fix(remediation): pass LINK_EXTRACTOR_VERSION_TS to the extraction-lag gate

countExtractionLag omitted versionTs, so its predicate diverged from the
counter it claims to share with doctor's links_extraction_lag check and
the extract --stale walk: pages stamped before an extractor version bump
(links_extracted_at < LINK_EXTRACTOR_VERSION_TS) lagged for doctor and
extract but never tripped the sync.repo/extract.all gate. Pass the stamp;
pin the version-bump arm with a backdated-page test (fails without it).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

src/commands/autopilot.ts

@@ -686,6 +686,7 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
       try {
         const { MinionQueue } = await import('../core/minions/queue.ts');
         const { computeRecommendations, embeddingProviderConfigured, HOSTED_EMBED_KEY_CONFIG } = await import('../core/brain-score-recommendations.ts');
+        const { countExtractionLag } = await import('../core/remediation/context.ts');
         const queue = new MinionQueue(engine);
         const slotMs = Math.floor(Date.now() / (baseInterval * 1000)) * baseInterval * 1000;
         const slot = new Date(slotMs).toISOString();
@@ -877,6 +878,9 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
             return !!(process.env[envVar] || (cfgField ? embedKeyCfg[cfgField] : undefined));
           }),
           hasChatApiKey: !!(process.env.ANTHROPIC_API_KEY || await engine.getConfig('anthropic_api_key')),
+          // Real extraction-lag gate for sync.repo/extract.all — same counter
+          // loadRecommendationContext uses (replaces the health.stale_pages proxy).
+          extractionLagPages: await countExtractionLag(engine),
         };
         // v0.41.18.0 (A5 + A19 + A22, T15): consult onboard recommendations
         // ALONGSIDE doctor's brain-score recommendations. Onboard's 4 new

src/commands/jobs.ts

@@ -2059,8 +2059,6 @@ export async function registerBuiltinHandlers(
         sourceId,
         windowSeconds,
         brainDir: repoPath,
-        // #2750: worker cancel/timeout/lock-loss propagates into the drain.
-        abortSignal: job.signal,
       });
     } catch (e) {
       if (e instanceof LockUnavailableError) {

src/core/brain-score-recommendations.ts

@@ -146,6 +146,16 @@ export interface RecommendationContext {
   chatModel?: string;
   /** Whether the chat provider has a usable API key. */
   hasChatApiKey?: boolean;
+  /**
+   * Count of pages needing link/timeline extraction — the SAME staleness the
+   * `gbrain extract --stale` walk and doctor's `links_extraction_lag` check use
+   * (`engine.countStalePagesForExtraction`). Gates the sync→extract pipeline
+   * (sync.repo / extract.all). Replaces the old `health.stale_pages` gate, which
+   * counted "pages whose updated_at predates their newest timeline entry" — a
+   * proxy that broke when the updated_at-on-timeline-insert trigger was dropped
+   * (migration v10) and never reflected real extraction work.
+   */
+  extractionLagPages?: number;
 }
 
 /** Triage result for one check. */
@@ -192,20 +202,28 @@ export function computeRecommendations(
   const source = ctx.sourceId ?? 'default';
 
   // ---------------------------------------------------------------------
-  // sync.repo — fires when sync hasn't run recently OR pages are stale
+  // sync.repo + extract.all — the materialization pipeline, gated on the REAL
+  // extraction lag (pages whose link/timeline edges are stale), NOT on the
+  // legacy `health.stale_pages` proxy. `extractionLagPages` comes from the same
+  // counter the `extract --stale` walk + doctor's `links_extraction_lag` use, so
+  // the recommendation can only fire when running extract will actually reduce
+  // it (and clear the rec). See RecommendationContext.extractionLagPages.
+  // sync.repo is the prerequisite: re-sync so pages are current before extract
+  // materializes their edges.
   // ---------------------------------------------------------------------
-  if (ctx.repoPath && health.stale_pages > 0) {
+  const extractionLag = ctx.extractionLagPages ?? 0;
+  if (ctx.repoPath && extractionLag > 0) {
     const params = { repoPath: ctx.repoPath, sourceId: ctx.sourceId, noEmbed: true };
     out.push({
       id: 'sync.repo',
       job: 'sync',
       params,
       idempotency_key: idemKey(source, 'sync', params),
-      severity: health.stale_pages > 50 ? 'high' : 'medium',
-      est_seconds: Math.min(600, 30 + health.stale_pages * 0.5),
+      severity: extractionLag > 50 ? 'high' : 'medium',
+      est_seconds: Math.min(600, 30 + extractionLag * 0.5),
       est_usd_cost: 0,  // sync is fs+DB only
       depends_on: [],
-      rationale: `${health.stale_pages} stale page${health.stale_pages === 1 ? '' : 's'} on disk`,
+      rationale: `Sync before extracting ${extractionLag} page${extractionLag === 1 ? '' : 's'} with stale link/timeline edges`,
       status: 'remediable',
     });
   }
@@ -237,7 +255,7 @@ export function computeRecommendations(
       est_seconds: Math.min(3600, 5 + health.missing_embeddings * 0.05),
       est_usd_cost,
       // sync should run first so embed sees fresh pages.
-      depends_on: ctx.repoPath && health.stale_pages > 0 ? ['sync.repo'] : [],
+      depends_on: ctx.repoPath && extractionLag > 0 ? ['sync.repo'] : [],
       rationale: `${health.missing_embeddings} chunk${health.missing_embeddings === 1 ? '' : 's'} invisible to vector search`,
       status: 'remediable',
     });
@@ -267,7 +285,7 @@ export function computeRecommendations(
   // Triggered when sync.repo fires (because sync was set to noEmbed:true,
   // and noExtract:true after T5 lands → extract job is the materializer).
   // ---------------------------------------------------------------------
-  if (ctx.repoPath && health.stale_pages > 0) {
+  if (ctx.repoPath && extractionLag > 0) {
     const params = { mode: 'all', dir: ctx.repoPath };
     out.push({
       id: 'extract.all',
@@ -278,7 +296,7 @@ export function computeRecommendations(
       est_seconds: Math.min(600, 30 + health.page_count * 0.01),
       est_usd_cost: 0,
       depends_on: ['sync.repo'],
-      rationale: 'Materialize link + timeline edges from fresh pages',
+      rationale: `Materialize link + timeline edges for ${extractionLag} page${extractionLag === 1 ? '' : 's'} with stale extraction`,
       status: 'remediable',
     });
   }

src/core/cycle/extract-atoms-drain.ts

@@ -23,10 +23,6 @@
  */
 
 import type { BrainEngine } from '../engine.ts';
-import { anySignal } from '../abort-check.ts';
-
-/** Fresh cleanup budget for the lock release after the window signal fires. */
-const LOCK_RELEASE_GRACE_MS = 5_000;
 
 export interface ExtractAtomsDrainDeps {
   /**
@@ -34,13 +30,13 @@ export interface ExtractAtomsDrainDeps {
    * via `withRefreshingLock`. MUST throw when the lock is held by another
    * process (e.g. `LockUnavailableError`) — the drain lets that propagate so
    * the caller can report `cycle_already_running` and exit, matching the
-   * routine cycle's skip contract. The signal bounds lock acquisition too.
+   * routine cycle's skip contract.
    */
-  withLock: <T>(work: () => Promise<T>, signal: AbortSignal) => Promise<T>;
-  /** Process one batch. The signal fires at the drain wallclock deadline. */
-  runBatch: (signal: AbortSignal) => Promise<{ extracted: number; skipped: number }>;
+  withLock: <T>(work: () => Promise<T>) => Promise<T>;
+  /** Process one bounded batch (rediscovers eligibility). Returns counts. */
+  runBatch: () => Promise<{ extracted: number; skipped: number }>;
   /** Count remaining eligible-but-unextracted pages, or null on query error. */
-  countRemaining: (signal: AbortSignal) => Promise<number | null>;
+  countRemaining: () => Promise<number | null>;
   /** Injectable clock. Production: Date.now. */
   now: () => number;
   /** Optional progress sink (one line per batch). */
@@ -52,8 +48,6 @@ export interface ExtractAtomsDrainOpts {
   windowMs: number;
   /** Hard cap on batches (belt-and-suspenders against a 0-progress loop). Default 1000. */
   maxBatches?: number;
-  /** External caller cancellation (worker timeout / shutdown). */
-  abortSignal?: AbortSignal;
 }
 
 export interface ExtractAtomsDrainResult {
@@ -74,79 +68,35 @@ export async function runExtractAtomsDrain(
   opts: ExtractAtomsDrainOpts,
 ): Promise<ExtractAtomsDrainResult> {
   const maxBatches = opts.maxBatches ?? 1000;
-  const deadline = deps.now() + opts.windowMs;
-  // #2750: the window used to be checked only BETWEEN batches, so one slow
-  // batch (sequential LLM calls) or a hung lock/count/write overran it without
-  // bound (observed window=120s → 282.5s). A real-time deadline signal now
-  // cancels (Postgres) or abandons (PGLite, cooperative) whatever is in
-  // flight; the injected clock still drives loop-boundary checks so the pure
-  // loop stays unit-testable.
-  const signal = anySignal(
-    AbortSignal.timeout(Math.max(1, opts.windowMs)),
-    opts.abortSignal,
-  );
-  const result: ExtractAtomsDrainResult = await deps.withLock(async () => {
+  return deps.withLock(async () => {
+    const deadline = deps.now() + opts.windowMs;
     let extracted = 0;
     let skipped = 0;
     let batches = 0;
     let stopped: ExtractAtomsDrainResult['stopped'] = 'window';
 
