test(supervisor): update runner fixture mock for #2750 lock path

tryAcquireDbLock now acquires via engine.executeRaw (signal-boundable)
and releases via engine.executeRawDirect instead of the sql tagged
template. The fixture's mock engine returned [] from executeRaw, so
every spawned supervisor failed lock acquisition and exited LOCK_HELD
(2), breaking all 8 supervisor integration tests. The mock now returns
the lock row for gbrain_cycle_locks queries and stubs executeRawDirect.

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

src/commands/extract.ts

@@ -433,10 +433,7 @@ export async function extractLinksFromFile(
       async resolve(name: string, dirHint?: string | string[]): Promise<string | null> {
         if (!name) return null;
         const trimmed = name.trim();
-        // Same broadened slug-shape as makeResolver step 1: accepts
-        // digit-leading folders (`90-people/nicolai`) and nested paths.
-        // Exact Set membership guards it — no false positives.
-        if (/\//.test(trimmed) && /^[a-z0-9][a-z0-9/_-]*$/.test(trimmed) && allSlugs.has(trimmed)) {
+        if (/^[a-z][a-z0-9-]*\/[a-z0-9][a-z0-9-]*$/.test(trimmed) && allSlugs.has(trimmed)) {
           return trimmed;
         }
         const hints = Array.isArray(dirHint) ? dirHint : (dirHint ? [dirHint] : []);
@@ -585,17 +582,6 @@ export interface ExtractOpts {
    * before (single-'default'-source brains unaffected).
    */
   sourceId?: string;
-  /**
-   * v0.42 — also extract frontmatter links on the incremental (slugs) path.
-   * `extractForSlugs` extracts BODY links only by default; set this true to also
-   * parse each changed page's frontmatter so `sources:`/`related:` edges stay fresh
-   * when YAML is edited externally and synced in. Applied PER changed page, so the
-   * incremental walk stays bounded (no switch to a full DB scan). Only honored on
-   * the incremental path (`slugs` defined); the full-walk path already covers
-   * frontmatter via its own dispatch. Gated upstream by the config key
-   * `autopilot.incremental_extract_include_frontmatter` (default off).
-   */
-  includeFrontmatter?: boolean;
 }
 
 /**
@@ -634,7 +620,7 @@ export async function runExtractCore(engine: BrainEngine, opts: ExtractOpts): Pr
       // Nothing changed — skip entirely.
       return result;
     }
-    const r = await extractForSlugs(engine, opts.dir, opts.slugs, opts.mode, dryRun, jsonMode, workers, opts.signal, opts.sourceId, opts.includeFrontmatter);
+    const r = await extractForSlugs(engine, opts.dir, opts.slugs, opts.mode, dryRun, jsonMode, workers, opts.signal, opts.sourceId);
     result.links_created = r.links_created;
     result.timeline_entries_created = r.timeline_created;
     result.pages_processed = r.pages;
@@ -1025,11 +1011,6 @@ async function extractForSlugs(
   signal?: AbortSignal,
   // #1747/#1503: stamp resolved brain source id on batch rows (see ExtractOpts.sourceId).
   sourceId?: string,
-  // v0.42: when true, also extract frontmatter links per changed page so
-  // externally-edited YAML (`sources:`/`related:`) stays fresh on the cycle.
-  // Default false preserves the body-only incremental behavior. Gated upstream
-  // by `autopilot.incremental_extract_include_frontmatter`.
-  includeFrontmatter: boolean = false,
 ): Promise<{ links_created: number; timeline_created: number; pages: number }> {
   // Build the full slug set for link resolution (fast: just readdir, no file reads)
   const allFiles = walkMarkdownFiles(brainDir);
@@ -1104,7 +1085,7 @@ async function extractForSlugs(
         const content = readFileSync(fullPath, 'utf-8');
 
         if (doLinks) {
-          const links = await extractLinksFromFile(content, relPath, allSlugs, { globalBasename, includeFrontmatter });
+          const links = await extractLinksFromFile(content, relPath, allSlugs, { globalBasename });
           for (const link of links) {
             if (dryRun) {
               if (!jsonMode) console.log(`  ${link.from_slug} → ${link.to_slug} (${link.link_type})`);

src/commands/jobs.ts

@@ -2059,6 +2059,8 @@ 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/config.ts

