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-fanout.ts

@@ -186,18 +186,6 @@ export function isSourceStale(src: SourceRow, now = Date.now(), floorMin = FULL_
   return ageMin >= floorMin;
 }
 
-/**
- * #2060: count sources past the per-source cycle freshness floor. Consumed
- * by autopilot's dispatch decision — a stale source forces the fanout path
- * even when the doctor plan is small (score 70–94, plan ≤ 3, est < 300s),
- * so targeted mode can't leave cycle_freshness stale indefinitely.
- * dispatchPerSource's own throttles (skipped_fresh / fanoutMax / failure
- * cooldown) bound the resulting work.
- */
-export function countStaleSources(sources: SourceRow[], now = Date.now(), floorMin = FULL_CYCLE_FLOOR_MIN): number {
-  return sources.filter((s) => isSourceStale(s, now, floorMin)).length;
-}
-
 /**
  * Most recent SUCCESSFUL cycle for a source. Prefers `last_source_cycle_at`
  * (per-source phases, written by the split cycle) and falls back to the legacy

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
@@ -901,27 +905,13 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
         const FULL_CYCLE_FLOOR_MIN = 60;
         const minutesSinceLastFull = (Date.now() - lastFullCycleAt) / 60000;
 
-        // #2060: stale per-source cycle freshness is a dispatch input. Without
-        // it, a brain sitting at score 70–94 with a small targeted plan (≤3
-        // steps, <300s) stays in targeted mode indefinitely and no per-source
-        // cycle is ever dispatched — cycle_freshness never advances. A stale
-        // source forces the fanout path; dispatchPerSource's throttles
-        // (skipped_fresh / fanoutMax / failure cooldown) bound the work.
-        // Fail-open to 0: a read failure must not block dispatch.
-        let staleCycleSources = 0;
-        try {
-          const { countStaleSources } = await import('./autopilot-fanout.ts');
-          staleCycleSources = countStaleSources(await engine.listAllSources({ localPathOnly: true }));
-        } catch { /* fail-open: freshness is a dispatch hint, not a gate */ }
-
         const shouldFullCycle =
           (score >= 95 && plan.length === 0 && minutesSinceLastFull >= FULL_CYCLE_FLOOR_MIN) ||
           plan.length > 3 ||
           estTotal >= 300 ||
-          score < 70 ||
-          staleCycleSources > 0;
+          score < 70;
 
-        const shouldSleep = score >= 95 && plan.length === 0 && minutesSinceLastFull < FULL_CYCLE_FLOOR_MIN && staleCycleSources === 0;
+        const shouldSleep = score >= 95 && plan.length === 0 && minutesSinceLastFull < FULL_CYCLE_FLOOR_MIN;
 
         if (shouldSleep) {
           if (jsonMode) {

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.ts

@@ -854,10 +854,7 @@ interface SyncPhaseResult extends PhaseResult {
 /**
  * Resolve the source id for a brain directory by looking up the sources
  * table. Returns undefined when no registered source matches (falls back
- * to pre-v0.18 global config.sync.* keys) OR when MORE than one source
- * claims the path — an ambiguous match must not scope phases or stamp
- * last_full_cycle_at for an arbitrarily-picked source (the "freshness
- * stamp that lies" this resolution exists to prevent).
+ * to pre-v0.18 global config.sync.* keys).
  */
 async function resolveSourceForDir(
   engine: BrainEngine,
@@ -868,10 +865,10 @@ async function resolveSourceForDir(
   if (brainDir === null) return undefined;
   try {
     const rows = await engine.executeRaw<{ id: string }>(
-      `SELECT id FROM sources WHERE local_path = $1 LIMIT 2`,
+      `SELECT id FROM sources WHERE local_path = $1 LIMIT 1`,
       [brainDir],
     );
-    return rows.length === 1 ? rows[0]!.id : undefined;
+    return rows[0]?.id;
   } catch {
     // sources table might not exist on very old brains — fall through.
     return undefined;
@@ -2368,23 +2365,17 @@ export async function runCycle(
   }
 