-    while (deps.now() < deadline && !signal.aborted) {
+    while (deps.now() < deadline) {
       if (batches >= maxBatches) { stopped = 'max_batches'; break; }
 
-      let before: number | null;
-      try {
-        before = await deps.countRemaining(signal);
-      } catch (err) {
-        if (signal.aborted) break;
-        throw err;
-      }
+      const before = await deps.countRemaining();
       if (before === 0) { stopped = 'drained'; break; }
 
-      // The backlog count consumed the same wallclock budget — re-check so a
-      // slow count can't hand the batch a window that already expired.
-      if (deps.now() >= deadline || signal.aborted) break;
-
-      let r: { extracted: number; skipped: number };
-      try {
-        r = await deps.runBatch(signal);
-      } catch (err) {
-        if (signal.aborted) break;
-        throw err;
-      }
+      const r = await deps.runBatch();
       extracted += r.extracted;
       skipped += r.skipped;
       batches++;
       deps.onBatch?.({ batch: batches, extracted: r.extracted, remaining: before });
 
-      // A deadline abort inside the batch can surface as zero progress;
-      // window exhaustion wins over the generic no_progress label.
-      if (deps.now() >= deadline || signal.aborted) break;
-
       // Stop if a batch made zero forward progress — extraction is failing or
       // everything left is ineligible (e.g. all skipped). Prevents a hot loop
       // that spends budget without draining.
       if (r.extracted === 0 && r.skipped === 0) { stopped = 'no_progress'; break; }
     }
 
-    // After the window elapsed, don't spend more unbounded time on a final
-    // count — report remaining as unknown instead of overrunning further.
-    const windowElapsed = signal.aborted || deps.now() >= deadline;
-    let remaining: number | null = null;
-    if (!windowElapsed) {
-      try {
-        remaining = await deps.countRemaining(signal);
-      } catch (err) {
-        if (!signal.aborted) throw err;
-      }
-    }
+    const remaining = await deps.countRemaining();
     if (remaining === 0) stopped = 'drained';
     return { phase: 'extract_atoms', status: 'ok', extracted, skipped, remaining, batches, stopped };
-  }, signal);
-  // Internal window expiry is a normal partial result. An EXTERNAL abort
-  // (worker cancel/timeout/shutdown) must reject so Minion records the abort.
-  if (opts.abortSignal?.aborted) throw opts.abortSignal.reason;
-  return result;
+  });
 }
 
 // ─── Shared wiring helper (v0.42.x #1685 DECISION 5A) ──────────────────────
@@ -184,8 +134,6 @@ export interface DrainForSourceOpts {
   maxBatches?: number;
   /** Optional per-batch progress sink (stderr line in dream; job progress in the handler). */
   onBatch?: ExtractAtomsDrainDeps['onBatch'];
-  /** Worker cancellation / shutdown signal (Minion `job.signal`). */
-  abortSignal?: AbortSignal;
 }
 
 export async function runExtractAtomsDrainForSource(
@@ -201,17 +149,12 @@ export async function runExtractAtomsDrainForSource(
 
   return runExtractAtomsDrain(
     {
-      withLock: (work, signal) => withRefreshingLock(engine, lockId, work, {
-        ttlMinutes: 5,
-        signal,
-        releaseTimeoutMs: LOCK_RELEASE_GRACE_MS,
-      }),
-      runBatch: async (signal) => {
+      withLock: (work) => withRefreshingLock(engine, lockId, work, { ttlMinutes: 5 }),
+      runBatch: async () => {
         const r = await runPhaseExtractAtoms(engine, {
           sourceId: extractionSourceId,
           dryRun: false,
           brainDir: opts.brainDir,
-          abortSignal: signal,
         });
         const d = (r.details ?? {}) as Record<string, unknown>;
         return {
@@ -219,14 +162,10 @@ export async function runExtractAtomsDrainForSource(
           skipped: Number(d.duplicates_skipped ?? 0),
         };
       },
-      countRemaining: (signal) => countExtractAtomsBacklog(engine, extractionSourceId, signal),
+      countRemaining: () => countExtractAtomsBacklog(engine, extractionSourceId),
       now: Date.now,
       onBatch: opts.onBatch,
     },
-    {
-      windowMs: opts.windowSeconds * 1000,
-      maxBatches: opts.maxBatches,
-      abortSignal: opts.abortSignal,
-    },
+    { windowMs: opts.windowSeconds * 1000, maxBatches: opts.maxBatches },
   );
 }

src/core/cycle/extract-atoms.ts

@@ -58,10 +58,6 @@ import { createHash } from 'crypto';
 import { slugifySegment } from '../sync.ts';
 
 const DEFAULT_BUDGET_USD = 0.3;
-// #2750: fresh wallclock budget for the receipt/rollup bookkeeping writes when
-// the caller's deadline already fired — committed atoms must not lose their
-// cost/receipt trail, but the writes can't be unbounded either.
-const BOOKKEEPING_GRACE_MS = 5_000;
 
 // v0.42+ TODO: read atom_type enum from active pack manifest at runtime.
 const ATOM_TYPES = [
@@ -159,13 +155,6 @@ export interface ExtractAtomsOpts {
    * `heartbeat()` on the passed reporter.
    */
   progress?: ProgressReporter;
-  /**
-   * #2750: caller deadline/cancellation. Forwarded to every gateway call and
-   * DB query/write so the drain window bounds real lifetime, plus a
-   * cooperative between-item check (the PGLite path, where query abort only
-   * abandons the waiter).
-   */
-  abortSignal?: AbortSignal;
 }
 
 interface ExtractedAtom {
@@ -223,7 +212,6 @@ export async function discoverExtractablePages(
   engine: BrainEngine,
   sourceId: string,
   affectedSlugs?: string[],
-  abortSignal?: AbortSignal,
 ): Promise<DiscoveredPage[]> {
   const hasFilter = Array.isArray(affectedSlugs) && affectedSlugs.length > 0;
   const sql = `
@@ -263,16 +251,13 @@ export async function discoverExtractablePages(
       slug: string;
       compiled_truth: string;
       content_hash: string;
-    }>(sql, params, { signal: abortSignal });
+    }>(sql, params);
     return rows.map((r) => ({
       slug: r.slug,
       content: r.compiled_truth,
       contentHash: r.content_hash,
     }));
   } catch (err) {
-    // A deadline abort is not a fail-soft condition — propagate so the
-    // caller stops instead of proceeding with an empty page list.
-    if (abortSignal?.aborted) throw err;
     const msg = err instanceof Error ? err.message : String(err);
     console.error(`[extract_atoms] page-discovery query failed: ${msg}`);
     return []; // fail-soft: transcript path still proceeds
@@ -297,7 +282,6 @@ export async function discoverExtractablePages(
 export async function countExtractAtomsBacklog(
   engine: BrainEngine,
   sourceId?: string,
-  abortSignal?: AbortSignal,
 ): Promise<number | null> {
   try {
     // Two modes: scoped (the phase's per-source `remaining`) vs brain-wide
@@ -337,10 +321,9 @@ export async function countExtractAtomsBacklog(
     const params = scoped
       ? [sourceId, extractableTypes, MIN_PAGE_CHARS_FOR_EXTRACTION]
       : [extractableTypes, MIN_PAGE_CHARS_FOR_EXTRACTION];
-    const rows = await engine.executeRaw<{ cnt: string | number }>(sql, params, { signal: abortSignal });
+    const rows = await engine.executeRaw<{ cnt: string | number }>(sql, params);
     return Number(rows[0]?.cnt ?? 0);
   } catch (err) {
-    if (abortSignal?.aborted) throw err;
     const msg = err instanceof Error ? err.message : String(err);
     console.error(`[extract_atoms] backlog count failed: ${msg}`);
     return null;
@@ -367,7 +350,6 @@ export async function atomsExistingForHashes(
   engine: BrainEngine,
   sourceId: string,
   contentHash16s: string[],
-  abortSignal?: AbortSignal,
 ): Promise<Set<string>> {
   if (contentHash16s.length === 0) return new Set();
   try {
@@ -379,11 +361,9 @@ export async function atomsExistingForHashes(
           AND deleted_at IS NULL
           AND frontmatter->>'source_hash' = ANY($2::text[])`,
       [sourceId, contentHash16s],
-      { signal: abortSignal },
     );
     return new Set(rows.map(r => r.h));
   } catch (err) {
-    if (abortSignal?.aborted) throw err;
     const msg = err instanceof Error ? err.message : String(err);
     console.error(`[extract_atoms] batch idempotency check failed (assuming none extracted): ${msg}`);
     return new Set();
@@ -404,7 +384,6 @@ export async function runPhaseExtractAtoms(
 ): Promise<PhaseResult> {
   const sourceId = opts.sourceId ?? 'default';
   const chat = opts._chat ?? gatewayChat;
-  if (opts.abortSignal?.aborted) throw opts.abortSignal.reason;
 
