTypeFilter for --type back-compat (D14): legacy aliases route through mapping_rules → canonical+subtype before the SQL filter fires - 3 new onboard checks: pack_upgrade_available, type_proliferation, dangling_aliases (source-scoped per F12) - unify-types Minion handler (PROTECTED, manual_only via render.ts allowlist per D17): retype-explicit → retype-catch-all → page-to-link → page-to-alias → final sync → active-pack flip - alias_resolved 1.05x post-fusion search boost stage; KNOBS_HASH_VERSION bumped 5→6 (one-time cache miss on upgrade, self-healing in TTL) - ELIGIBLE_TYPES for facts extraction extended with v2 canonicals (codex F-ELIGIBLE: blocker not v0.43 follow-up) Tests: 79 new unit/integration cases + 3 E2E cases covering all 9 production clusters end-to-end. 124-case verification on the cache-key + build-llms fixes. KNOBS_HASH_VERSION assertions updated in 3 tests. Plan: ~/.claude/plans/system-instruction-you-are-working-transient-elephant.md (16 locked decisions D1-D17, 12 baseline fixes F7-F21 absorbed from codex outside voice). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * fix: CI verify failures — system-of-record allow-comment + schema-unify manifest registration Two CI failures on PR #1542: 1. check:system-of-record flagged page-to-link.ts:207 addLinksBatch as a direct write to a derived table. The call IS the reconcile surface for page_to_link mapping_rules — it converts edge-shaped pages into canonical link rows under the PROTECTED unify-types Minion handler, source-scoped, atomic per-rule. Added the canonical `// gbrain-allow-direct-insert: <reason>` comment on the same line. 2. check:resolver emitted 11 orphan_trigger warnings for `schema-unify` because the skill was added to skills/RESOLVER.md without a corresponding entry in skills/manifest.json. Added the registration under the existing skills[] array. bun run verify: 28/28 checks pass locally. * fix: CI test failures — schema-unify conformance + eligibility regression Six test failures across shards 2 + 10 on PR #1542: 1. resolver.test.ts: round-trip parser requires frontmatter triggers to be quoted (`- "..."` or `- '...'`). schema-unify shipped with bare YAML strings; quoted the 10 triggers to round-trip correctly. 2. skills-conformance.test.ts (×3): schema-unify SKILL.md was missing the required Contract, Anti-Patterns, and Output Format sections that every conformant skill must declare. Added all three: - Contract: inputs / outputs / side effects / failure modes - Anti-Patterns: 5 DON'Ts including the autopilot trust boundary - Output Format: per-phase stderr lines + celebration summary + JSON envelope shape 3. facts-eligibility.test.ts (×2): the v0.41.22 ELIGIBLE_TYPES expansion added `concept` to the eligible list, but the existing test suite pins concept as rejected (it's `extractable: true` in the schema pack but the v0.41.11 contract documented this as "cosmetic on the backstop path because backstop uses hardcoded ELIGIBLE_TYPES"). Removed `concept` from the expansion; other v2 canonicals (media, tweet, atom, analysis) stay. Comment updated to document the deliberate omission. All 6 failing tests now pass locally (370/370 across the 3 affected files). bun run verify: 28/28 checks green. * fix: harden findPackSuccessors test against shard pollution CI shard 8 reported 1 fail (1.00ms — too fast for any real loadActivePack file I/O) on `finds gbrain-base-v2 as successor of gbrain-base@1.0.0`. Local triple-run passes 9/9 in isolation. Root cause: the existing afterEach reset clears the module-level pack cache AFTER each test, but the FIRST test in the file inherits whatever state sibling files in the same bun shard process left behind. With 24+ schema-pack tests in shard 8 (mutate, mutate-audit, best-effort, registry-reload, manifest-v041_2, etc.) running before this file, the first test can read a poisoned cache. Fix: add `beforeEach(_resetPackCacheForTests)`. Two-sided reset guarantees clean state regardless of file ordering within the shard. bun run verify: 28/28 checks pass. * fix: quarantine two flaky tests to serial runner CI shard 1 + shard 8 each surfaced one intermittent failure: shard 1: buildBrainTools > execute() on put_page with valid namespace shard 8: findPackSuccessors > finds gbrain-base-v2 as successor Both pass cleanly in isolation. Both are concurrency races against shared in-shard state: - brain-allowlist.test.ts shares a singleton PGLiteEngine across 18 tests with a beforeEach DELETE FROM pages. With max-concurrency=4, two put_page tests can interleave their TRUNCATE + write phases, so the auto-link/extract sub-steps inside put_page race against the sibling test's DELETE. - schema-pack-find-pack-successors.test.ts reads bundled YAML packs via loadActivePack. The module-level pack cache is shared across parallel tests in the same shard; the previous beforeEach reset helped but didn't fully isolate against concurrent file reads under CI load. Fix per CLAUDE.md test-isolation lint rule R2 (concurrency-fragile files belong in the .serial.test.ts quarantine): rename both files to *.serial.test.ts. Serial runner picks them up at max-concurrency=1. 49/49 serial files pass locally. 28/28 verify checks pass. * fix: quarantine embed-stale test to serial runner CI shard 9 reported 6 failures, all from the embedStaleForSource describe block, all ~120-150ms each — classic shared-engine concurrency race shape. Passes 7/7 locally in isolation. Root cause: embed-stale.test.ts shares a singleton PGLiteEngine across 7 tests with beforeEach resetPgliteState. Under bun's max-concurrency=4 in the parallel shard, two tests can interleave their TRUNCATE + seedPage + upsertChunks + embedStaleForSource flow, so one test's stale-chunk count sees another test's mid-flight writes. Same fix as brain-allowlist.serial.test.ts and schema-pack-find-pack-successors.serial.test.ts: rename to *.serial.test.ts so the serial runner picks it up at max-concurrency=1. bun run verify: 28/28 checks pass. 7/7 embed-stale tests pass via serial. --------- Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com> |
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a74e5d90fc |
v0.41.20.0 feat: gbrain status + doctor --scope=brain (fix wave 2: items #6 + #7) (#1544)
* feat(doctor): doctor-categories foundation — BRAIN/SKILL/OPS/META sets + drift guard
Categorizes every doctor check name into exactly one of four categories. Exported
constants + categorizeCheck(name) helper are the single source of truth for the
v0.41.20.0 brain_checks_score + category_scores + --scope=brain wave. Drift guard
test parses doctor.ts source for both inline {name: 'foo'} and helper
const name = 'foo' patterns; CI fires if any check name lacks a category.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
* feat(doctor): brain_checks_score + category_scores + --scope=brain skip-computation
Extends Check with optional category and DoctorReport with brain_checks_score +
category_scores (additive — schema_version stays at 2; back-compat health_score
math byte-identical). buildChecks gains --scope=brain with explicit early-skip
gates around the SKILL check group (resolver_health + skill_conformance +
skill_brain_first + whoknows_health). Sub-second doctor on a brain with thousands
of skills. computeDoctorReport tags every check via categorizeCheck() at compute
time. Human output leads with the brain figure and renders the weighted
BrainHealth.brain_score alongside.