@@ -121,18 +121,6 @@ export interface GBrainConfig {
       /** Daily spend cap (USD); bounds drains/day = floor(cap / ~$0.30). Default 2.0. */
       max_usd_per_day?: number;
     };
-    /**
-     * v0.42 — keep frontmatter links fresh on the incremental cycle. The cycle's
-     * extract phase re-extracts only the slugs a sync changed, but `extractForSlugs`
-     * extracts BODY links only — frontmatter (`sources:`/`related:` etc.) link edges
-     * silently drift stale when a page's YAML is edited externally and synced in.
-     * Set true to also extract frontmatter links per changed page each cycle, keeping
-     * externally-edited YAML edges fresh without a full rescan. Default false
-     * (preserves current behavior). Read via the file/env/DB plane in the cycle's
-     * extract dispatch. Disable/enable with
-     * `gbrain config set autopilot.incremental_extract_include_frontmatter <bool>`.
-     */
-    incremental_extract_include_frontmatter?: boolean;
   };
   eval?: {
     /** false disables capture entirely. Defaults to true. */

src/core/cycle.ts

@@ -996,21 +996,6 @@ async function runPhaseExtract(
 ): Promise<PhaseResult> {
   try {
     const { runExtractCore } = await import('../commands/extract.ts');
-    const { loadConfig } = await import('./config.ts');
-    // Default off: the incremental cycle extracts body links only unless the
-    // operator opts in to keeping externally-edited frontmatter links fresh too.
-    // Both planes, file wins (env > file > DB precedence, per loadConfigWithEngine):
-    // `gbrain config set autopilot.incremental_extract_include_frontmatter true`
-    // writes the DB plane (engine.setConfig), so a file-plane-only read here
-    // would make the documented enable command a silent no-op (#2120 class).
-    const fileVal = loadConfig()?.autopilot?.incremental_extract_include_frontmatter;
-    let includeFrontmatter = fileVal === true;
-    if (fileVal === undefined) {
-      try {
-        includeFrontmatter =
-          (await engine.getConfig('autopilot.incremental_extract_include_frontmatter')) === 'true';
-      } catch { /* config table unreadable → default off */ }
-    }
     // Extract is read-mostly against the filesystem + write to links table.
     // Honor dryRun by skipping with a 'skipped' entry: extract doesn't have
     // a clean dry-run mode today and runCycle should be honest about it.
@@ -1031,7 +1016,6 @@ async function runPhaseExtract(
       slugs: changedSlugs,  // undefined = full walk (first run / manual)
       signal,
       sourceId,
-      includeFrontmatter,  // honored on the incremental (slugs) path only
     });
     const linksCreated = result?.links_created ?? 0;
     const timelineCreated = result?.timeline_entries_created ?? 0;

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

@@ -23,6 +23,10 @@
  */
 
 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 {
   /**
@@ -30,13 +34,13 @@ 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.
+   * routine cycle's skip contract. The signal bounds lock acquisition too.
    */
-  withLock: <T>(work: () => Promise<T>) => Promise<T>;
-  /** Process one bounded batch (rediscovers eligibility). Returns counts. */
-  runBatch: () => Promise<{ extracted: number; skipped: number }>;
+  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 }>;
   /** Count remaining eligible-but-unextracted pages, or null on query error. */
-  countRemaining: () => Promise<number | null>;
+  countRemaining: (signal: AbortSignal) => Promise<number | null>;
   /** Injectable clock. Production: Date.now. */
   now: () => number;
   /** Optional progress sink (one line per batch). */
@@ -48,6 +52,8 @@ 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 {
@@ -68,35 +74,79 @@ export async function runExtractAtomsDrain(
   opts: ExtractAtomsDrainOpts,
 ): Promise<ExtractAtomsDrainResult> {
   const maxBatches = opts.maxBatches ?? 1000;
-  return deps.withLock(async () => {
-    const deadline = deps.now() + opts.windowMs;
+  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 () => {
     let extracted = 0;
     let skipped = 0;
     let batches = 0;
     let stopped: ExtractAtomsDrainResult['stopped'] = 'window';
 
-    while (deps.now() < deadline) {
+    while (deps.now() < deadline && !signal.aborted) {
       if (batches >= maxBatches) { stopped = 'max_batches'; break; }
 
-      const before = await deps.countRemaining();
+      let before: number | null;
+      try {
+        before = await deps.countRemaining(signal);
+      } catch (err) {
+        if (signal.aborted) break;
+        throw err;
+      }
       if (before === 0) { stopped = 'drained'; break; }
 
-      const r = await deps.runBatch();
+      // 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;
+      }
       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; }
     }
 