   // 1a. Get transcripts (test seam OR production discovery).
   //     v0.41.2.1: config loader switched to loadConfigWithEngine() so the
@@ -446,7 +425,7 @@ export async function runPhaseExtractAtoms(
   if (opts._pages !== undefined) {
     pages = opts._pages;
   } else {
-    pages = await discoverExtractablePages(engine, sourceId, opts.affectedSlugs, opts.abortSignal);
+    pages = await discoverExtractablePages(engine, sourceId, opts.affectedSlugs);
   }
 
   // 2. Apply transcript-side source-hash idempotency in ONE batch query
@@ -458,7 +437,7 @@ export async function runPhaseExtractAtoms(
   // Surface a heartbeat before the batch query so even an instant
   // short-circuit shows a sign of life (closes Issue 2 silent-phase pain).
   opts.progress?.heartbeat(`checking existing atoms for ${allHashes16.length} transcripts`);
-  const existingHashes = await atomsExistingForHashes(engine, sourceId, allHashes16, opts.abortSignal);
+  const existingHashes = await atomsExistingForHashes(engine, sourceId, allHashes16);
   for (const t of transcripts) {
     if (existingHashes.has(t.contentHash.slice(0, 16))) {
       duplicatesSkipped++;
@@ -522,7 +501,6 @@ export async function runPhaseExtractAtoms(
   const failures: Array<{ source: string; error: string }> = [];
   let estimatedSpendUsd = 0;
   const budgetCap = DEFAULT_BUDGET_USD;
-  let deadlineAborted = false;
 
   // v0.41.19.0 (T3): throttled yield helper. Fires `opts.yieldDuringPhase`
   // every 30s. Cycle.ts threads `buildYieldDuringPhase(lock, outer)` so
@@ -548,12 +526,6 @@ export async function runPhaseExtractAtoms(
   }
 
   for (const item of work) {
-    // #2750: cooperative between-item abort. Works on every engine — this is
-    // the primary bound on PGLite, where query abort only abandons the waiter.
-    if (opts.abortSignal?.aborted) {
-      deadlineAborted = true;
-      break;
-    }
     await maybeYield();
     if (estimatedSpendUsd >= budgetCap) {
       if (item.kind === 'transcript') transcriptsSkipped++;
@@ -572,22 +544,16 @@ export async function runPhaseExtractAtoms(
           },
         ],
         maxTokens: 2000,
-        abortSignal: opts.abortSignal,
       });
-      // Rough cost estimate — Haiku at ~$0.80/M input + $4/M output.
-      // A completed gateway call is billable even if the deadline fires
-      // immediately afterward, so record usage BEFORE the abort check.
-      estimatedSpendUsd +=
-        (result.usage.input_tokens * 0.8 + result.usage.output_tokens * 4.0) / 1_000_000;
-      if (opts.abortSignal?.aborted) {
-        deadlineAborted = true;
-        break;
-      }
       // Post-await yield: closes the "long LLM call past TTL" hazard
       // codex flagged. The 30s throttle inside maybeYield bounds the
       // actual refresh rate so this is cheap when calls are fast.
       await maybeYield();
 
+      // Rough cost estimate — Haiku at ~$0.80/M input + $4/M output
+      estimatedSpendUsd +=
+        (result.usage.input_tokens * 0.8 + result.usage.output_tokens * 4.0) / 1_000_000;
+
       const atoms = parseAtomsResponse(result.text);
       if (atoms.length === 0) {
         if (item.kind === 'transcript') transcriptsProcessed++;
@@ -626,7 +592,7 @@ export async function runPhaseExtractAtoms(
               },
               timeline: '',
             },
-            { sourceId, signal: opts.abortSignal },
+            { sourceId },
           );
           totalAtomsExtracted++;
         }
@@ -639,11 +605,6 @@ export async function runPhaseExtractAtoms(
       // Reporter rate-limits to ~1 line/sec; safe to tick every iter.
       opts.progress?.tick(1, `${totalAtomsExtracted} atoms / ${duplicatesSkipped} skipped`);
     } catch (err) {
-      // A deadline abort is a partial result, not a per-item failure.
-      if (opts.abortSignal?.aborted) {
-        deadlineAborted = true;
-        break;
-      }
       failures.push({
         source: originLabel,
         error: err instanceof Error ? err.message : String(err),
@@ -654,12 +615,6 @@ export async function runPhaseExtractAtoms(
   // v0.42 Wave B2: write extract receipt + rollup row when the phase
   // actually extracted atoms. Both are best-effort per F-OUT-19 —
   // audit-trail / search-visibility surfaces don't block the phase result.
-  //
-  // #2750: bookkeeping runs on a FRESH short grace signal, never the caller's
-  // work deadline — the deadline may have already fired (partial run) and
-  // committed atoms must not lose their receipt/cost trail; but the writes
-  // stay bounded so the overrun is capped at the grace window.
-  const bookkeepingSignal = opts.dryRun ? undefined : AbortSignal.timeout(BOOKKEEPING_GRACE_MS);
   if (!opts.dryRun && totalAtomsExtracted > 0) {
     const runId = `atoms-${Date.now().toString(36)}-${sourceId.slice(0, 4)}`;
     try {
@@ -674,24 +629,19 @@ export async function runPhaseExtractAtoms(
         summary:
           `Extracted ${totalAtomsExtracted} atoms from ` +
           `${transcriptsProcessed} transcripts + ${pagesProcessed} pages.`,
-      }, { signal: bookkeepingSignal });
+      });
     } catch (err) {
       console.error(`[extract_atoms] receipt write failed: ${(err as Error).message}`);
     }
   }
   if (!opts.dryRun) {
-    try {
-      await upsertExtractRollup(engine, {
-        kind: 'atoms',
-        source_id: sourceId,
-        cost_delta: estimatedSpendUsd,
-        // A deadline-truncated run is not a completed round.
-        round_completed_delta: failures.length === 0 && !deadlineAborted ? 1 : 0,
-        halt_delta: failures.length > 0 ? 1 : 0,
-      }, { signal: bookkeepingSignal });
-    } catch (err) {
-      console.error(`[extract_atoms] rollup write failed: ${(err as Error).message}`);
-    }
+    await upsertExtractRollup(engine, {
+      kind: 'atoms',
+      source_id: sourceId,
+      cost_delta: estimatedSpendUsd,
+      round_completed_delta: failures.length === 0 ? 1 : 0,
+      halt_delta: failures.length > 0 ? 1 : 0,
+    });
   }
 
   return {
@@ -720,7 +670,6 @@ export async function runPhaseExtractAtoms(
       budget_usd: budgetCap,
       source_id: sourceId,
       dry_run: opts.dryRun ?? false,
-      deadline_aborted: deadlineAborted,
     },
   };
 }

src/core/db-lock.ts

@@ -26,8 +26,7 @@ import type { BrainEngine } from './engine.ts';
 
 export interface DbLockHandle {
   id: string;
-  /** Optional signal bounds the release DELETE (deadline-bound callers). */
-  release: (signal?: AbortSignal) => Promise<void>;
+  release: () => Promise<void>;
   refresh: () => Promise<void>;
 }
 
@@ -174,7 +173,6 @@ export async function tryAcquireDbLock(
   engine: BrainEngine,
   lockId: string,
   ttlMinutes: number = DEFAULT_TTL_MINUTES,
-  opts: { signal?: AbortSignal } = {},
 ): Promise<DbLockHandle | null> {
   const pid = process.pid;
   const host = hostname();
@@ -207,26 +205,20 @@ export async function tryAcquireDbLock(
     // `gbrain sync --break-lock --max-age <s>` uses last_refreshed_at (not
     // acquired_at) to identify wedged-but-alive holders without stealing
     // healthy long-running holders that are actively refreshing.
-    // #2750: routed through executeRaw so a deadline-bound caller's signal
-    // can cancel a hung acquire (pool exhaustion). Cancellation is
-    // transactional; in the rare ambiguous-commit case the row's TTL is the
-    // backstop (drain locks use a short 5-minute TTL).
-    const rows = await engine.executeRaw<{ id: string }>(
-      `INSERT INTO gbrain_cycle_locks (id, holder_pid, holder_host, acquired_at, ttl_expires_at, last_refreshed_at)
-       VALUES ($1, $2, $3, NOW(), NOW() + $4::interval, NOW())
-       ON CONFLICT (id) DO UPDATE
-         SET holder_pid = $2,
-             holder_host = $3,
-             acquired_at = NOW(),
-             ttl_expires_at = NOW() + $4::interval,
-             last_refreshed_at = NOW()
-         WHERE gbrain_cycle_locks.ttl_expires_at < NOW()
-           AND (gbrain_cycle_locks.last_refreshed_at IS NULL
-                OR gbrain_cycle_locks.last_refreshed_at < NOW() - $5 * INTERVAL '1 second')
-       RETURNING id`,
-      [lockId, pid, host, ttl, stealGraceSeconds],
-      { signal: opts.signal },
-    );
+    const rows: Array<{ id: string }> = await sql`
+      INSERT INTO gbrain_cycle_locks (id, holder_pid, holder_host, acquired_at, ttl_expires_at, last_refreshed_at)
+      VALUES (${lockId}, ${pid}, ${host}, NOW(), NOW() + ${ttl}::interval, NOW())
+      ON CONFLICT (id) DO UPDATE
+        SET holder_pid = ${pid},
+            holder_host = ${host},
+            acquired_at = NOW(),
+            ttl_expires_at = NOW() + ${ttl}::interval,
+            last_refreshed_at = NOW()
+        WHERE gbrain_cycle_locks.ttl_expires_at < NOW()
+          AND (gbrain_cycle_locks.last_refreshed_at IS NULL
+               OR gbrain_cycle_locks.last_refreshed_at < NOW() - ${stealGraceSeconds} * INTERVAL '1 second')
+      RETURNING id
+    `;
     if (rows.length === 0) return null;
     const deregister = registerCleanup(`db-lock:${lockId}`, async () => {
       await sql`
@@ -249,17 +241,12 @@ export async function tryAcquireDbLock(
           [ttl, lockId, pid],
         );
       },
-      release: async (signal?: AbortSignal) => {
+      release: async () => {
         deregister();
-        // Direct session pool (same rationale as refresh, #1794) + optional
-        // signal so a deadline-bound caller's release can't hang forever on
-        // an exhausted pooler. TTL is the backstop if the DELETE is cancelled.
-        await engine.executeRawDirect(
-          `DELETE FROM gbrain_cycle_locks
-            WHERE id = $1 AND holder_pid = $2`,
-          [lockId, pid],
-          { signal },
-        );
+        await sql`
+          DELETE FROM gbrain_cycle_locks
+          WHERE id = ${lockId} AND holder_pid = ${pid}
+        `;
       },
     };
   }
@@ -316,11 +303,6 @@ export async function tryAcquireDbLock(
   const first = await acquireOnce();
   if (first) return first;
 