Test seam fix in test/doctor-home-dir-in-worktree.test.ts: the pre-existing
fragile JSON parser walked back from "checks" to find the envelope's outer
brace; v0.41.20.0's new nested category_scores object broke that heuristic.
Anchored on the canonical {"schema_version" envelope prefix instead.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
* feat(status): gbrain status — single-screen brain health dashboard + get_status_snapshot MCP op
NEW gbrain status command (src/commands/status.ts) composes 6 sections:
sync (per-source last_sync_at + staleness via buildSyncStatusReport),
cycle (TWO rows: last autopilot-cycle + last autopilot-* of any kind —
reflects v0.36.4.0 health-aware autopilot's targeted handler routing;
totals read from result.report.totals per the canonical handler shape),
locks (gbrain_cycle_locks active rows), workers (readSupervisorEvents +
summarizeCrashes), queue (LIVE counts NO time-window — old stuck jobs
are exactly what status surfaces), autopilot (PID liveness via kill -0).
Stable --json envelope (schema_version: 1). Exit codes 0=ok / 1=snapshot
failed / 2=usage. --section filter.
Thin-client mode routes Sync + Cycle through NEW get_status_snapshot MCP
op (admin scope, NOT localOnly; payload deliberately omits Locks /
Workers / Queue / Autopilot so feature creep can't quietly widen the
admin-scoped data exposure). Local-only sections render "local-only —
N/A on remote brain" honestly instead of pretending the local install's
empty state is the remote brain's.
CLI dispatch: pre-engine-bind branch for thin-client (no PGLite needed)
+ engine-connected dispatch case for local mode. CLI-only architecture
per codex MAJOR-4 (status owns its own thin-client branch inside
runStatus, not routed through op dispatch).
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
* chore: bump version to v0.41.20.0 + CHANGELOG + TODOS + llms regen
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
* fix(doctor-categories): categorize batch_retry_health from v0.41.19.0 Supavisor wave
The drift guard correctly caught a new check introduced by master's v0.41.19.0
Supavisor Retry Cathedral (PR #1537). batch_retry_health surfaces batch-write
retry events from the new src/core/audit/batch-retry-audit.ts module — OPS
category (infrastructure liveness).
This is exactly why the drift guard exists: any future check added to doctor.ts
without a category entry fails CI immediately instead of silently degrading
to 'meta'.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
---------
Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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10816cba38 |
v0.41.18.0: gbrain onboard — the activation surface gbrain didn't have before (#1521)
* feat(schema): migrations v98/v99/v100 for onboard wave (A6 A10 A11 A13 A25, codex #1 #9 #10 #11 #12) Three schema additions supporting the gbrain onboard wave: v98 — links.link_kind nullable column (A10, codex finding #12). The NER extraction was originally going to add a new link_source='ner' provenance, but that would have forced every existing link_source='mentions' query (backlink-count filter, orphan-ratio, doctor checks) to update or metrics would drift across the cutover. Instead: keep link_source='mentions' for the storage layer AND add a nullable link_kind column. Three kinds: 'plain', 'typed_ner', NULL (legacy/unknown — semantically 'plain'). NOT in the links UNIQUE constraint so the storage shape stays compatible. v99 — timeline_entries dedup widening (A11, codex finding #11). Pre-v99 dedup key was (page_id, date, summary). The new --from-meetings extraction writes timeline entries with source='extract-timeline-from- meetings:<meeting-slug>', and codex caught that two meetings with the same date+summary on the same entity page would silently DO NOTHING — the second meeting's provenance is lost. Widened to (page_id, date, summary, source). Legacy rows (source='') preserve current dedup behavior. v100 — migration_impact_log table + content_chunks_stale_idx partial (A6 + A25 + A13 + codex findings #10 + #9). Bundled because both are consumed by the onboard pipeline and ship together. Impact log captures before/after metric stats so gbrain onboard --history shows real deltas; attribution columns (job_id, source_id, brain_id, started_at, idempotency_key) prevent concurrent runs misattributing to wrong migrations. content_chunks_stale_idx partial WHERE embedding IS NULL supports gbrain embed --stale + --priority recent (outer ORDER BY p.updated_at DESC uses existing idx_pages_updated_at_desc via JOIN). Plain NUMERIC columns; delta computed at read time (NOT a stored GENERATED column per eng-review D2 — zero PGLite parity risk). Slot history note: plan originally proposed v97/v98/v99 but master had already used v95 (links 'mentions' CHECK widening), v96 (facts conversation session index), and v97 (pages_dedup_partial_index) by ship time. Codex caught the collision; renumbered to v98/v99/v100. Test pin: test/schema-bootstrap-coverage.test.ts (100/100 migrations apply clean on PGLite), test/migrate.test.ts (152 cases pass). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * refactor(remediation): extract doctor remediation library (A1, codex finding #2) Pre-fix: src/commands/doctor.ts contained two CLI-shaped functions (runRemediationPlan + runRemediate) with hardcoded argv parsing, process.exit calls, and console.log emission. Onboard CLI shell and the upcoming MCP run_onboard op couldn't compose against them — the plan file's "100-LOC thin wrapper" assumption didn't survive codex's review of the actual source. Post-fix: src/core/remediation/ exports a library shape that all three consumers (doctor CLI, onboard CLI, MCP run_onboard) wrap. src/core/remediation/types.ts RemediationPlanOpts, RemediationPlan, RemediationOpts, RemediationResult, StepResult, RemediationHooks (the observability seam — library never calls console.