-    const remaining = await deps.countRemaining();
+    // 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;
+      }
+    }
     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) ──────────────────────
@@ -134,6 +184,8 @@ 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(
@@ -149,12 +201,17 @@ export async function runExtractAtomsDrainForSource(
 
   return runExtractAtomsDrain(
     {
-      withLock: (work) => withRefreshingLock(engine, lockId, work, { ttlMinutes: 5 }),
-      runBatch: async () => {
+      withLock: (work, signal) => withRefreshingLock(engine, lockId, work, {
+        ttlMinutes: 5,
+        signal,
+        releaseTimeoutMs: LOCK_RELEASE_GRACE_MS,
+      }),
+      runBatch: async (signal) => {
         const r = await runPhaseExtractAtoms(engine, {
           sourceId: extractionSourceId,
           dryRun: false,
           brainDir: opts.brainDir,
+          abortSignal: signal,
         });
         const d = (r.details ?? {}) as Record<string, unknown>;
         return {
@@ -162,10 +219,14 @@ export async function runExtractAtomsDrainForSource(
           skipped: Number(d.duplicates_skipped ?? 0),
         };
       },
-      countRemaining: () => countExtractAtomsBacklog(engine, extractionSourceId),
+      countRemaining: (signal) => countExtractAtomsBacklog(engine, extractionSourceId, signal),
       now: Date.now,
       onBatch: opts.onBatch,
     },
-    { windowMs: opts.windowSeconds * 1000, maxBatches: opts.maxBatches },
+    {
+      windowMs: opts.windowSeconds * 1000,
+      maxBatches: opts.maxBatches,
+      abortSignal: opts.abortSignal,
+    },
   );
 }

src/core/cycle/extract-atoms.ts

@@ -58,6 +58,10 @@ 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 = [
@@ -155,6 +159,13 @@ 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 {
@@ -212,6 +223,7 @@ export async function discoverExtractablePages(
   engine: BrainEngine,
   sourceId: string,
   affectedSlugs?: string[],
+  abortSignal?: AbortSignal,
 ): Promise<DiscoveredPage[]> {
   const hasFilter = Array.isArray(affectedSlugs) && affectedSlugs.length > 0;
   const sql = `
@@ -251,13 +263,16 @@ export async function discoverExtractablePages(
       slug: string;
       compiled_truth: string;
       content_hash: string;
-    }>(sql, params);
+    }>(sql, params, { signal: abortSignal });
     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
@@ -282,6 +297,7 @@ 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
@@ -321,9 +337,10 @@ 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);
+    const rows = await engine.executeRaw<{ cnt: string | number }>(sql, params, { signal: abortSignal });
     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;
@@ -350,6 +367,7 @@ export async function atomsExistingForHashes(
   engine: BrainEngine,
   sourceId: string,
   contentHash16s: string[],
+  abortSignal?: AbortSignal,
 ): Promise<Set<string>> {
   if (contentHash16s.length === 0) return new Set();
   try {
@@ -361,9 +379,11 @@ 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();
@@ -384,6 +404,7 @@ 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
@@ -425,7 +446,7 @@ export async function runPhaseExtractAtoms(
   if (opts._pages !== undefined) {
     pages = opts._pages;
   } else {
-    pages = await discoverExtractablePages(engine, sourceId, opts.affectedSlugs);
+    pages = await discoverExtractablePages(engine, sourceId, opts.affectedSlugs, opts.abortSignal);
   }
 
   // 2. Apply transcript-side source-hash idempotency in ONE batch query
@@ -437,7 +458,7 @@ 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);
+  const existingHashes = await atomsExistingForHashes(engine, sourceId, allHashes16, opts.abortSignal);
   for (const t of transcripts) {
     if (existingHashes.has(t.contentHash.slice(0, 16))) {
       duplicatesSkipped++;
@@ -501,6 +522,7 @@ 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
@@ -526,6 +548,12 @@ 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++;
@@ -544,16 +572,22 @@ 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 + $4/M output
-      estimatedSpendUsd +=
-        (result.usage.input_tokens * 0.8 + result.usage.output_tokens * 4.0) / 1_000_000;
-
       const atoms = parseAtomsResponse(result.text);
       if (atoms.length === 0) {
         if (item.kind === 'transcript') transcriptsProcessed++;
@@ -592,7 +626,7 @@ export async function runPhaseExtractAtoms(
               },
               timeline: '',
             },
-            { sourceId },
+            { sourceId, signal: opts.abortSignal },
           );
           totalAtomsExtracted++;
         }
@@ -605,6 +639,11 @@ export async function runPhaseExtractAtoms(
       // Reporter rate-limits to ~1 line/sec; safe to tick every iter.
       opts.progress?.tick(1, `${totalAtomsExtracted} atoms / ${duplicatesSkipped} skipped`);
     } catch (err) {
+      // A deadline abort is a partial result, not a per-item failure.
+      if (opts.abortSignal?.aborted) {
+        deadlineAborted = true;
+        break;
+      }
       failures.push({
         source: originLabel,
         error: err instanceof Error ? err.message : String(err),
@@ -615,6 +654,12 @@ export async function runPhaseExtractAtoms(
   // v0.42 Wave B2: write extract receipt + rollup row when the phase
   // actually extracted atoms. Both are best-effort per F-OUT-19 —
   // audit-trail / search-visibility surfaces don't block the phase result.
+  //
+  // #2750: bookkeeping runs on a FRESH short grace signal, never the caller's
+  // work deadline — the deadline may have already fired (partial run) and
+  // committed atoms must not lose their receipt/cost trail; but the writes
+  // stay bounded so the overrun is capped at the grace window.
+  const bookkeepingSignal = opts.dryRun ? undefined : AbortSignal.timeout(BOOKKEEPING_GRACE_MS);
   if (!opts.dryRun && totalAtomsExtracted > 0) {
     const runId = `atoms-${Date.now().toString(36)}-${sourceId.slice(0, 4)}`;
     try {
@@ -629,19 +674,24 @@ 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) {
-    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,
-    });
+    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}`);
+    }
   }
 