-  // #2750: deadline-bound callers prefer an honest busy result over the
-  // best-effort same-host takeover below, whose inspect/delete/retry calls
-  // are not signal-bounded. The initial upsert already reclaims expired locks.
-  if (opts.signal) return null;
-
   // v0.42 (#1780 Gap 3): the lock is held and its TTL hasn't expired (the
   // upsert's ON CONFLICT ... WHERE ttl_expires_at < NOW() returned no row).
   // If the holder is on THIS host, provably dead, and past the grace window,
@@ -814,10 +796,6 @@ export interface WithRefreshingLockOpts {
   ttlMinutes?: number;
   /** Heartbeat-fail threshold in ms — abort if SELECT 1 takes longer. Default 30000. */
   heartbeatTimeoutMs?: number;
-  /** #2750: bound lock acquisition with the caller's deadline signal. */
-  signal?: AbortSignal;
-  /** Fresh cleanup budget for the release DELETE when `signal` is set. Default 5000. */
-  releaseTimeoutMs?: number;
 }
 
 /**
@@ -837,7 +815,7 @@ export async function withRefreshingLock<T>(
   // Refresh 6x per TTL window so a missed tick doesn't expire the lock.
   const refreshIntervalMs = Math.max(15000, (ttlMinutes * 60 * 1000) / 6);
 
-  const handle = await tryAcquireDbLock(engine, lockId, ttlMinutes, { signal: opts.signal });
+  const handle = await tryAcquireDbLock(engine, lockId, ttlMinutes);
   if (!handle) throw new LockUnavailableError(lockId);
 
   let healthOk = true;
@@ -876,13 +854,7 @@ export async function withRefreshingLock<T>(
     return await work();
   } finally {
     clearInterval(interval);
-    // #2750: when the caller is deadline-bound, its work signal may already
-    // have fired — release on a FRESH short grace signal so cleanup neither
-    // inherits the spent deadline nor hangs unbounded. TTL is the backstop.
-    const releaseSignal = opts.signal
-      ? AbortSignal.timeout(opts.releaseTimeoutMs ?? 5_000)
-      : undefined;
-    try { await handle.release(releaseSignal); } catch { /* idempotent; TTL backstop */ }
+    try { await handle.release(); } catch { /* idempotent */ }
     if (!healthOk) {
       // Surface that the heartbeat detected backend trouble — caller can
       // log to the connection-events audit if desired.

src/core/engine.ts

@@ -696,16 +696,8 @@ export interface BrainEngine {
    * is included in the INSERT column list so ON CONFLICT (source_id, slug)
    * DO UPDATE actually targets the intended row instead of fabricating a
    * duplicate at (default, slug). Multi-source brains MUST pass sourceId.
-   *
-   * `opts.signal` (#2750): optional cancellation for deadline-bound writers.
-   * Postgres cancels the in-flight statement; PGLite pre-checks only (query
-   * cancellation is not possible in-process — cooperative abort between calls).
    */
-  putPage(
-    slug: string,
-    page: PageInput,
-    opts?: { sourceId?: string; signal?: AbortSignal },
-  ): Promise<Page>;
+  putPage(slug: string, page: PageInput, opts?: { sourceId?: string }): Promise<Page>;
   /**
    * v0.41.13 (#1309) — identity-based dedup pre-check for the import pipeline.
    *

src/core/extract/receipt-writer.ts

@@ -187,7 +187,6 @@ function buildReceiptFrontmatter(input: ExtractReceiptInput): Record<string, unk
 export async function writeReceipt(
   engine: BrainEngine,
   input: ExtractReceiptInput,
-  opts?: { signal?: AbortSignal },
 ): Promise<{ slug: string; page: Page }> {
   const slug = receiptSlug(input);
   const title = `${input.kind} — ${input.round} — ${input.source_id}`;
@@ -202,7 +201,7 @@ export async function writeReceipt(
       compiled_truth,
       frontmatter,
     },
-    { sourceId: input.source_id, signal: opts?.signal },
+    { sourceId: input.source_id },
   );
 
   return { slug, page };

src/core/extract/rollup-writer.ts

@@ -70,7 +70,6 @@ function today(): string {
 export async function upsertExtractRollup(
   engine: BrainEngine,
   input: RollupUpsertInput,
-  opts?: { signal?: AbortSignal },
 ): Promise<{ ok: boolean; error?: string }> {
   const day = input.day ?? today();
   const cost = input.cost_delta ?? 0;
@@ -97,12 +96,9 @@ export async function upsertExtractRollup(
          rollup_write_failures  = extract_rollup_7d.rollup_write_failures  + EXCLUDED.rollup_write_failures,
          updated_at             = now()`,
       [input.kind, input.source_id, day, cost, halts, evalFails, evalPasses, completed, failures],
-      { signal: opts?.signal },
     );
     return { ok: true };
   } catch (err) {
-    // Signal-bounded callers get the abort surfaced, not a swallowed `ok:false`.
-    if (opts?.signal?.aborted) throw err;
     const msg = (err as Error).message || String(err);
     // Don't spam: log once per process per (kind, day) error class.
     rollupErrorLogOnce(input.kind, day, msg);

src/core/pglite-engine.ts

@@ -1003,15 +1003,7 @@ export class PGLiteEngine implements BrainEngine {
     return { slug: r.slug, id: Number(r.id) };
   }
 
-  async putPage(
-    slug: string,
-    page: PageInput,
-    opts?: { sourceId?: string; signal?: AbortSignal },
-  ): Promise<Page> {
-    // #2750: PGLite is in-process WASM — no query cancellation. Pre-check so
-    // an already-fired deadline skips the write; abort is cooperative
-    // between calls (same posture as executeRaw's documented gap).
-    if (opts?.signal?.aborted) throw new DOMException('aborted', 'AbortError');
+  async putPage(slug: string, page: PageInput, opts?: { sourceId?: string }): Promise<Page> {
     slug = validateSlug(slug);
     const hash = page.content_hash || contentHash(page);
     const frontmatter = page.frontmatter || {};

src/core/postgres-engine.ts

@@ -72,32 +72,6 @@ function escapeSqlStringLiteral(value: string): string {
   return value.replace(/'/g, "''");
 }
 
-/**
- * #2750: race a promise against an AbortSignal, detaching the listener once
- * settled (long-lived drain signals are reused across many calls, so a bare
- * Promise.race would leak one listener per call). The abandoned promise keeps
- * running; used only for pool-acquisition waits where that is harmless.
- */
-function waitForSignal<T>(work: Promise<T>, signal?: AbortSignal): Promise<T> {
-  if (!signal) return work;
-  if (signal.aborted) return Promise.reject(new DOMException('aborted', 'AbortError'));
-  return new Promise<T>((resolve, reject) => {
-    let settled = false;
-    const finish = (fn: () => void) => {
-      if (settled) return;
-      settled = true;
-      signal.removeEventListener('abort', onAbort);
-      fn();
-    };
-    const onAbort = () => finish(() => reject(new DOMException('aborted', 'AbortError')));
-    signal.addEventListener('abort', onAbort, { once: true });
-    work.then(
-      (value) => finish(() => resolve(value)),
-      (err) => finish(() => reject(err)),
-    );
-  });
-}
-
 export function getPostgresSchema(
   dims: number = DEFAULT_EMBEDDING_DIMENSIONS,
   model: string = DEFAULT_EMBEDDING_MODEL,
@@ -1087,12 +1061,7 @@ export class PostgresEngine implements BrainEngine {
     });
   }
 