* itself). src/core/remediation/context.ts loadRecommendationContext moved verbatim from doctor.ts. Re-exports RecommendationContext from brain-score-recommendations.ts since that's still the canonical home for the type (consumed by computeRecommendations). src/core/remediation/plan.ts computeRemediationPlan(engine, opts): Promise<RemediationPlan>. Pure read; produces the stable JSON envelope downstream agents bind to. Pulls in computeRecommendations + classifyChecks + maxReachableScore behind one library entry point. src/core/remediation/run.ts runRemediation(engine, opts, hooks): Promise<RemediationResult>. Orchestrator with BudgetTracker, checkpoint resume, D5 dep cascade, D7 per-step recheck. Returns a result object instead of process.exit calls; the CLI shell maps result.budget_exhausted / .target_unreachable / .submitted to exit codes. src/core/remediation/index.ts Barrel for the three modules above. doctor.ts is now a thin wrapper: runRemediationPlan: parse argv → computeRemediationPlan → human/JSON render runRemediate: parse argv → TTY confirm gate → runRemediation(hooks: console.*) The TTY confirmation step deliberately stays in the CLI shell — the library never asks for confirmation; that's a CLI concern. Net: ~340 LOC removed from doctor.ts; ~470 LOC added across the library module (with full JSDoc + per-A-decision rationale comments). Functional behavior preserved bit-for-bit: 67 tests pass across doctor.test.ts + v0_37_gap_fill.serial.test.ts. The Lane E.4 source-text test (test/v0_37_gap_fill.serial.test.ts:329) followed loadRecommendationContext to its new home at src/core/remediation/context.ts — assertions otherwise unchanged. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * refactor(remediation): generalize computeRecommendations to accept extras (A2, codex finding #3) Pre-fix: computeRecommendations at brain-score-recommendations.ts:170 was a hardcoded planner for 5 synthetic check categories. Adding a Check.remediation field to a new doctor check would NOT auto-wire into --remediation-plan — the planner simply ignored it. Codex caught this when reviewing the plan's "checks ARE specs" framing. Post-fix: optional third arg `extraRemediations: RemediationStep[]` lets callers inject step entries discovered outside the hardcoded planner. The existing 5-category surface is preserved bit-for-bit; on id collision the hardcoded entry wins, so an extra accidentally duplicating a hardcoded id doesn't shadow legacy behavior. RemediationPlanOpts gains the matching field; computeRemediationPlan in src/core/remediation/plan.ts threads opts.extraRemediations through. The 4 new doctor checks (T4) will produce per-check helper functions that return RemediationStep[]; onboard's render layer (T12) aggregates them into the opts.extraRemediations slot. doctor's existing --remediation-plan call passes empty (no behavior change for legacy CLI). 84 tests pass across brain-score-recommendations + doctor suites. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * feat(doctor): 4 new onboard checks (embed_staleness, link_coverage, timeline_coverage, takes_count) (A16, T4) Adds src/core/onboard/checks.ts: 4 check helpers + a runAllOnboardChecks aggregator. Each helper returns {check, remediations}, so doctor pushes the Check entry (for human/JSON rendering) AND onboard's plan path collects the RemediationStep[] (via T3's new extraRemediations seam in computeRecommendations). embed_staleness: COUNT(*) on content_chunks WHERE embedding IS NULL. Cheap thanks to content_chunks_stale_idx partial (v100). warn at 1+ stale, fail at 1000+; remediation points at embed-catch-up handler (built in T6). entity_link_coverage: fraction of entity pages with inbound links. Per A21 + codex #15: TABLESAMPLE BERNOULLI on PG when total_pages > 50K with pinned sample formula (LEAST 100, GREATEST 2, target ~5000 rows) AND ±sqrt(p(1-p)/n) confidence interval embedded in message ("coverage: 31% ± 1.3%") so warn/fail decisions show their margin of error. PGLite path: full scan (rare >50K). warn <70%, fail <40%; remediation points at extract-ner handler. timeline_coverage: same TABLESAMPLE policy. warn <90%, fail <70%; remediation points at extract-timeline-from-meetings handler. takes_count: COUNT(*) on takes table. Per A12 two-gate consent: the remediation only emits when `takes.bootstrap_enabled` config is true. Otherwise the check shows "0 takes (takes.bootstrap_enabled is false; opt in to enable)" without an autopilot-eligible remediation. Prevents unattended LLM-bearing extractions on brains that haven't opted in. runDoctor wires runAllOnboardChecks at the end of the DB-checks block (after stale_locks); fast-mode skipped to preserve --fast UX. Thin-client parity (A16 spec) deferred to T16 — the MCP run_onboard op will run these helpers server-side where engine.executeRaw works, which is the real federated path. Adding them to doctor-remote.ts would duplicate the logic without functional benefit since the helpers are server-side queries. 55 doctor tests pass; typecheck clean. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * feat(engine): listStaleChunks --priority recent + executeRaw AbortSignal (A13/A20, codex #7 #9) Two interface extensions on BrainEngine, with parity across postgres-engine and pglite-engine. Plus a follow-on fix for v99's timeline_entries dedup widening. listStaleChunks gains: - orderBy?: 'page_id' | 'updated_desc' (default 'page_id' = legacy) - afterUpdatedAt?: string | null (composite cursor for updated_desc) When orderBy === 'updated_desc' the query JOINs pages and orders by p.updated_at DESC NULLS LAST, p.id ASC, cc.chunk_index ASC backed by idx_pages_updated_at_desc + content_chunks_stale_idx partial (both indexes added in v100). The cursor "next row" semantic with DESC NULLS LAST + ASC tiebreakers is: (updated_at < prev) OR (updated_at = prev AND page_id > prev_page_id) OR (updated_at = prev AND page_id = prev_page_id AND chunk_index > prev_chunk_index) First page (afterUpdatedAt undefined AND afterPageId 0) bypasses the cursor predicate. Both engines parity-tested via 100/100 pglite-engine tests; Postgres path mirrors the same WHERE clause structure. executeRaw gains: - opts?: {signal?: AbortSignal} Postgres impl: real cancellation via postgres.js's .cancel() on the pending query. Pre-aborted signal short-circuits before the network round-trip; mid-flight abort fires .cancel(). The query throws on abort which the caller catches. PGLite impl: in-process WASM has no kernel-level cancellation. Best-effort: pre-check, then race the query against a signal-rejection promise. The query keeps running in WASM but the awaited result is discarded (DOMException AbortError thrown). Documented gap. ReservedConnection.executeRaw extends the signature for type compatibility but doesn't wire the signal (its only callers are migrations + cycle-lock writes that explicitly don't want cancellation). V99 timeline dedup follow-on: the dedup widening in migration v99 changed the unique index from (page_id, date, summary) to (page_id, date, summary, source). The ON CONFLICT clauses in both engines' addTimelineEntriesBatch + addTimelineEntry impls were still using the old 3-tuple, causing 12 PGLite tests to fail with SQLSTATE 42P10 "no unique constraint matching ON CONFLICT specification". Updated all 4 sites (2 per engine) to the 4-tuple. Typecheck clean, 100/100 PGLite engine tests pass. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * feat(embed): --batch-size + --priority recent + --catch-up + embed-catch-up handler (A13) CLI surface on gbrain embed gains 3 flags: --batch-size N Override hardcoded PAGE_SIZE=2000 (clamped 1..10000) --priority recent Walk stale chunks newest-first (page.updated_at DESC) backed by content_chunks_stale_idx + idx_pages_updated_at_desc via T5's listStaleChunks(orderBy='updated_desc') extension. Composite cursor (updated_at, page_id, chunk_index). --catch-up Removes the GBRAIN_EMBED_TIME_BUDGET_MS wall-clock cap; loops until countStaleChunks() returns 0. EmbedOpts gains matching fields; embedAll + embedAllStale plumb them through. The cursor tracking in embedAllStale now advances (afterUpdatedAt, afterPageId, afterChunkIndex) instead of just (afterPageId, afterChunkIndex) when in 'updated_desc' mode. The engine returns p.updated_at as Date|string; the caller normalizes to ISO string for the next page's cursor. New Minion handler `embed-catch-up` registered in jobs.ts. Wraps runEmbedCore with stale=true + catchUp=true + the priority/batchSize the caller supplies. NOT in PROTECTED_JOB_NAMES (embedding spend only — same posture as the existing embed-backfill handler). Consumed by the gbrain onboard remediation pipeline (T11) when embed_staleness check fires. 63 embed tests pass; typecheck clean. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * feat(extract): NER link extraction via schema-pack inference.regex (A10, T7, codex #12) NEW src/core/extract-ner.ts: extractNerLinks(engine, opts). Walks pages, reuses the by-mention gazetteer, applies the active schema-pack's link_types[].inference.regex patterns to assign a typed verb to each mention ("CEO of Acme" + Acme is a company → 'works_at' linking the source page to Acme). Codex finding #12 design: do NOT split link_source='ner' as a new provenance. NER is still mention-derived; splitting would break every existing link_source='mentions' query (backlink-count, orphan-ratio, doctor checks). Instead: keep link_source='mentions' AND set link_kind='typed_ner' (v98 column). LinkBatchInput type gains link_kind field. Both engines' addLinksBatch impls add the column to the INSERT projection + unnest() tuple (column #11). The links UNIQUE constraint excludes link_kind so an existing plain mention row + a typed_ner row for the same (from, to, type, source, origin) collide DO NOTHING; the typed link goes in as a separate row with a DIFFERENT link_type (the inferred verb), so they don't collide on the typical case. CLI: `gbrain extract links --ner` (DB source only). Combined `--by-mention --ner` walk shares ONE gazetteer build across both passes — saves a full walk on big brains. Either flag alone runs its pass solo. Each gets its own --source-id filter inheritance. Minion handler: `extract-ner` (NOT in PROTECTED_JOB_NAMES — regex-only, no LLM spend). Consumed by onboard's entity_link_coverage remediation when coverage <70%. Target-type lookup: one round-trip SELECT slug, source_id, type FROM pages WHERE type IN ('person', 'company', 'organization', 'entity') AND deleted_at IS NULL — built once at extraction start, consulted per-mention. Avoids the N+1 getPage cost. Pack best-effort: when no active pack OR no link_types declared OR no inference.regex on any link_type, returns pack_unavailable=true and 0 created. CLI prints a one-line note; handler returns silently. 122 tests pass (pglite-engine + by-mention); typecheck clean. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * feat(extract): timeline from meetings — gbrain extract timeline --from-meetings (A11, T8, codex #11) NEW src/core/extract-timeline-from-meetings.ts: extractTimelineFromMeetings(engine, opts). Walks meeting pages, finds discussed entities via two sources, writes a timeline entry on each entity page. Discussed-entity sources merged: 1. Existing 'attended' links from the meeting (canonical attendees). One round-trip SELECT pulls all attended edges for the loaded meeting set; in-memory Map<meetingSlug → attendees[]> for O(1) lookup per meeting. 2. Body-text mentions via the existing by-mention gazetteer (findMentionedEntities + cross-source guard). Catches entities discussed in the meeting body even when no explicit 'attended' link exists. De-duped via Map<sourceId::slug → entity> within each meeting so a person who's both an attendee AND mentioned in the body gets exactly one timeline row per meeting, not two. Timeline write uses TimelineBatchInput with: source = 'extract-timeline-from-meetings:<meeting-slug>' summary = 'Discussed in <meeting-title>' date = meeting.effective_date Per v99 dedup widening (codex #11): the source field is now in the uniqueness key (page_id, date, summary, source). Two meetings on the same date with the same summary on the same entity page survive as distinct rows — the second meeting's provenance is no longer silently dropped. CLI: `gbrain extract timeline --from-meetings` (DB source only). Mode dispatch — runs SOLO (does not combine with --by-mention/--ner; those are links passes). Minion handler: `extract-timeline-from-meetings` (NOT in PROTECTED_JOB_NAMES — pure SQL + string scan). Consumed by onboard's timeline_coverage remediation when coverage <90%. Typecheck clean. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * feat(takes): takes-bootstrap from concept/atom/lore pages (A12, A24, T9) NEW src/core/extract-takes-from-pages.ts: Haiku classifier loop. Walks pages WHERE type IN ('concept','atom','lore','briefing','writing', 'originals') AND deleted_at IS NULL AND length(compiled_truth) > 200, ordered by updated_at DESC. Each page is truncated to 20K chars and sent to Haiku with a strict-JSON classifier prompt: {"claim", "kind": fact|take|bet|hunch, "weight": 0..1} Inserts via addTakesBatch with source='cli:takes-bootstrap-from-pages'. Two-gate consent per A12: 1. `takes.bootstrap_enabled` config (default false) — even the manual CLI refuses without it explicitly set. 2. --yes flag (CLI) — interactive confirmation that this sends content to Haiku. The handler-side gate also reads takes.bootstrap_enabled, so even a trusted local Minion submitter (allowProtectedSubmit=true) cannot fire takes-bootstrap on a brain that hasn't opted in. CLI: `gbrain takes extract --from-pages [--yes] [--dry-run] [--source-id X] [--max-pages N] [--holder name]`. Surfaces consent-gate-blocked vs llm-unavailable distinctly so users see the actual blocker. Minion handler `extract-takes-from-pages` added to PROTECTED_JOB_NAMES. Consumed by onboard's takes_count remediation when count=0 AND takes.bootstrap_enabled=true (handler-side double-check). Per A24: ships with classifier infrastructure ONLY. Per-prompt eval suite deferred to v0.42.1 follow-up; autopilot remediation tier for takes-bootstrap stays manual_only until eval coverage catches up. Manual `gbrain takes extract --from-pages --yes` is the only path that triggers it in v0.42.0. parseClaimsJson exported for unit testing — strict JSON parse + ```json fence strip + kind allowlist filter, returns [] on any parse failure. Typecheck clean. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * feat(minions): recordMinionJobSpend primitive for MCP client_id attribution (A7+A23, codex finding #4) NEW src/core/minion-spend.ts: small primitive that closes the per-OAuth- client spend chain gap codex flagged when MCP run_onboard submits child Minion jobs. Pre-fix: only subagent loops via budget-meter.ts recorded spend against the originating OAuth client. Generic Minion handlers (embed-catch-up, extract-ner, extract-timeline-from-meetings, extract-takes-from-pages) wrote to the gateway with no per-client attribution — admin-scope tokens would have unbounded indirect spend via the run_onboard fan-out. Convention for v0.42.0 (deferred schema column to v0.42.1): - run_onboard MCP op sets job.data.client_id when submitting each child handler. - Handlers that spend LLM/embedding budget call recordMinionJobSpend(engine, job, {operation, spendCents, ...}) which reads job.data.client_id and writes mcp_spend_log with the right attribution. - Local-submitted jobs (CLI, autopilot tick) pass no client_id; the row still lands with client_id=null for global accounting. Two exports: getJobClientId(job): undefined for local jobs; the OAuth client_id string for MCP-submitted ones. recordMinionJobSpend(engine, job, entry): wraps recordSpend with job-aware attribution. Best-effort throughout — spend telemetry failures MUST NOT fail the user's call. A23 full schema column (minion_jobs.client_id + index) deferred to v0.42.1; today's JSONB-pass-through is sufficient for the MCP run_onboard chain to land per-client attribution end-to-end. Handlers adopt the primitive over time; no behavior change for callers that haven't migrated. Typecheck clean. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * feat(onboard): impact capture module + writeImpactLogRow primitive (A6 + A25 + A17, T11) NEW src/core/onboard/impact-capture.ts. Three exports: captureMetric(engine, metric) Pure-ish: returns the current numeric value for one of 5 metrics (orphan_count, stale_count, entity_link_coverage, timeline_coverage, takes_count). Returns null on any throw per A17 best-effort posture — a stat-query failure MUST NOT block the extraction itself. writeImpactLogRow(engine, attribution, metric, before, after, details?) Best-effort INSERT into v100's migration_impact_log table. Attribution columns (job_id, source_id, brain_id, started_at, idempotency_key, applied_by) per A25 + codex finding #10 so concurrent runs can't misattribute deltas. withImpactCapture(engine, attribution, metric, runner, details?) Convenience: capture-before → run → capture-after → write log row. Per A17 the log row lands even when the runner throws (after-on-fail + error in details), so downstream consumers see a "ran but impact unknown" entry instead of silent loss. Designed to be picked up by the 4 new Minion handlers (embed-catch-up, extract-ner, extract-timeline-from-meetings, extract-takes-from-pages) when they wrap their main runner. Handlers stay decoupled from the log-write path — they just call withImpactCapture with the metric they move. Per-handler integration follows in T12/T13/T15 as those wrappers land. Typecheck clean. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * feat(onboard): types + render layer (A8, T12) NEW src/core/onboard/types.ts: OnboardRecommendation (extends RemediationStep with apply_policy + prompt_text + migration_id), OnboardReport (stable JSON envelope), OnboardOpts. NEW src/core/onboard/render.ts: toOnboardRecommendation(step): RemediationStep → OnboardRecommendation Sets apply_policy per A8 tiered rules: - protected + job === extract-takes-from-pages → 'manual_only' (A12/A24) - protected + other → 'prompt_required' - non-protected → 'auto_apply' buildOnboardReport(plan, opts?): assembles the stable JSON envelope. renderHuman(report): string. Echoes the "Recommendation + WHY" framing the CEO + Eng + Codex reviews settled on; CLI shell prints to stdout. Stable JSON envelope shape: schema_version: 1 brain_id?: string recommendations: OnboardRecommendation[] summary: { total, auto_eligible, prompt_required, manual_only, est_total_usd } history?: Array<{ remediation_id, metric_name, metric_before, metric_after, delta, applied_at }> Library-shaped — no console.* / process.exit. T13 (onboard CLI shell) calls these from the wrapping CLI. MCP run_onboard (T16) returns the JSON envelope unmodified. Typecheck clean. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * feat(onboard): gbrain onboard CLI shell (A1, T13) NEW src/commands/onboard.ts (~180 LOC). Thin wrapper that composes: - T2 library (computeRemediationPlan + runRemediation) - T4 onboard checks (runAllOnboardChecks → extraRemediations) - T12 render layer (buildOnboardReport + renderHuman) Three modes: --check (default): print plan, no submission. Computes plan via T2 library with T4 check-derived extraRemediations. Renders human (default) or JSON envelope (--json). --auto: submit auto_apply tier. Requires --max-usd N (cron-safety per A12 + A20 — refuses without explicit cap to avoid surprise spend). --auto --yes: also submit prompt_required tier. --history: dump last 50 migration_impact_log entries. Library hooks wired into stderr (per CLI/library separation): onStepStart, onStepEnd, onBudgetRefused, onBudgetExhausted, onNothingToDo, onTargetUnreachable. Final JSON envelope (--json) or human summary lands on stdout. CLI dispatch: registered in src/cli.ts CLI_ONLY set + case dispatch between 'takes' and 'founder'. Typecheck clean. Manual smoke-test pending T20 E2E (DATABASE_URL gated). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * feat(onboard): init nudge + upgrade banner (A4, A18, A20, T14) NEW src/core/onboard/init-nudge.ts exports two fail-open hooks: runInitNudge(engine): Post-initSchema 5-query AbortSignal-bound parallel check against a 3-second wallclock budget. Per A20: uses REAL cancellation via the T5 executeRaw signal extension — Promise.race against a timer was codex's #7 wrong shape. Postgres queries actually .cancel(); PGLite documented gap. Partial-results path: if some checks complete and the budget fires on others, prints what landed + a fallthrough hint pointing at `gbrain onboard --check` for the full picture. Per A18: fail-open — ANY throw is caught, logged to stderr, and suppressed so init returns successfully. Bypass: GBRAIN_NO_ONBOARD_NUDGE=1 short-circuits. Non-TTY default short-circuits too (CI/scripted callers see nothing). Nudge format: one-line summary of opportunities ("Brain has opportunities: 23000 stale chunks, link coverage 32%, 0 takes") + a 'gbrain onboard --check' nudge. runUpgradeBanner(_engine): Lighter post-upgrade banner. Doesn't engine-query — just prints a one-line nudge that upgrades may surface new opportunities. Same fail-open posture. Wired into: src/commands/init.ts:initPGLite (end-of-function, after reportModStatus) src/commands/init.ts:initPostgres (same) src/commands/upgrade.ts:runPostUpgrade (end-of-function, after postUpgradeReferenceSweep) Each wire site uses dynamic import + try/catch so even an import failure can't crash init/upgrade. Typecheck clean. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * feat(autopilot): tick consults onboard recommendations (A5, A19, A22, T15) Pre-fix: autopilot tick's per-source recommendation walk called computeRecommendations(health, ctx) — doctor's hardcoded 5-category planner. The 4 new onboard checks (embed_staleness, entity_link_coverage, timeline_coverage, takes_count) had nowhere to hook in, so even with takes.bootstrap_enabled flipped on, autopilot never noticed 0 takes and never proposed bootstrap. Post-fix: tick body now ALSO calls runAllOnboardChecks(engine) and threads the result's RemediationStep[] into the T3-generalized third arg of computeRecommendations. The planner merges onboard's extras with the legacy hardcoded entries (hardcoded wins on id collision). Per A19 fail-open: any throw in the onboard-checks path is caught, logged to stderr, and suppressed. The legacy plan (without extras) runs as before — autopilot can't crash from an onboard-check failure. A22 (idempotency-key dedupe across concurrent manual + autopilot runs): inherits from the existing computeRecommendations → remediation.idempotency_key chain. T7-T9 handlers each get their content-hash key from the makeRemediationStep factory; an autopilot tick + a manual `gbrain onboard --auto` submitting the same step in the same brain produce the SAME key, so queue.add(...) dedupes. No behavior change for brains where all 4 onboard metrics already look healthy (extras=[]; legacy plan unchanged). Typecheck clean. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * feat(mcp): run_onboard op with run_protected_onboard scope binding (A7, T16, codex finding #5) NEW MCP op `run_onboard`. Admin scope (NOT localOnly) so federated / thin-client brain installs can probe brain health + submit auto-eligible remediation handlers over OAuth-authenticated MCP. Two-tier authorization per A7 + codex #5: - Admin scope: sufficient for mode='check' (read-only OnboardReport JSON) AND for submitting non-protected handlers in mode='auto'/'auto-with-prompt'. - run_protected_onboard scope (NEW, additive): MUST be granted in addition to admin for any PROTECTED_JOB_NAMES handler to fire (synthesize, patterns, consolidate, extract-takes-from-pages, contextual_reindex_per_chunk). Without the new scope tier, an admin-scoped OAuth token would silently bypass the same protected-name gate `submit_job` enforces at operations.ts:2288. The codex finding #5 caught this: admin scope alone was insufficient guard. Now the run_onboard op explicitly FILTERS protected extras from the recommendation plan when the caller lacks run_protected_onboard; filtered items appear in the response as skipped_missing_scope[] so the caller knows what would have been available with the right grants. Modes: check — read-only OnboardReport JSON envelope. auto — submits auto_apply tier (plus prompt_required when --yes/auto-with-prompt). auto-with-prompt — adds prompt_required tier. Both auto modes REQUIRE max_usd per A12 + A20 cron-safety (rejects with invalid_params if missing). Per A26 source-scope: future extension will scope plans by ctx.sourceId / ctx.auth.allowedSources. Today the recommendation planner is brain-wide; the source-scope thread doesn't change correctness, just optimization. Per A19 fail-open: any error in runAllOnboardChecks during plan-build caught + suppressed; the plan still returns with extras=[] rather than crashing the op. Typecheck clean. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * chore(verify): add check-source-scope-onboard lint (A26, T17) NEW scripts/check-source-scope-onboard.sh. Grep guard for SQL sites in onboard surfaces (src/core/onboard/, src/commands/onboard.ts) that touch source_id-bearing tables (pages, content_chunks, takes, links, timeline_entries) WITHOUT either: (a) source_id / sourceIds in the WHERE clause, OR (b) the opt-out marker `sourcescope:brain-wide` within 4 lines above the SQL. File-level opt-out: `sourcescope:file-brain-wide` in the file header (first 30 lines) treats every SQL site in that file as intentionally brain-wide. Used by onboard/checks.ts, onboard/impact-capture.ts, and commands/onboard.ts because the onboard CHECKS are explicitly brain-wide aggregates (orphan_count, stale_count, link_coverage are reported across all sources by design). Wired into bun run verify (23 checks total now, all green). Without this gate, any future onboard SQL touching per-source data without source-scoping would silently leak rows across sources — exactly the class of bug v0.34.1's P0 seal closed at the engine layer. The lint adds an explicit forcing function for new code in the onboard surface. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * docs(install): onboard surface agent prescription (D13, T18) Adds a v0.42.0+ section to INSTALL_FOR_AGENTS.md describing: - First-connect probe: gbrain onboard --check --json - Post-upgrade re-probe (after gbrain upgrade) - Unattended remediation: gbrain onboard --auto --max-usd 5 - MCP run_onboard op for federated/thin-client installs - run_protected_onboard scope requirement for LLM-bearing handlers - Two-gate consent for takes-bootstrap (takes.bootstrap_enabled + --yes) - GBRAIN_NO_ONBOARD_NUDGE=1 bypass for CI Per D13: agents should run --check on first connect AND after every upgrade as a hygiene step. The autopilot path makes this auto-improve on a 24h cycle; the explicit agent probe surfaces opportunities immediately on connect rather than waiting for the next autopilot tick. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * test(e2e): hermetic onboard surface contracts (T20) NEW test/e2e/onboard-full-flow.test.ts. 13 hermetic PGLite cases (no DATABASE_URL needed) covering the key onboard contracts: captureMetric — all 5 metrics return expected values on empty brain (0 for counts; 1 for coverage = vacuous truth). runAllOnboardChecks — returns exactly 4 results with correct names; empty brain shows stale/link/timeline ok BUT takes_count warns (0 takes); 0 remediations emitted because takes.bootstrap_enabled defaults to false per A12 two-gate consent. computeRemediationPlan — extras (T3 generalization) thread through to plan.plan output; stable schema_version: 2 envelope. buildOnboardReport — stable schema_version: 1 envelope with the right summary fields populated. toOnboardRecommendation tier policy (A8): - non-protected job → auto_apply - extract-takes-from-pages → manual_only (A12 + A24) - other protected jobs (synthesize, patterns, ...) → prompt_required Full DATABASE_URL-gated end-to-end (real Postgres, actual extractions through Minion handlers) deferred to v0.42.1 once the per-handler test seam lands; the hermetic suite covers the data-shape contracts that matter for downstream consumers binding to the JSON envelopes. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * v0.42.0.0 gbrain onboard mega PR — activation surface (closes #1383, completes #1409) VERSION + package.json bumped to 0.42.0.0. CHANGELOG with full ELI10 lead + "What you can do that you couldn't before" itemized list + "To take advantage of v0.42.0.0" upgrade steps per CLAUDE.md voice rules. TODOS.md: 9 follow-up items filed (TODO-A through TODO-I) for the v0.42.1+ wave: pack-aware linkable types, LLM-disambiguation NER, onboard --explain, live-brain impact measurement, 100+-case takes classifier eval, admin SPA UI, full DATABASE_URL E2E, minion_jobs client_id schema column, thin-client doctor-remote parity. llms-full.txt regenerated per CLAUDE.md rule (every CHANGELOG edit followed by bun run build:llms in the same commit). 23/23 verify checks pass. Full implementation across 21 commits on this branch (T0-T21): T0 merge master T1 schema migrations v98/v99/v100 T2 extract doctor remediation library T3 generalize computeRecommendations T4 4 new doctor checks T5 engine API: listStaleChunks orderBy + executeRaw AbortSignal T6 embed --batch-size / --priority recent / --catch-up T7 NER extraction + extract-ner handler T8 timeline-from-meetings + extract-timeline-from-meetings handler T9 takes-bootstrap + extract-takes-from-pages handler T10 recordMinionJobSpend primitive T11 impact capture module + writeImpactLogRow T12 onboard render layer (types + render) T13 gbrain onboard CLI shell T14 init nudge + upgrade banner T15 autopilot tick consults onboard T16 MCP run_onboard + run_protected_onboard scope T17 check-source-scope-onboard lint T18 INSTALL_FOR_AGENTS.md agent prescription T20 hermetic PGLite E2E (13 cases) T21 ship (this commit) Reviews: CEO + Eng + Codex on plan ~/.claude/plans/system-instruction-you-are-working-lively-hollerith.md. 27 A-decisions locked; 18 codex findings absorbed. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * fix(ci): connection-resilience regex + doctor warn-not-fail + v0.41.18.0 Two CI fixes from PR #1521 + version renumber per user request. Why fix #1 (connection-resilience.test.ts): T5/A20 extended PostgresEngine.executeRaw signature to accept an optional `opts?: { signal?: AbortSignal }` 3rd arg and rewrote the body as multi-line. The regression test's regex was anchored to the legacy single-line `(sql: string, params?: unknown[])` shape and the assertions banned `try {` / `catch` (which T5 legitimately added for AbortSignal cancellation swallow, NOT for retry). Updated regex to tolerate both shapes; replaced the wrong `not.toContain('conn.unsafe( sql, params')` assertion (which incorrectly flagged the legitimate single call) with a count assertion: `conn.unsafe(` must appear exactly ONCE in the body. Preserves the original D3 intent (no per-call retry — recovery is supervisor-driven via reconnect()) while accepting the new try/catch shape that swallows AbortSignal aborts. Why fix #2 (src/core/onboard/checks.ts): Three of the four new onboard doctor checks (entity_link_coverage, timeline_coverage, embed_staleness) emitted `status = 'fail'` on healthy DBs that simply hadn't run extractions yet. This flipped `gbrain doctor`'s exit code to non-zero on freshly initialized brains, breaking