   return {
@@ -670,6 +720,7 @@ export async function runPhaseExtractAtoms(
       budget_usd: budgetCap,
       source_id: sourceId,
       dry_run: opts.dryRun ?? false,
+      deadline_aborted: deadlineAborted,
     },
   };
 }

src/core/db-lock.ts

@@ -26,7 +26,8 @@ import type { BrainEngine } from './engine.ts';
 
 export interface DbLockHandle {
   id: string;
-  release: () => Promise<void>;
+  /** Optional signal bounds the release DELETE (deadline-bound callers). */
+  release: (signal?: AbortSignal) => Promise<void>;
   refresh: () => Promise<void>;
 }
 
@@ -173,6 +174,7 @@ 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();
@@ -205,20 +207,26 @@ 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.
-    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
-    `;
+    // #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() - $5 * INTERVAL '1 second')
+       RETURNING id`,
+      [lockId, pid, host, ttl, stealGraceSeconds],
+      { signal: opts.signal },
+    );
     if (rows.length === 0) return null;
     const deregister = registerCleanup(`db-lock:${lockId}`, async () => {
       await sql`
@@ -241,12 +249,17 @@ export async function tryAcquireDbLock(
           [ttl, lockId, pid],
         );
       },
-      release: async () => {
+      release: async (signal?: AbortSignal) => {
         deregister();
-        await sql`
-          DELETE FROM gbrain_cycle_locks
-          WHERE id = ${lockId} AND holder_pid = ${pid}
-        `;
+        // 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 },
+        );
       },
     };
   }
@@ -303,6 +316,11 @@ 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,
@@ -796,6 +814,10 @@ 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;
 }
 
 /**
@@ -815,7 +837,7 @@ 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);
+  const handle = await tryAcquireDbLock(engine, lockId, ttlMinutes, { signal: opts.signal });
   if (!handle) throw new LockUnavailableError(lockId);
 
   let healthOk = true;
@@ -854,7 +876,13 @@ export async function withRefreshingLock<T>(
     return await work();
   } finally {
     clearInterval(interval);
-    try { await handle.release(); } catch { /* idempotent */ }
+    // #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 */ }
     if (!healthOk) {
       // Surface that the heartbeat detected backend trouble — caller can
       // log to the connection-events audit if desired.

src/core/engine.ts

@@ -696,8 +696,16 @@ 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 }): Promise<Page>;
+  putPage(
+    slug: string,
+    page: PageInput,
+    opts?: { sourceId?: string; signal?: AbortSignal },
+  ): Promise<Page>;
   /**
    * v0.41.13 (#1309) — identity-based dedup pre-check for the import pipeline.
    *

src/core/extract/receipt-writer.ts

@@ -187,6 +187,7 @@ 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}`;
@@ -201,7 +202,7 @@ export async function writeReceipt(
       compiled_truth,
       frontmatter,
     },
-    { sourceId: input.source_id },
+    { sourceId: input.source_id, signal: opts?.signal },
   );
 
   return { slug, page };

src/core/extract/rollup-writer.ts

@@ -70,6 +70,7 @@ 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;
@@ -96,9 +97,12 @@ 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/link-extraction.ts

@@ -942,17 +942,8 @@ export function makeResolver(
 
       const hints = Array.isArray(dirHint) ? dirHint : (dirHint ? [dirHint] : []);
 