-  async putPage(
-    slug: string,
-    page: PageInput,
-    opts?: { sourceId?: string; signal?: AbortSignal },
-  ): Promise<Page> {
-    if (opts?.signal?.aborted) throw new DOMException('aborted', 'AbortError');
+  async putPage(slug: string, page: PageInput, opts?: { sourceId?: string }): Promise<Page> {
     slug = validateSlug(slug);
     const sql = this.sql;
     const hash = page.content_hash || contentHash(page);
@@ -1127,7 +1096,7 @@ export class PostgresEngine implements BrainEngine {
     const sourceUri = page.source_uri ?? null;
     const ingestedVia = page.ingested_via ?? null;
     const ingestedAt = (sourceKind || sourceUri || ingestedVia) ? new Date() : null;
-    const pending = sql`
+    const rows = await sql`
       INSERT INTO pages (source_id, slug, type, page_kind, title, compiled_truth, timeline, frontmatter, content_hash, updated_at, effective_date, effective_date_source, import_filename, chunker_version, source_path, source_kind, source_uri, ingested_via, ingested_at)
       VALUES (${sourceId}, ${slug}, ${page.type}, ${pageKind}, ${page.title}, ${page.compiled_truth}, ${page.timeline || ''}, ${sql.json(frontmatter as Parameters<typeof sql.json>[0])}, ${hash}, now(), ${effectiveDate}, ${effectiveDateSource}, ${importFilename}, COALESCE(${chunkerVersion}::smallint, ${MARKDOWN_CHUNKER_VERSION}), ${sourcePath}, ${sourceKind}, ${sourceUri}, ${ingestedVia}, ${ingestedAt})
       ON CONFLICT (source_id, slug) DO UPDATE SET
@@ -1150,22 +1119,6 @@ export class PostgresEngine implements BrainEngine {
         ingested_at           = COALESCE(EXCLUDED.ingested_at,           pages.ingested_at)
       RETURNING id, source_id, slug, type, title, compiled_truth, timeline, frontmatter, content_hash, created_at, updated_at, effective_date, effective_date_source, import_filename, source_kind, source_uri, ingested_via, ingested_at
     `;
-    // #2750: cancel the in-flight statement when the caller's deadline fires,
-    // same .cancel() wiring as runUnsafe (postgres.js pending queries).
-    if (opts?.signal) {
-      const signal = opts.signal;
-      const onAbort = () => {
-        try { (pending as unknown as { cancel?: () => void }).cancel?.(); } catch { /* best-effort */ }
-      };
-      signal.addEventListener('abort', onAbort, { once: true });
-      try {
-        const rows = await pending;
-        return rowToPage(rows[0]);
-      } finally {
-        signal.removeEventListener('abort', onAbort);
-      }
-    }
-    const rows = await pending;
     return rowToPage(rows[0]);
   }
 
@@ -5854,16 +5807,11 @@ export class PostgresEngine implements BrainEngine {
     params?: unknown[],
     opts?: { signal?: AbortSignal },
   ): Promise<T[]> {
-    // #2750: an already-fired signal short-circuits BEFORE any pool routing,
-    // and the direct-pool acquisition itself is signal-bounded — under pooler
-    // exhaustion `ddl()` can stall indefinitely, which used to make even a
-    // "bounded" lock release hang past its caller's deadline.
-    if (opts?.signal?.aborted) throw new DOMException('aborted', 'AbortError');
     // Inside an open transaction, _sql is the reserved tx connection (set via
     // defineProperty in transaction()); never reroute off it.
     const inTransaction = this._sql !== null && this.connectionManager?.peekReadPool() !== this._sql;
     const conn = (!inTransaction && this.connectionManager?.isDualPoolActive())
-      ? await waitForSignal(this.connectionManager.ddl(), opts?.signal)
+      ? await this.connectionManager.ddl()
       : this.sql;
     return this.runUnsafe<T>(conn, sql, params, opts);
   }

src/core/remediation/context.ts

@@ -8,6 +8,7 @@
 
 import type { BrainEngine } from '../engine.ts';
 import type { RecommendationContext } from '../brain-score-recommendations.ts';
+import { LINK_EXTRACTOR_VERSION_TS } from '../link-extraction.ts';
 
 // Re-export so consumers can `import { RecommendationContext } from '../remediation'`
 // — the canonical RecommendationContext type still lives in
@@ -68,5 +69,29 @@ export async function loadRecommendationContext(
     embeddingDimensions,
     embeddingProviderConfigured: embeddingConfigured,
     hasChatApiKey: !!(process.env.ANTHROPIC_API_KEY || fileCfg?.anthropic_api_key),
+    extractionLagPages: await countExtractionLag(engine),
   };
 }
+
+/**
+ * Real extraction-lag count — the SAME staleness `gbrain extract --stale`
+ * processes (engine.countStalePagesForExtraction with
+ * versionTs=LINK_EXTRACTOR_VERSION_TS, matching doctor's links_extraction_lag
+ * check — without versionTs, pages stamped before an extractor version bump
+ * would lag for doctor/extract but never trip this gate). Drives the
+ * sync→extract recommendation pipeline; replaces the legacy
+ * `health.stale_pages` proxy that no longer reflected real extraction work
+ * after the v10 trigger drop.
+ *
+ * Shared by loadRecommendationContext AND the D7 per-step recheck in
+ * runRemediation — the recheck MUST refresh this gate alongside getHealth,
+ * or a completed extract step keeps re-firing off the frozen initial count.
+ */
+export async function countExtractionLag(engine: BrainEngine): Promise<number> {
+  try {
+    return await engine.countStalePagesForExtraction({ versionTs: LINK_EXTRACTOR_VERSION_TS });
+  } catch {
+    /* counter unavailable (very old brain / mid-migration) — treat as 0 */
+    return 0;
+  }
+}

src/core/remediation/run.ts

@@ -16,7 +16,7 @@ import {
   computeRecommendations,
 } from '../brain-score-recommendations.ts';
 import type { RemediationStep } from '../remediation-step.ts';
-import { loadRecommendationContext } from './context.ts';
+import { countExtractionLag, loadRecommendationContext } from './context.ts';
 import { computeRemediationPlan } from './plan.ts';
 import type {
   RemediationHooks,
@@ -65,7 +65,7 @@ export async function runRemediation(
     clearRemediationCheckpoint,
   } = await import('../remediation-checkpoint.ts');
 
-  const ctx = await loadRecommendationContext(engine);
+  let ctx = await loadRecommendationContext(engine);
 
   // Pre-flight ceiling check via the shared plan computation.
   const initialPlan = await computeRemediationPlan(engine, { targetScore });
@@ -305,6 +305,11 @@ export async function runRemediation(
       // steps with bumped retry suffix (D1).
       if (recs.length === 0 || stepCount >= maxJobs) break;
       const freshHealth = await engine.getHealth();
+      // Refresh the extraction-lag gate alongside health: ctx was loaded once
+      // before the loop, and a completed sync/extract step is exactly what
+      // drives the count down. Reusing the frozen initial count would re-fire
+      // sync.repo/extract.all every recheck until maxJobs.
+      ctx = { ...ctx, extractionLagPages: await countExtractionLag(engine) };
       recs = computeRecommendations(freshHealth, ctx).filter((r) => r.status === 'remediable');
     }
   };

src/core/types.ts

@@ -1423,6 +1423,15 @@ export interface BrainStats {
 export interface BrainHealth {
   page_count: number;
   embed_coverage: number;
+  /**
+   * LEGACY proxy: count of pages whose `updated_at` predates their newest
+   * timeline entry. This bumped meaningfully only while a trigger updated
+   * `pages.updated_at` on timeline insert; that trigger was dropped in
+   * migration v10, so the metric no longer reflects real "needs work" state.
+   * NO LONGER gates remediations — the sync→extract pipeline now gates on
+   * `RecommendationContext.extractionLagPages` (the real extraction-lag from
+   * `countStalePagesForExtraction`). Retained for the CLI health line + back-compat.
+   */
   stale_pages: number;
   /**
    * Islanded pages — zero inbound AND zero outbound links. A hub page

test/brain-score-recommendations.test.ts

@@ -119,13 +119,12 @@ describe('computeRecommendations', () => {
     expect(recs.find((r) => r.id === 'embed.stale')).toBeUndefined();
   });
 
-  test('stale pages + dead links produce sync + backlinks + extract', () => {
+  test('extraction lag + dead links produce sync + backlinks + extract', () => {
     const health = makeHealth({
-      stale_pages: 25,
       dead_links: 8,
       brain_score: 70,
     });
-    const recs = computeRecommendations(health, { repoPath: '/brain', embeddingProviderConfigured: true });
+    const recs = computeRecommendations(health, { repoPath: '/brain', embeddingProviderConfigured: true, extractionLagPages: 25 });
     const ids = recs.map((r) => r.id);
     expect(ids).toContain('sync.repo');
     expect(ids).toContain('backlinks.fix');
@@ -133,18 +132,17 @@ describe('computeRecommendations', () => {
   });
 
   test('extract.all depends on sync.repo (D14: stable ids)', () => {
-    const health = makeHealth({ stale_pages: 10 });
-    const recs = computeRecommendations(health, { repoPath: '/brain', embeddingProviderConfigured: true });
+    const health = makeHealth();
+    const recs = computeRecommendations(health, { repoPath: '/brain', embeddingProviderConfigured: true, extractionLagPages: 10 });
     const extract = recs.find((r) => r.id === 'extract.all');
     expect(extract?.depends_on).toContain('sync.repo');
   });
 
