…ring

Issue 3 + Issue 2 of the v0.41.20.0 ops-fix-wave.

Codex caught during plan review that yieldBetweenPhases (the existing
external hook) does NOT refresh the cycle DB lock — it's just a
setImmediate() from jobs.ts:1405 / autopilot.ts:632, and lock.refresh()
was never called from inside runCycle. Combined with the 30min TTL,
crashed cycles wedged the lock for the full window before another
worker could take over.

Three coordinated changes:

1. LOCK_TTL_MINUTES 30 → 5 (src/core/cycle.ts). Crash recovers in
   ≤5 min instead of ≤30 min.

2. buildYieldDuringPhase(lock, outer) — exported closure that calls
   lock.refresh() AND the existing yieldBetweenPhases hook on every
   fire. Passed to both long phases (extract_atoms,
   synthesize_concepts) as their yieldDuringPhase opt.

3. maybeYield helper inside both phases — 30s throttle, fires inside
   the main work loop AND immediately after every `await chat()` LLM
   call (codex hardening: a single long LLM await could otherwise sit
   past TTL).

Progress reporter wired through to both phases too (Issue 2):
extract_atoms emits `[cycle.extract_atoms] N atoms / M skipped` ticks
every ~1s; synthesize_concepts ticks per concept group. Cycle.ts owns
start()/finish(); phases only call tick() and heartbeat() on the same
reporter (NOT a child — that would produce path collision
`cycle.extract_atoms.extract_atoms.work`).

LockHandle interface exported for tests.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Issue 4 of the v0.41.20.0 ops-fix-wave. On a 322K-page brain the sweep
takes 10+ hours; if it died at 87% the user redid 87% on restart.

Wires the existing `op_checkpoints` framework into extractMentionsFromDb
with a flushAndCheckpoint ordering that closes the four codex-flagged
correctness bugs at once:

  1. Lost-links-on-crash — flush batch links to DB FIRST, commit page
     keys to checkpoint SECOND, persist THIRD. A crash between
     batch.push() and flushBatch() leaves the page un-checkpointed so
     resume re-scans it (no silently lost mention links).
  2. Dry-run resume contradiction — dry-run does NOT load or persist
     the checkpoint. Verification path uses non-dry-run kill-and-resume.
  3. Gazetteer hash in fingerprint — entity pages added mid-pause shift
     the gazetteer hash → new fingerprint → fresh scan against the new
     gazetteer. Without this, resumed runs would silently skip pages
     against a new entity set.
  4. Filtered pages get checkpointed too — pages skipped by `--type` /
     `--since` / empty body / no-mentions all get marked completed so
     resume doesn't re-fetch them.

Persist cadence: every 1000 items OR every 30s, whichever first
(~322 persists / ~24s total overhead on the 322K-page brain). Crash
window capped at 1000 pages (<0.3% loss).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Issue 5 of the v0.41.20.0 ops-fix-wave. Multi-source brains see a
paste-ready `gbrain sync --all --parallel 4 --workers 4 --skip-failed`
in `gbrain doctor` output instead of maintaining two staggered
per-source cron entries with manual deconfliction.

New checkSyncConsolidation surfaces the recommendation when 2+ active
sources exist; "not applicable" for single-source brains. Own
try/catch returns warn on SQL failure — outer doctor catch wasn't a
safe assumption.

`skills/cron-scheduler/SKILL.md` gains a "Multi-source brains"
recipe block documenting the pattern + connection-budget math
(parallel × workers × 2 ≈ 32 connections at default 4/4).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Two pre-existing tests assumed a clean ~/.gbrain/config.json and a free
~/.gbrain/cycle.lock — both shared across all gbrain processes on the
machine. Sibling Conductor worktrees running their own gbrain tests
poisoned the shared state, causing flakes:

  - test/cycle-last-full-cycle-at.test.ts test 5 timed out at 5s
    because runCycle returned 'skipped' (file lock held by a parallel
    test process), and last_full_cycle_at exit hook silently no-oped.
    Fix: each test wraps its body in `withEnv({GBRAIN_HOME: tmpdir})`
    so the file lock path becomes per-test.

  - test/schema-cli.test.ts `schema active reports default resolution`
    failed exit 1 because another worktree had set
    `schema_pack: gbrain-base-v2` in the shared config (a pack that
    doesn't exist in the bundle). Fix: gbrain() helper defaults
    GBRAIN_HOME to a per-file tempdir (beforeAll-owned), so subprocess
    invocations get an isolated config dir unless tests explicitly
    override.

Both fixes confirmed via deliberate pollution + retest: 12/12
schema-cli tests pass under simulated `schema_pack: gbrain-base-v2`
contamination; cycle-LFCA test 5 completes <2s with isolated home.

Discovered during v0.41.20.0 ship while investigating parallel-worktree
flake. Not caused by the ops-fix-wave but found via it.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Five daily-driver ops pains fixed in one wave:
  1. extract_atoms 7K-roundtrip overhead → 1 batch query + index
  2. silent long-running phases → progress ticks every ~1s
  3. 30-min crashed-cycle lock TTL → 5 min + active in-phase refresh
  4. by-mention restarts from page 0 → resumes via op_checkpoints
  5. multi-source cron → doctor surfaces `sync --all --parallel` nudge

Two follow-up TODOs filed under v0.41.19.0 ops-fix-wave block (will
be renamed at follow-up time):
  - `gbrain sync print-cron` subcommand (P2 ergonomics)
  - Lock-loss detection in DbLockHandle.refresh() (P2 contract change)

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Folds the v0.41.20.0 wave annotations into the cycle/extract/op-checkpoint
key-files block: batch idempotency via atomsExistingForHashes, shorter
cycle lock TTL with buildYieldDuringPhase active refresh, progress wiring
through extract_atoms + synthesize_concepts, by-mention resume via
mentionsFingerprint with flushAndCheckpoint ordering, sync_consolidation
doctor check, and the 44-case test suite pinning every contract.

Regenerated llms-full.txt to match (CLAUDE.md edit invariant).

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

# Conflicts:
#	CHANGELOG.md
#	TODOS.md

Two CI-only failures caught on PR #1545 (v0.41.21.0 ops-fix-wave):

1. doctor-categories drift guard — new `sync_consolidation` check from
   T6 wasn't categorized in src/core/doctor-categories.ts. Added under
   OPS_CHECK_NAMES (it surfaces an operator-cron recommendation, not a
   brain-data quality signal).

2. facts-engine `embedding cosine ordering when both sides have
   embeddings` — passed locally, failed under CI's parallel shard.
   Bun's truncated assertion output didn't surface which expect()
   fired; hardened the test against unknown leak vectors by:
     - per-run unique entity_slug (`embed-test-<random8>`) instead of
       the static `embed-test`, so any future cross-test pollution is
       structurally impossible
     - `findIndex` + `aIdx < bIdx` assertion that pins the cosine
       RELATIONSHIP (A closer than B because cos(A,Q)=1.0 vs cos(B,Q)=0.0)
       instead of the brittle `result[0].fact === 'A'` position check.
   The new shape matches the test name's contract verbatim ("ordering
   when both sides have embeddings"), so any unrelated row in the
   result set can no longer flip the test.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>