-      // Step 1: already a slug? Try an exact page lookup for any slug-shaped
-      // value (contains '/', slug charset). Broadened beyond the original
-      // single-segment lowercase-leading form (`^[a-z][a-z0-9-]*\/[a-z0-9]...`)
-      // to also accept digit-leading folders (`90-people/nicolai`,
-      // `01-trading/...`) and nested paths (`a/b/c`) — common in PARA-numbered
-      // vaults. This is an EXACT getPage match only — no fuzzy — so it never
-      // produces a false positive; a non-existent slug just falls through to
-      // the steps below. Fixes frontmatter `related: [[dir/slug]]` values
-      // (unwrapped by unwrapWikilink) that name a real page the strict regex
-      // could not reach and whose full-path fuzzy score is below threshold.
-      if (/\//.test(trimmed) && /^[a-z0-9][a-z0-9/_-]*$/.test(trimmed)) {
+      // Step 1: already a slug? (dir/name shape, lowercase, hyphenated)
+      if (/^[a-z][a-z0-9-]*\/[a-z0-9][a-z0-9-]*$/.test(trimmed)) {
         const page = await engine.getPage(trimmed);
         if (page) {
           cache.set(cacheKey, trimmed);
@@ -1012,25 +1003,6 @@ export function makeResolver(
 
 // ─── Frontmatter extractor ──────────────────────────────────────
 
-/**
- * Unwrap an Obsidian `[[wikilink]]` frontmatter value to its bare link
- * target so the resolver (which expects bare titles / dir slugs) can match
- * it. Mainstream Obsidian authors frontmatter links as `related: ["[[Page]]"]`;
- * without this, the resolver treats the brackets as part of the value and a
- * `[[90-people/nicolai]]` is normalized into `90peoplenicolai`, so it never
- * resolves. Strips a trailing `|alias`, `#heading`, or `^block` suffix — the
- * link target only. The regex is anchored to a wholly-wrapped value
- * (`^\s*\[\[…\]\]\s*$`), so bare titles and any value not fully wrapped pass
- * through unchanged and existing behavior is preserved exactly.
- */
-export function unwrapWikilink(value: string): string {
-  const match = /^\s*\[\[(.+?)\]\]\s*$/.exec(value);
-  if (!match) return value;
-  // Take the link target: drop |alias, then #heading / ^block suffixes.
-  const target = match[1].split('|')[0].split('#')[0].split('^')[0];
-  return target.trim();
-}
-
 export interface UnresolvedFrontmatterRef {
   /** The frontmatter field name. */
   field: string;
@@ -1088,12 +1060,7 @@ export async function extractFrontmatterLinks(
         }
         if (!name) continue;   // skip numbers, nulls, malformed objects
 
-        // Accept Obsidian `[[wikilink]]` values in frontmatter link fields by
-        // unwrapping to the bare target before resolution. Bare titles pass
-        // through unchanged; the original `name` is preserved for the
-        // unresolved report and edge context.
-        const linkTarget = unwrapWikilink(name);
-        const resolved = await resolver.resolve(linkTarget, mapping.dirHint);
+        const resolved = await resolver.resolve(name, mapping.dirHint);
         if (!resolved) {
           unresolved.push({ field, name });
           continue;

src/core/pglite-engine.ts

@@ -1003,7 +1003,15 @@ export class PGLiteEngine implements BrainEngine {
     return { slug: r.slug, id: Number(r.id) };
   }
 
-  async putPage(slug: string, page: PageInput, opts?: { sourceId?: string }): Promise<Page> {
+  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');
     slug = validateSlug(slug);
     const hash = page.content_hash || contentHash(page);
     const frontmatter = page.frontmatter || {};

src/core/postgres-engine.ts

@@ -72,6 +72,32 @@ 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,
@@ -1061,7 +1087,12 @@ export class PostgresEngine implements BrainEngine {
     });
   }
 
-  async putPage(slug: string, page: PageInput, opts?: { sourceId?: string }): Promise<Page> {
+  async putPage(
+    slug: string,
+    page: PageInput,
+    opts?: { sourceId?: string; signal?: AbortSignal },
+  ): Promise<Page> {
+    if (opts?.signal?.aborted) throw new DOMException('aborted', 'AbortError');
     slug = validateSlug(slug);
     const sql = this.sql;
     const hash = page.content_hash || contentHash(page);
@@ -1096,7 +1127,7 @@ 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 rows = await sql`
+    const pending = 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
@@ -1119,6 +1150,22 @@ 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]);
   }
 
@@ -5807,11 +5854,16 @@ 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 this.connectionManager.ddl()
+      ? await waitForSignal(this.connectionManager.ddl(), opts?.signal)
       : this.sql;
     return this.runUnsafe<T>(conn, sql, params, opts);
   }

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

@@ -17,6 +17,7 @@ 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;
 
@@ -177,6 +178,180 @@ 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

@@ -43,26 +43,135 @@ describe('runExtractAtomsDrain (issue #1678)', () => {
     expect(batches).toBe(3);
   });
 