-  test('embed.stale depends on sync.repo when sync also needed', () => {
+  test('embed.stale depends on sync.repo when extraction also needed', () => {
     const health = makeHealth({
-      stale_pages: 10,
       missing_embeddings: 100,
     });
-    const recs = computeRecommendations(health, { repoPath: '/brain', embeddingProviderConfigured: true });
+    const recs = computeRecommendations(health, { repoPath: '/brain', embeddingProviderConfigured: true, extractionLagPages: 10 });
     const embed = recs.find((r) => r.id === 'embed.stale');
     expect(embed?.depends_on).toContain('sync.repo');
   });
@@ -159,9 +157,9 @@ describe('computeRecommendations', () => {
   test('severity ordering: critical before high before medium', () => {
     const health = makeHealth({
       missing_embeddings: 100,  // critical
-      stale_pages: 80,          // high
     });
-    const recs = computeRecommendations(health, { repoPath: '/brain', embeddingProviderConfigured: true });
+    // extractionLagPages > 50 → sync.repo fires at 'high' severity.
+    const recs = computeRecommendations(health, { repoPath: '/brain', embeddingProviderConfigured: true, extractionLagPages: 80 });
     const critIdx = recs.findIndex((r) => r.severity === 'critical');
     const highIdx = recs.findIndex((r) => r.severity === 'high');
     expect(critIdx).toBeLessThan(highIdx);
@@ -170,11 +168,10 @@ describe('computeRecommendations', () => {
   // D6 #5 — THE critical regression test for the agent contract.
   test('D6 #5: determinism — same input twice produces identical output', () => {
     const health = makeHealth({
-      stale_pages: 10,
       missing_embeddings: 50,
       dead_links: 3,
     });
-    const ctx = { repoPath: '/brain', embeddingProviderConfigured: true, sourceId: 'default' };
+    const ctx = { repoPath: '/brain', embeddingProviderConfigured: true, sourceId: 'default', extractionLagPages: 10 };
     const run1 = computeRecommendations(health, ctx);
     const run2 = computeRecommendations(health, ctx);
     expect(JSON.stringify(run1)).toBe(JSON.stringify(run2));

test/cycle/extract-atoms-synthesize-concepts.test.ts

@@ -17,7 +17,6 @@ import { runPhaseExtractAtoms, parseAtomsResponse } from '../../src/core/cycle/e
 import { runPhaseSynthesizeConcepts } from '../../src/core/cycle/synthesize-concepts.ts';
 import { resetPgliteState } from '../helpers/reset-pglite.ts';
 import type { ChatResult, ChatOpts } from '../../src/core/ai/gateway.ts';
-import type { BrainEngine } from '../../src/core/engine.ts';
 
 let engine: PGLiteEngine;
 
@@ -178,180 +177,6 @@ describe('v0.41 T5: runPhaseExtractAtoms via stubbed chat', () => {
     expect((result.details?.failures as unknown[]).length).toBe(1);
   });
 
-  // ── #2750: caller deadline bounds the phase ────────────────────────────
-
-  test('caller deadline aborts a hung chat before processing the next item', async () => {
-    let calls = 0;
-    const chat = async (opts: ChatOpts) => {
-      calls++;
-      return await new Promise<never>((_resolve, reject) => {
-        const signal = opts.abortSignal;
-        if (!signal) return reject(new Error('missing abort signal'));
-        if (signal.aborted) return reject(signal.reason);
-        signal.addEventListener('abort', () => reject(signal.reason), { once: true });
-      });
-    };
-    const started = Date.now();
-    const result = await runPhaseExtractAtoms(engine, {
-      _transcripts: [
-        { filePath: '/hung.txt', content: 'a', contentHash: 'hung-a' },
-        { filePath: '/never.txt', content: 'b', contentHash: 'hung-b' },
-      ],
-      _pages: [],
-      _chat: chat as typeof import('../../src/core/ai/gateway.ts').chat,
-      abortSignal: AbortSignal.timeout(25),
-    });
-    expect(Date.now() - started).toBeLessThan(2_000);
-    expect(calls).toBe(1);
-    expect(result.status).toBe('ok');
-    expect(result.details?.deadline_aborted).toBe(true);
-    expect(result.details?.atoms_extracted).toBe(0);
-    expect(result.details?.failures).toEqual([]);
-  });
-
-  test('billable chat usage is counted when the deadline fires as the response resolves', async () => {
-    const controller = new AbortController();
-    const chat = async (opts: ChatOpts): Promise<ChatResult> => {
-      controller.abort(new DOMException('deadline', 'TimeoutError'));
-      return stubChat(`[{"title":"late","atom_type":"insight","body":"b"}]`, {
-        input_tokens: 1_000,
-        output_tokens: 500,
-      })(opts);
-    };
-    const result = await runPhaseExtractAtoms(engine, {
-      _transcripts: [{ filePath: '/late.txt', content: 'a', contentHash: 'late' }],
-      _pages: [],
-      _chat: chat,
-      abortSignal: controller.signal,
-    });
-    expect(result.details?.deadline_aborted).toBe(true);
-    expect(Number(result.details?.estimated_spend_usd)).toBeGreaterThan(0);
-    expect(result.details?.atoms_extracted).toBe(0);
-  });
-
-  test('deadline after partial progress still writes receipt and incomplete rollup', async () => {
-    const controller = new AbortController();
-    let calls = 0;
-    let notifySecondChat!: () => void;
-    const secondChatStarted = new Promise<void>((resolve) => { notifySecondChat = resolve; });
-    const chat = async (opts: ChatOpts): Promise<ChatResult> => {
-      calls++;
-      if (calls === 1) {
-        return stubChat(`[{"title":"committed","atom_type":"insight","body":"b"}]`)(opts);
-      }
-      notifySecondChat();
-      return await new Promise<never>((_resolve, reject) => {
-        const signal = opts.abortSignal;
-        if (!signal) return reject(new Error('missing abort signal'));
-        signal.addEventListener('abort', () => reject(signal.reason), { once: true });
-      });
-    };
-
-    const pending = runPhaseExtractAtoms(engine, {
-      _transcripts: [
-        { filePath: '/committed.txt', content: 'a', contentHash: 'committed-a' },
-        { filePath: '/hung.txt', content: 'b', contentHash: 'hung-b' },
-      ],
-      _pages: [],
-      _chat: chat,
-      abortSignal: controller.signal,
-    });
-    await secondChatStarted;
-    controller.abort(new DOMException('deadline', 'TimeoutError'));
-    const result = await pending;
-
-    const atoms = await engine.executeRaw<{ n: number }>(
-      `SELECT COUNT(*)::int AS n FROM pages WHERE type = 'atom'`,
-    );
-    const receipts = await engine.executeRaw<{ n: number }>(
-      `SELECT COUNT(*)::int AS n FROM pages WHERE type = 'extract_receipt'`,
-    );
-    const rollups = await engine.executeRaw<{
-      cost_usd: string | number;
-      round_completed_count: string | number;
-    }>(
-      `SELECT cost_usd, round_completed_count
-         FROM extract_rollup_7d
-        WHERE kind = 'atoms' AND source_id = 'default'`,
-    );
-    expect(result.details?.deadline_aborted).toBe(true);
-    expect(atoms[0].n).toBe(1);
-    expect(receipts[0].n).toBe(1);
-    expect(Number(rollups[0].cost_usd)).toBeGreaterThan(0);
-    expect(Number(rollups[0].round_completed_count)).toBe(0);
-  });
-
-  test('bookkeeping runs on a fresh grace signal, not the fired work deadline', async () => {
-    const controller = new AbortController();
-    let putCalls = 0;
-    let receiptSignal: AbortSignal | undefined;
-    let rollupSignal: AbortSignal | undefined;
-    const signalAwareEngine = {
-      executeRaw: async (sql: string, _params?: unknown[], opts?: { signal?: AbortSignal }) => {
-        if (sql.includes('INSERT INTO extract_rollup_7d')) rollupSignal = opts?.signal;
-        return [];
-      },
-      putPage: async (_slug: string, _page: unknown, opts?: { signal?: AbortSignal }) => {
-        putCalls++;
-        if (putCalls === 1) {
-          // Atom write in flight; the work deadline fires before bookkeeping.
-          controller.abort(new DOMException('work deadline', 'TimeoutError'));
-        } else {
-          receiptSignal = opts?.signal;
-        }
-        return {};
-      },
-    } as unknown as BrainEngine;
-
-    const result = await runPhaseExtractAtoms(signalAwareEngine, {
-      _transcripts: [{ filePath: '/one.txt', content: 'a', contentHash: 'one' }],
-      _pages: [],
-      _chat: stubChat(`[{"title":"one","atom_type":"insight","body":"b"}]`),
-      abortSignal: controller.signal,
-    });
-
-    expect(result.details?.atoms_extracted).toBe(1);
-    expect(putCalls).toBe(2); // atom write + receipt write
-    expect(receiptSignal).toBeDefined();
-    expect(receiptSignal).not.toBe(controller.signal);
-    expect(receiptSignal?.aborted).toBe(false);
-    expect(rollupSignal).toBe(receiptSignal);
-  });
-
-  test('caller deadline cancels a hung atom write and stops the phase', async () => {
-    const controller = new AbortController();
-    let notifyWriteStarted!: () => void;
-    const writeStarted = new Promise<void>((resolve) => { notifyWriteStarted = resolve; });
-    let writeCalls = 0;
-    const signalAwareEngine = {
-      executeRaw: async () => [],
-      putPage: async (_slug: string, _page: unknown, opts?: { signal?: AbortSignal }) => {
-        writeCalls++;
-        notifyWriteStarted();
-        return await new Promise<never>((_resolve, reject) => {
-          const signal = opts?.signal;
-          if (!signal) return reject(new Error('missing abort signal'));
-          if (signal.aborted) return reject(signal.reason);
-          signal.addEventListener('abort', () => reject(signal.reason), { once: true });
-        });
-      },
-    } as unknown as BrainEngine;
-
-    const pending = runPhaseExtractAtoms(signalAwareEngine, {
-      _transcripts: [{ filePath: '/hung-write.txt', content: 'a', contentHash: 'hung-write' }],
-      _pages: [],
-      _chat: stubChat(`[{"title":"hung write","atom_type":"insight","body":"b"}]`),
-      abortSignal: controller.signal,
-    });
-    await writeStarted;
-    controller.abort(new DOMException('deadline', 'TimeoutError'));
-    const result = await pending;
-
-    expect(writeCalls).toBe(1);
-    expect(result.details?.deadline_aborted).toBe(true);
-    expect(result.details?.atoms_extracted).toBe(0);
-  });
-
   // v0.41.2.1 regression case (D9 #14 wording): with _pages:[] and same
   // _transcripts, all PRE-EXISTING PhaseResult.details fields match
   // pre-fix values byte-for-byte. The new fields (pages_processed,