test/e2e/mechanical.test.ts:1280 ("gbrain doctor exits 0 on healthy DB"). Downgraded all three to `status = 'warn'` — these are remediation opportunities, not assertion failures. Doctor exit codes are reserved for actual failures; remediation surfaces use warn-level signaling so they can be picked up by `--remediate` without polluting the exit code. Why fix #3 (version renumber 0.42.0.0 → 0.41.18.0): Per user directive, this wave ships as v0.41.18.0 rather than v0.42.0.0. Master is at 0.41.16.0; 0.41.17.0 is reserved for an in-flight wave. Renamed every reference my branch added (54 files touched): VERSION, package.json, CHANGELOG.md header, TODOS.md, plus inline version-stamp comments across src/, test/, and scripts/. Preserved 13 files with PRE-EXISTING `v0.42.0.0` references on master (from earlier waves originally planned for v0.42 that landed at v0.41.x — those stay as historical record). Verified via per-file diff against origin/master: every renamed reference is one I added in this branch. Audit trio aligned: VERSION=0.41.18.0, package.json=0.41.18.0, CHANGELOG topmost entry=[0.41.18.0]. llms-full.txt regenerated to match CLAUDE.md updates. Bisect contract: this commit fixes CI test failures from PR #1521's landing. Typecheck clean; connection-resilience suite 26/26 pass. Refs A20 (executeRaw AbortSignal), A16 (4 new onboard checks), codex #1 (master collision avoidance via renumber). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com> |
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v0.41.16.0 feat: conversation parser cathedral + progressive-batch primitive (closes #1461) (#1510)
* v0.41.15.0 feat: conversation parser cathedral + progressive-batch primitive (closes #1461) Replaces PR #1461's single-format Telegram regex with a 12-pattern built-in registry covering iMessage/Slack, Telegram (×2), Discord (×2), WhatsApp (×2 locales), Signal, Matrix/Element, IRC (×2), Teams. Each pattern is hand-vetted from public format docs (signal-cli, DiscordChatExporter, Telegram Desktop, WhatsApp export docs, Element matrix-archive, irssi/weechat defaults); module-load validation runs test_positive[] + test_negative[] for every pattern at startup so a typo makes gbrain refuse to start. PR #1461 contributor's BRACKET_TIME_RX + cleanSpeaker survive verbatim as the `telegram-bracket` built-in pattern + DEFAULT_SPEAKER_CLEAN export. All 33 of their test cases pass against the new orchestrator. Three layers per page (orchestrator chooses): 1. Built-in pattern registry (zero-cost, deterministic) 2. User-declared simple_pattern via config (deferred to v0.42+) 3. Opt-IN LLM polish + fallback (privacy-first; chat content goes to Anthropic only when user explicitly enables) D18 priority scoring picks the highest-match-rate pattern across the first 10 lines (not first-wins) so overlapping formats don't silently mis-route. D5 multi_line per-pattern + D11 quick_reject prefix screen + D19 timezone_policy per-pattern complete the registry shape. Companion: src/core/progressive-batch/ primitive (rule of three satisfied across 12+ ad-hoc cost-prompt sites). Wintermute-inspired ramp shape (trial 10 → 100 → 500 → full with verification at each stage), productionized with verifier+policy injection (callers describe HOW TO MEASURE SUCCESS, not WHEN TO WAIT FOR CTRL-C). D3 fail-closed budget gate: null tracker + null Policy.maxCostUsd → abort_cost_cap reason='no_budget_safety_net'. D20 discriminated Verifier union (output_count | idempotent_mutation | noop). extract-conversation-facts is the one proven consumer in v0.41.15.0; 9-site retrofit deferred to v0.41.16.0+ per TODOS.md. Codex outside-voice review absorbed 8 substantive findings: - Privacy posture (LLM polish/fallback flipped to opt-IN) - ReDoS theater (dropped arbitrary user regex; v0.42+ uses RE2) - LLM-inferred-regex persistence as silent-corruption machine - Pattern priority scoring across first 10 lines - Timezone policy on every PatternEntry - Verifier shape discriminated union - Behavior parity for sites that "jumped straight to full" - Real-corpus-redacted fixture gap (v0.42+ TODO) CI gates: - bun run check:conversation-parser (13 fixtures, --no-llm, deterministic) - bun run check:fixture-privacy (banned-token grep) Doctor surfaces 3 new checks: conversation_format_coverage, progressive_batch_audit_health, conversation_parser_probe_health. Tests: 198/198 across primitive + parser + LLM + nightly probe + eval CLI + debug CLI + doctor checks + migration v97 round-trip + E2E parser ↔ engine integration. Real bug caught + fixed during gap audit: IdempotentMutationVerifier was comparing absolute mutated-count vs per-stage expected (failed silently on stage 2+); now uses per-stage delta semantics matching OutputCountVerifier. Schema migration v97: conversation_parser_llm_cache table with (content_sha256, model_id, call_shape) composite key. NO inferred_patterns table (D17: silent-corruption machine). Plan + 23 decisions + codex outside-voice absorption at ~/.claude/plans/system-instruction-you-are-working-cuddly-hollerith.md. Co-Authored-By: garrytan-agents (PR #1461) <noreply@github.com> Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * fix(check-privacy): allowlist scripts/check-fixture-privacy.sh The new sibling privacy guard literally names the banned tokens in its BANNED_TOKENS array — same meta-exception that check-privacy.sh itself gets. Without this allowlist entry, bun run verify rejects the file post-merge because the banned name appears in the rule-definition script. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * chore: renumber v0.41.15.0 → v0.41.16.0 (queue drift) Mechanical rename across all surfaces: VERSION, package.json, CHANGELOG (header + body refs), CLAUDE.md, TODOS.md, src/core/ migrate.ts (migration v98 comment), all src/core/conversation-parser/* and src/core/progressive-batch/* file headers, all test/ headers, scripts/check-privacy.sh allowlist comment, llms-full.txt regenerated. Audit clean: VERSION + package.json + CHANGELOG header all show 0.41.16.0. verify 24/24, touched tests 179/179. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> --------- Co-authored-by: garrytan-agents (PR #1461) <noreply@github.com> Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com> |