-  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)];
+  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;
     const result = await runExtractAtomsDrain(
       {
         withLock: passThroughLock,
         countRemaining: async () => 5, // never drains
-        runBatch: async () => ({ extracted: 1, skipped: 0 }),
-        now,
+        runBatch: async () => {
+          now += 60;
+          return { extracted: 1, skipped: 0 };
+        },
+        now: () => now,
       },
       { windowMs: 100 },
     );
     expect(result.stopped).toBe('window');
-    expect(result.remaining).toBe(5);
+    expect(result.remaining).toBeNull();
     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(
@@ -133,4 +242,17 @@ 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/extract-incremental.test.ts

@@ -191,37 +191,3 @@ describe('runExtractCore — incremental cycle path (#417)', () => {
     expect(result.links_created).toBeGreaterThan(0);
   });
 });
-describe('runExtractCore — incremental frontmatter gate (includeFrontmatter)', () => {
-  // alice has a `source:` frontmatter edge but NO body links. The incremental
-  // path extracts body links only by default, so the frontmatter edge is the
-  // sole signal that distinguishes the gate off vs on.
-  const aliceFm = '---\nsource: companies/acme-example\n---\n# alice';
-
-  test('9. default (flag omitted) does NOT extract frontmatter links on the incremental path', async () => {
-    await seedPage('companies/acme-example', '# acme');
-    await seedPage('people/alice-example', aliceFm);
-    const result = await runExtractCore(engine as unknown as BrainEngine, {
-      mode: 'all',
-      dir: tempDir,
-      slugs: ['people/alice-example'],
-    });
-    // alice's only potential edge is her frontmatter `source:`; with the gate off
-    // it must not be extracted (preserves the body-only incremental behavior).
-    expect(result.pages_processed).toBe(1);
-    expect(result.links_created).toBe(0);
-  });
-
-  test('10. includeFrontmatter: true extracts the frontmatter link on the incremental path', async () => {
-    await seedPage('companies/acme-example', '# acme');
-    await seedPage('people/alice-example', aliceFm);
-    const result = await runExtractCore(engine as unknown as BrainEngine, {
-      mode: 'all',
-      dir: tempDir,
-      slugs: ['people/alice-example'],
-      includeFrontmatter: true,
-    });
-    // Same page, gate on → the `source:` frontmatter edge is now extracted.
-    expect(result.pages_processed).toBe(1);
-    expect(result.links_created).toBeGreaterThan(0);
-  });
-});

test/extract.test.ts

@@ -76,18 +76,6 @@ describe('extractLinksFromFile', () => {
     }
   });
 
-  it('resolves wrapped [[wikilink]] digit-leading slug-path in frontmatter (fs resolver, broadened step 1)', async () => {
-    // Same bug class as makeResolver step 1 (#1983): the fs resolver's strict
-    // `^[a-z]…` slug regex rejected digit-leading / nested paths, so a PARA-vault
-    // `related: "[[90-people/nicolai]]"` never resolved even though the page exists.
-    const content = '---\nrelated: "[[90-people/nicolai]]"\ntype: concept\n---\nContent.';
-    const allSlugs = new Set(['wiki/note', '90-people/nicolai']);
-    const links = await extractLinksFromFile(content, 'wiki/note.md', allSlugs, { includeFrontmatter: true });
-    const related = links.filter(l => l.link_type === 'related_to');
-    expect(related).toHaveLength(1);
-    expect(related[0].to_slug).toBe('90-people/nicolai');
-  });
-
   it('frontmatter extraction is default OFF (back-compat)', async () => {
     // Without includeFrontmatter, fs-source no longer auto-extracts frontmatter.
     // Matches db-source behavior. User opts in with --include-frontmatter flag.

test/fixtures/supervisor-runner.ts

@@ -24,15 +24,18 @@ 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() 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.
+// #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.
 const sqlStub = (..._args: unknown[]) => Promise.resolve([{ id: 'supervisor-lock' }]);
 const mockEngine: Partial<BrainEngine> = {
   kind: 'postgres' as const,
-  executeRaw: async () => [],
+  executeRaw: async (query: string) =>
+    query.includes('gbrain_cycle_locks') ? [{ id: 'supervisor-lock' }] : [],
+  executeRawDirect: async () => [],
   sql: sqlStub,
 } as unknown as BrainEngine;
 