test/extract-atoms-drain.test.ts

@@ -43,135 +43,26 @@ describe('runExtractAtomsDrain (issue #1678)', () => {
     expect(batches).toBe(3);
   });
 
-  it('stops at the wallclock window; remaining is unknown (no post-window count)', async () => {
-    // Each batch consumes 60ms of the 100ms window: two batches fit, the
-    // third boundary check sees 120 ≥ 100 and stops. #2750: after the window
-    // elapses the final countRemaining is SKIPPED (it would overrun the
-    // window), so remaining reports null.
-    let now = 0;
+  it('stops at the wallclock window with remaining > 0', async () => {
+    // SYNC stepping clock: now() #1 sets deadline (0+100=100); the while-check
+    // then sees 50, 50 (two batches), then 999999 → past deadline → stop.
+    const times = [0, 50, 50, 999_999];
+    let ti = 0;
+    const now = () => times[Math.min(ti++, times.length - 1)];
     const result = await runExtractAtomsDrain(
       {
         withLock: passThroughLock,
         countRemaining: async () => 5, // never drains
-        runBatch: async () => {
-          now += 60;
-          return { extracted: 1, skipped: 0 };
-        },
-        now: () => now,
+        runBatch: async () => ({ extracted: 1, skipped: 0 }),
+        now,
       },
       { windowMs: 100 },
     );
     expect(result.stopped).toBe('window');
-    expect(result.remaining).toBeNull();
+    expect(result.remaining).toBe(5);
     expect(result.batches).toBe(2);
   });
 
-  it('passes one drain-level deadline signal into count and batch', async () => {
-    const seen: AbortSignal[] = [];
-    const controller = new AbortController();
-    let now = 0;
-    const result = await runExtractAtomsDrain(
-      {
-        withLock: passThroughLock,
-        countRemaining: async (signal) => {
-          seen.push(signal);
-          return 5;
-        },
-        runBatch: async (signal) => {
-          seen.push(signal);
-          now = 100;
-          return { extracted: 1, skipped: 0 };
-        },
-        now: () => now,
-      },
-      { windowMs: 100, abortSignal: controller.signal },
-    );
-    expect(result.stopped).toBe('window');
-    expect(result.batches).toBe(1);
-    expect(seen.length).toBe(2);
-    expect(seen[0]).toBe(seen[1]);
-    // Combined (timeout + external) signal, not the raw external one.
-    expect(seen[0]).not.toBe(controller.signal);
-  });
-
-  it('aborts a hung backlog count at the window deadline and releases the lock', async () => {
-    let released = false;
-    const result = await runExtractAtomsDrain(
-      {
-        withLock: async (work) => {
-          try { return await work(); }
-          finally { released = true; }
-        },
-        // Hangs until the drain's real-time deadline signal fires (10ms).
-        countRemaining: (signal) => new Promise((_resolve, reject) => {
-          signal.addEventListener('abort', () => reject(signal.reason), { once: true });
-        }),
-        runBatch: async () => ({ extracted: 0, skipped: 0 }),
-        now: () => 0, // injected clock never advances — the SIGNAL must save us
-      },
-      { windowMs: 10 },
-    );
-    expect(result.stopped).toBe('window');
-    expect(result.remaining).toBeNull();
-    expect(released).toBe(true);
-  });
-
-  it('rethrows external cancellation after releasing the lock', async () => {
-    const controller = new AbortController();
-    let released = false;
-    const pending = runExtractAtomsDrain(
-      {
-        withLock: async (work) => {
-          try { return await work(); }
-          finally { released = true; }
-        },
-        countRemaining: (signal) => new Promise((_resolve, reject) => {
-          signal.addEventListener('abort', () => reject(signal.reason), { once: true });
-        }),
-        runBatch: async () => ({ extracted: 0, skipped: 0 }),
-        now: () => 0,
-      },
-      { windowMs: 1_000_000, abortSignal: controller.signal },
-    );
-    controller.abort(new DOMException('worker timeout', 'AbortError'));
-    await expect(pending).rejects.toThrow('worker timeout');
-    expect(released).toBe(true);
-  });
-
-  it('classifies a deadline-exhausted zero-progress batch as window, not no_progress', async () => {
-    let now = 0;
-    const result = await runExtractAtomsDrain(
-      {
-        withLock: passThroughLock,
-        countRemaining: async () => 5,
-        runBatch: async () => {
-          now = 100; // batch consumed the whole window and returned nothing
-          return { extracted: 0, skipped: 0 };
-        },
-        now: () => now,
-      },
-      { windowMs: 100 },
-    );
-    expect(result.stopped).toBe('window');
-    expect(result.batches).toBe(1);
-  });
-
-  it('bounds a hung lock acquisition with the drain deadline signal', async () => {
-    const started = Date.now();
-    await expect(runExtractAtomsDrain(
-      {
-        withLock: (_work, signal) => new Promise((_resolve, reject) => {
-          signal.addEventListener('abort', () => reject(signal.reason), { once: true });
-        }),
-        countRemaining: async () => 1,
-        runBatch: async () => ({ extracted: 0, skipped: 0 }),
-        now: Date.now,
-      },
-      { windowMs: 10 },
-    )).rejects.toThrow();
-    expect(Date.now() - started).toBeLessThan(1_000);
-  });
-
   it('stops on a zero-progress batch (no hot loop)', async () => {
     let batches = 0;
     const result = await runExtractAtomsDrain(
@@ -242,17 +133,4 @@ describe('shared wiring helper holds the cycle lock (5A)', () => {
     expect(src).toContain('cycleLockIdFor(opts.sourceId)');
     expect(src).toContain('withRefreshingLock(engine, lockId');
   });
-
-  // #2750: the deadline signal must reach the phase, the backlog count, AND
-  // the lock wrapper — and the transcript path (brainDir) must stay wired
-  // exactly as the routine callers expect (PR #2752 takeover reverted its
-  // unsanctioned transcript-suppression scope change).
-  it('threads the drain deadline signal through phase, count, and lock', () => {
-    const jobsSrc = readFileSync(join(import.meta.dir, '../src/commands/jobs.ts'), 'utf8');
-    expect(src).toContain('abortSignal: signal');
-    expect(src).toContain('countExtractAtomsBacklog(engine, extractionSourceId, signal)');
-    expect(src).toContain('brainDir: opts.brainDir');
-    expect(src).not.toContain('_transcripts');
-    expect(jobsSrc).toContain('abortSignal: job.signal');
-  });
 });

test/fixtures/supervisor-runner.ts

@@ -24,18 +24,15 @@ import type { BrainEngine } from '../../src/core/engine.ts';
 // Mock engine: healthCheck() calls engine.executeRaw; return empty rows so
 // the query path exercises without needing Postgres.
 //
-// #1849: start() acquires the queue-scoped DB singleton lock via
-// tryAcquireDbLock. #2750 routed the acquire upsert through engine.executeRaw
-// (signal-boundable) and release through engine.executeRawDirect, so the
-// stub returns a single row from the lock upsert (length 1 → acquired) and
-// empty rows everywhere else. Each spawned runner is a fresh process, so
-// there's no cross-test lock state to clean up.
+// #1849: start() now acquires the queue-scoped DB singleton lock via
+// tryAcquireDbLock, which uses the postgres `sql` tagged-template escape hatch.
+// The stub returns a single row from every call so acquire succeeds (length 1
+// → acquired) and refresh/release are no-ops. Each spawned runner is a fresh
+// process, so there's no cross-test lock state to clean up.
 const sqlStub = (..._args: unknown[]) => Promise.resolve([{ id: 'supervisor-lock' }]);
 const mockEngine: Partial<BrainEngine> = {
   kind: 'postgres' as const,
-  executeRaw: async (query: string) =>
-    query.includes('gbrain_cycle_locks') ? [{ id: 'supervisor-lock' }] : [],
-  executeRawDirect: async () => [],
+  executeRaw: async () => [],
   sql: sqlStub,
 } as unknown as BrainEngine;
 

test/postgres-execute-raw-direct.test.ts

@@ -98,39 +98,14 @@ describe('PostgresEngine.executeRawDirect — routing decision (PR #1816)', () =
   });
 
   test('already-aborted signal short-circuits with AbortError before routing the query', async () => {
-    let unsafeCalls = 0;
-    let ddlCalls = 0;
-    const readConn: FakeSql = { unsafe: async () => { unsafeCalls++; return []; } };
+    const readConn = fakeSql('read');
     const directConn = fakeSql('direct');
     const engine = makeEngine({ dualPoolActive: true, readConn, directConn });
-    const e = engine as unknown as { connectionManager: { ddl: () => Promise<FakeSql> } };
-    e.connectionManager.ddl = async () => { ddlCalls++; return directConn; };
 
     const ac = new AbortController();
     ac.abort();
     await expect(
       engine.executeRawDirect('UPDATE minion_jobs SET x=1', [], { signal: ac.signal }),
     ).rejects.toThrow(/abort/i);
-    // #2750: short-circuits BEFORE pool routing — no ddl(), no unsafe().
-    expect(ddlCalls).toBe(0);
-    expect(unsafeCalls).toBe(0);
-  });
-
-  test('#2750: signal bounds a stalled direct-pool acquisition before unsafe starts', async () => {
-    let unsafeCalls = 0;
-    const readConn: FakeSql = { unsafe: async () => { unsafeCalls++; return []; } };
-    const directConn = fakeSql('direct');
-    const engine = makeEngine({ dualPoolActive: true, readConn, directConn });
-    const e = engine as unknown as { connectionManager: { ddl: () => Promise<FakeSql> } };
-    e.connectionManager.ddl = () => new Promise<FakeSql>(() => {}); // pooler exhausted: never resolves
-
-    const started = Date.now();
-    await expect(engine.executeRawDirect(
-      'DELETE FROM gbrain_cycle_locks',
-      [],
-      { signal: AbortSignal.timeout(10) },
-    )).rejects.toThrow(/abort/i);
-    expect(Date.now() - started).toBeLessThan(1_000);
-    expect(unsafeCalls).toBe(0);
   });
 });

test/remediation-context-extraction-lag.test.ts

@@ -0,0 +1,62 @@
+// test/remediation-context-extraction-lag.test.ts
+//
+// Pins the v-next fix: the sync→extract remediation pipeline gates on REAL
+// extraction lag, not the legacy `health.stale_pages` proxy (which counted
+// "updated_at predates newest timeline entry" — meaningless after the v10
+// trigger drop). loadRecommendationContext now populates `extractionLagPages`
+// from `engine.countStalePagesForExtraction` — the SAME counter the
+// `gbrain extract --stale` walk and doctor's `links_extraction_lag` use — so a
+// recommendation can only fire when running extract will actually reduce it.
+
+import { afterAll, beforeAll, describe, expect, it } from 'bun:test';
+import { PGLiteEngine } from '../src/core/pglite-engine.ts';
+import { loadRecommendationContext } from '../src/core/remediation/context.ts';
+
+let engine: PGLiteEngine;
+
+beforeAll(async () => {
+  engine = new PGLiteEngine();
+  await engine.connect({});
+  await engine.initSchema();
+});
+
+afterAll(async () => {
+  await engine.disconnect();
+});
+
+describe('loadRecommendationContext — extractionLagPages wiring', () => {
+  it('is 0 on an empty brain (nothing to extract)', async () => {
+    const ctx = await loadRecommendationContext(engine);
+    expect(ctx.extractionLagPages).toBe(0);
+  });
+
+  it('reflects the real extraction-lag count once a page needs extraction', async () => {
+    // A freshly-imported page has links_extracted_at = NULL, which the canonical
+    // countStalePagesForExtraction predicate counts as stale-for-extraction.
+    await engine.putPage('p0', {
+      title: 'p0',
+      type: 'note' as never,
+      compiled_truth: 'body that is long enough to pass any minimum-length guards in the codebase',
+      timeline: '',
+      frontmatter: {},
+      source_path: 'p0.md',
+    });
+    const ctx = await loadRecommendationContext(engine);
+    expect(ctx.extractionLagPages).toBeGreaterThan(0);
+  });
+
+  it('counts pages stamped before LINK_EXTRACTOR_VERSION_TS (version-bump arm)', async () => {
+    // Backdate p0 so BOTH the NULL arm and the updated_at arm are quiet:
+    // updated_at < links_extracted_at, but links_extracted_at predates the
+    // extractor version stamp. doctor's links_extraction_lag and
+    // `extract --stale` both count this page; the remediation gate must too.
+    await engine.executeRaw(
+      `UPDATE pages SET updated_at = '2020-01-01T00:00:00Z'::timestamptz,
+                        links_extracted_at = '2020-01-02T00:00:00Z'::timestamptz
+        WHERE slug = 'p0'`,
+      [],
+    );
+    const ctx = await loadRecommendationContext(engine);
+    expect(ctx.extractionLagPages).toBeGreaterThan(0);
+  });
+});

test/remediation-run-d7-refresh.serial.test.ts

@@ -0,0 +1,81 @@
+// test/remediation-run-d7-refresh.serial.test.ts
+//
+// Pins the D7-recheck half of the extraction-lag gate fix: runRemediation
+// loads RecommendationContext ONCE before the step loop, and the per-step
+// recheck (D7) must REFRESH ctx.extractionLagPages alongside getHealth.
+// Without the refresh, a completed sync/extract step keeps re-firing off
+// the frozen initial count — the plan never converges and the loop burns
+// steps until maxJobs.
+//
+// SERIAL (R2): uses top-level mock.module for the minion queue +
+// wait-for-completion so no real worker is needed — mocks leak across
+// files in a shard process, so this file must run in its own process.
+
+import { describe, expect, mock, test } from 'bun:test';
+
+// The fake brain: sync.repo clears the extraction lag when it "runs"
+// (today's sync materializes link/timeline edges; extract.all is the
+// explicit re-materializer). The frozen-ctx bug makes runRemediation
+// ignore that and resubmit sync.repo on every D7 recheck.
+let extractionLag = 25;
+const submittedJobs: string[] = [];
+
+mock.module('../src/core/minions/queue.ts', () => ({
+  MinionQueue: class {
+    constructor(_engine: unknown) {}
+    async add(job: string): Promise<{ id: number }> {
+      submittedJobs.push(job);
+      if (job === 'sync' || job === 'extract') extractionLag = 0;
+      return { id: submittedJobs.length };
+    }
+  },
+}));
+
+mock.module('../src/core/minions/wait-for-completion.ts', () => ({
+  waitForCompletion: async () => ({ status: 'completed' }),
+}));
+
+const health = () => ({
+  page_count: 100,
+  embed_coverage: 1.0,
+  stale_pages: 0, // legacy proxy stays 0 — the real counter drives the gate
+  orphan_pages: 0,
+  missing_embeddings: 0,
+  brain_score: 70,
+  dead_links: 0,
+  link_coverage: 1.0,
+  timeline_coverage: 1.0,
+  most_connected: [],
+  embed_coverage_score: 35,
+  link_density_score: 25,
+  timeline_coverage_score: 15,
+  no_orphans_score: 15,
+  no_dead_links_score: 10,
+});
+
+const fakeEngine = {
+  kind: 'pglite' as const,
+  getHealth: async () => health(),
+  getConfig: async (key: string) =>
+    key === 'sync.repo_path' ? '/tmp/brain-example' : null,
+  countStalePagesForExtraction: async () => extractionLag,
+};
+
+describe('runRemediation D7 recheck — extraction-lag gate refresh', () => {
+  test('a completed materializer step clears the gate; the pipeline is not resubmitted', async () => {
+    const { runRemediation } = await import('../src/core/remediation/run.ts');
+    const result = await runRemediation(
+      // Only the methods the orchestrator touches are needed.
+      fakeEngine as never,
+      { targetScore: 0, maxJobs: 6 },
+    );
+    // Frozen-ctx bug: extractionLagPages stays 25 forever, so every D7
+    // recheck re-introduces the sync/extract pipeline and the loop burns
+    // all 6 maxJobs. With the refresh, the plan converges after the first
+    // completed step: no step id is ever submitted twice.
+    const ids = result.submitted.map((s) => s.id);
+    expect(new Set(ids).size).toBe(ids.length);
+    expect(submittedJobs.length).toBeLessThan(3);
+    expect(extractionLag).toBe(0);
+  });
+});