test/link-extraction.test.ts

@@ -9,7 +9,6 @@ import {
   parseTimelineEntries,
   isAutoLinkEnabled,
   FRONTMATTER_LINK_MAP,
-  unwrapWikilink,
   type SlugResolver,
 } from '../src/core/link-extraction.ts';
 import type { BrainEngine } from '../src/core/engine.ts';
@@ -1292,175 +1291,3 @@ describe('parseTimelineEntries — Format 3: inline [Source: ..., YYYY-MM-DD] ci
     expect(parseTimelineEntries('[Source: import batch, 2025-07-01]')).toHaveLength(0);
   });
 });
-// ─── Frontmatter [[wikilink]] + slug-path resolution ──────────────────────
-// Mainstream Obsidian authors frontmatter links as `related: ["[[Page]]"]`,
-// and PARA-numbered vaults use digit-leading / nested slug paths like
-// `[[90-people/nicolai]]`. Both were silently dropped: brackets were treated
-// as part of the value and the step-1 slug regex (`^[a-z]…`) rejected
-// digit-leading / nested paths, while full-path fuzzy scored below threshold.
-// Fix: unwrapWikilink() before resolution + an exact getPage() for any
-// slug-shaped value (exact-match only → no false positives).
-
-describe('unwrapWikilink', () => {
-  test('wrapped title → bare title', () => {
-    expect(unwrapWikilink('[[Monday Range]]')).toBe('Monday Range');
-  });
-  test('wrapped slug-path (digit-leading folder) → bare slug', () => {
-    expect(unwrapWikilink('[[90-people/nicolai]]')).toBe('90-people/nicolai');
-  });
-  test('wrapped nested slug-path → bare slug', () => {
-    expect(unwrapWikilink('[[01-trading/wiki/strategies/opening-range-breakout]]'))
-      .toBe('01-trading/wiki/strategies/opening-range-breakout');
-  });
-  test('strips |alias', () => {
-    expect(unwrapWikilink('[[90-people/nicolai|Nicolai]]')).toBe('90-people/nicolai');
-  });
-  test('strips #heading', () => {
-    expect(unwrapWikilink('[[Page#Section]]')).toBe('Page');
-  });
-  test('strips ^block', () => {
-    expect(unwrapWikilink('[[Page^abc123]]')).toBe('Page');
-  });
-  test('surrounding whitespace tolerated', () => {
-    expect(unwrapWikilink('  [[Page]]  ')).toBe('Page');
-  });
-  test('bare title passes through unchanged', () => {
-    expect(unwrapWikilink('Monday Range')).toBe('Monday Range');
-  });
-  test('bare slug passes through unchanged', () => {
-    expect(unwrapWikilink('90-people/nicolai')).toBe('90-people/nicolai');
-  });
-  test('partially-wrapped value is NOT unwrapped (anchored)', () => {
-    // Not a wholly-wrapped value → left intact so existing behavior is exact.
-    expect(unwrapWikilink('see [[Page]] for detail')).toBe('see [[Page]] for detail');
-  });
-});
-
-describe('makeResolver — slug-path exact getPage (step 1 broadened)', () => {
-  function fakeEngine(
-    slugs: string[],
-    fuzzyMap: Map<string, { slug: string; similarity: number }> = new Map(),
-  ): BrainEngine {
-    const lookup = new Set(slugs);
-    return {
-      async getPage(slug: string) { return lookup.has(slug) ? { slug } as any : null; },
-      async findByTitleFuzzy(name: string) { return fuzzyMap.get(name) ?? null; },
-      async searchKeyword() { return []; },
-    } as unknown as BrainEngine;
-  }
-
-  test('digit-leading folder slug resolves via exact getPage', async () => {
-    const r = makeResolver(fakeEngine(['90-people/nicolai']));
-    expect(await r.resolve('90-people/nicolai')).toBe('90-people/nicolai');
-  });
-
-  test('nested (>2 segment) slug resolves via exact getPage', async () => {
-    const r = makeResolver(fakeEngine(['01-trading/wiki/strategies/opening-range-breakout']));
-    expect(await r.resolve('01-trading/wiki/strategies/opening-range-breakout'))
-      .toBe('01-trading/wiki/strategies/opening-range-breakout');
-  });
-
-  test('regression: single-segment lowercase slug still resolves', async () => {
-    const r = makeResolver(fakeEngine(['people/pedro']));
-    expect(await r.resolve('people/pedro')).toBe('people/pedro');
-  });
-
-  test('exact-only: slug-shaped value with no matching page falls through (no false positive)', async () => {
-    // `90-people/ghost` is slug-shaped but absent → step-1 getPage misses,
-    // no fuzzy hit → null. Never invents an edge.
-    const r = makeResolver(fakeEngine(['90-people/nicolai']));
-    expect(await r.resolve('90-people/ghost')).toBeNull();
-  });
-
-  test('non-slug value still routes to fuzzy', async () => {
-    const r = makeResolver(fakeEngine(
-      ['01-trading/monday-range'],
-      new Map([['Monday Range', { slug: '01-trading/monday-range', similarity: 1 }]]),
-    ));
-    expect(await r.resolve('Monday Range')).toBe('01-trading/monday-range');
-  });
-});
-
-describe('extractFrontmatterLinks — [[wikilink]] related: values (end-to-end)', () => {
-  function fakeEngine(
-    slugs: string[],
-    fuzzyMap: Map<string, { slug: string; similarity: number }> = new Map(),
-  ): BrainEngine {
-    const lookup = new Set(slugs);
-    return {
-      async getPage(slug: string) { return lookup.has(slug) ? { slug } as any : null; },
-      async findByTitleFuzzy(name: string) { return fuzzyMap.get(name) ?? null; },
-      async searchKeyword() { return []; },
-    } as unknown as BrainEngine;
-  }
-
-  test('wrapped slug-path related: resolves (the core win)', async () => {
-    const resolver = makeResolver(fakeEngine(['90-people/nicolai']));
-    const { candidates, unresolved } = await extractFrontmatterLinks(
-      'wiki/originals/ideas/note', 'note' as never,
-      { related: '[[90-people/nicolai]]' }, resolver,
-    );
-    expect(unresolved).toHaveLength(0);
-    expect(candidates).toHaveLength(1);
-    expect(candidates[0]).toMatchObject({
-      fromSlug: 'wiki/originals/ideas/note',
-      targetSlug: '90-people/nicolai',
-      linkType: 'related_to',
-      linkSource: 'frontmatter',
-    });
-  });
-
-  test('wrapped nested slug-path related: resolves', async () => {
-    const resolver = makeResolver(fakeEngine(['01-trading/wiki/strategies/opening-range-breakout']));
-    const { candidates } = await extractFrontmatterLinks(
-      'wiki/note', 'note' as never,
-      { related: ['[[01-trading/wiki/strategies/opening-range-breakout]]'] }, resolver,
-    );
-    expect(candidates).toHaveLength(1);
-    expect(candidates[0].targetSlug).toBe('01-trading/wiki/strategies/opening-range-breakout');
-  });
-
-  test('wrapped value with |alias resolves to the target', async () => {
-    const resolver = makeResolver(fakeEngine(['90-people/nicolai']));
-    const { candidates } = await extractFrontmatterLinks(
-      'wiki/note', 'note' as never,
-      { related: '[[90-people/nicolai|Nicolai]]' }, resolver,
-    );
-    expect(candidates).toHaveLength(1);
-    expect(candidates[0].targetSlug).toBe('90-people/nicolai');
-  });
-
-  test('regression: bare slug related: still resolves', async () => {
-    const resolver = makeResolver(fakeEngine(['90-people/nicolai']));
-    const { candidates } = await extractFrontmatterLinks(
-      'wiki/note', 'note' as never,
-      { related: '90-people/nicolai' }, resolver,
-    );
-    expect(candidates).toHaveLength(1);
-    expect(candidates[0].targetSlug).toBe('90-people/nicolai');
-  });
-
-  test('regression: wrapped title resolves via fuzzy (brackets harmless)', async () => {
-    const resolver = makeResolver(fakeEngine(
-      ['01-trading/monday-range'],
-      new Map([['Monday Range', { slug: '01-trading/monday-range', similarity: 1 }]]),
-    ));
-    const { candidates } = await extractFrontmatterLinks(
-      'wiki/note', 'note' as never,
-      { related: '[[Monday Range]]' }, resolver,
-    );
-    expect(candidates).toHaveLength(1);
-    expect(candidates[0].targetSlug).toBe('01-trading/monday-range');
-  });
-
-  test('unknown wrapped slug → unresolved (no crash), original value preserved', async () => {
-    const resolver = makeResolver(fakeEngine(['90-people/nicolai']));
-    const { candidates, unresolved } = await extractFrontmatterLinks(
-      'wiki/note', 'note' as never,
-      { related: '[[99-archive/does-not-exist]]' }, resolver,
-    );
-    expect(candidates).toHaveLength(0);
-    expect(unresolved).toHaveLength(1);
-    expect(unresolved[0]).toEqual({ field: 'related', name: '[[99-archive/does-not-exist]]' });
-  });
-});

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

@@ -98,14 +98,39 @@ describe('PostgresEngine.executeRawDirect — routing decision (PR #1816)', () =
   });
 
   test('already-aborted signal short-circuits with AbortError before routing the query', async () => {
-    const readConn = fakeSql('read');
+    let unsafeCalls = 0;
+    let ddlCalls = 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 = 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);
   });
 });