   // v0.38 (codex r1 P0-5): persist per-source cycle completion timestamp
-  // when the cycle ran successfully against a resolvable source. Read by
-  // autopilot's per-source freshness gate next tick.
-  //
-  // #1993: keyed off `cycleSourceId` (opts.sourceId ?? the source resolved
-  // from brainDir) — the SAME id the cycle locked + scoped its phases to —
-  // NOT raw opts.sourceId. The autopilot's inline cycle sets brainDir but
-  // passes no explicit sourceId, so keying off opts.sourceId alone never
-  // advanced last_full_cycle_at and cycle_freshness stayed stale even while
-  // the autopilot cycled every interval. Skipped when:
-  //   - no source resolves (engine null, or no checkout AND no opts.sourceId)
+  // when the cycle ran successfully against an explicit source. Read by
+  // autopilot's per-source freshness gate next tick. Skipped when:
+  //   - opts.sourceId is unset (legacy callers — autopilot still here)
+  //   - engine is null (no-DB path)
   //   - status is 'failed' or 'skipped' (don't mark a non-run as fresh)
   //   - dryRun (writes are out of scope)
   //
   // Best-effort: a write failure does NOT change the CycleReport status.
   // The cost of writing the wrong timestamp post-failure is higher than
   // the cost of missing a successful write (next cycle will redo work).
-  if (cycleSourceId && engine && !dryRun && !aborted && (status === 'ok' || status === 'clean' || status === 'partial')) {
+  if (opts.sourceId && engine && !dryRun && !aborted && (status === 'ok' || status === 'clean' || status === 'partial')) {
     try {
       const nowIso = new Date().toISOString();
       // #2194 fix #3 (the cycle split): `last_source_cycle_at` is the NEW gate
@@ -2394,13 +2385,13 @@ export async function runCycle(
       // phases (those gate on autopilot.last_global_at), so writing it on a
       // source-only cycle does not re-introduce the freshness poisoning codex
       // flagged in the rejected skip-based design.
-      await engine.updateSourceConfig(cycleSourceId, {
+      await engine.updateSourceConfig(opts.sourceId, {
         last_source_cycle_at: nowIso,
         last_full_cycle_at: nowIso,
       });
     } catch (e) {
       // Best-effort; cycle already succeeded by the time we get here.
-      console.warn(`[cycle] failed to write last_source_cycle_at for source ${cycleSourceId}: ${e instanceof Error ? e.message : String(e)}`);
+      console.warn(`[cycle] failed to write last_source_cycle_at for source ${opts.sourceId}: ${e instanceof Error ? e.message : String(e)}`);
     }
   }
 

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/autopilot-fanout-wiring.test.ts

@@ -54,20 +54,6 @@ describe('autopilot.ts ↔ dispatchPerSource wiring', () => {
     expect(AUTOPILOT_SRC).toMatch(/lastFullCycleAt\s*=\s*Date\.now\(\)/);
   });
 
-  test('stale per-source cycle freshness is a shouldFullCycle input (#2060)', () => {
-    // Targeted mode (score 70–94, plan ≤3, est <300s) must not be able to
-    // starve per-source cycle dispatch: a stale source (per countStaleSources
-    // over listAllSources) forces the fanout path, and the sleep gate must
-    // not fire while stale sources exist. Without these terms, cycle
-    // freshness never advances for a brain that always lands in targeted mode.
-    expect(AUTOPILOT_SRC).toMatch(/countStaleSources/);
-    const fullCycleDeclIdx = AUTOPILOT_SRC.indexOf('const shouldFullCycle');
-    expect(fullCycleDeclIdx).toBeGreaterThan(-1);
-    const decl = AUTOPILOT_SRC.slice(fullCycleDeclIdx, fullCycleDeclIdx + 700);
-    expect(decl).toMatch(/staleCycleSources\s*>\s*0/);
-    expect(decl).toMatch(/const shouldSleep[^;]*staleCycleSources\s*===\s*0/);
-  });
-
   test('does NOT regress to the single-job dispatch on the full-cycle path', () => {
     // Pre-PR: the shouldFullCycle branch did:
     //   const job = await queue.add('autopilot-cycle', { repoPath }, {

test/autopilot-fanout.test.ts

@@ -14,7 +14,6 @@ import { describe, test, expect } from 'bun:test';
 import {
   readLastFullCycleAt,
   isSourceStale,
-  countStaleSources,
   selectSourcesForDispatch,
   resolveFanoutMax,
   dispatchPerSource,
@@ -75,23 +74,6 @@ describe('isSourceStale', () => {
   });
 });
 
-describe('countStaleSources (#2060 dispatch-decision input)', () => {
-  const NOW = Date.parse('2026-05-22T12:00:00.000Z');
-  test('counts never-cycled + past-floor sources, ignores fresh', () => {
-    const sources = [
-      src('never-cycled'), // stale (null)
-      src('old', new Date(NOW - 2 * 60 * 60_000).toISOString()), // stale (2h)
-      src('fresh', new Date(NOW - 30 * 60_000).toISOString()), // fresh (30min)
-    ];
-    expect(countStaleSources(sources, NOW)).toBe(2);
-  });
-  test('returns 0 for all-fresh and for empty list', () => {
-    const fresh = src('a', new Date(NOW - 10 * 60_000).toISOString());
-    expect(countStaleSources([fresh], NOW)).toBe(0);
-    expect(countStaleSources([], NOW)).toBe(0);
-  });
-});
-
 describe('selectSourcesForDispatch', () => {
   const NOW = Date.parse('2026-05-22T12:00:00.000Z');
   const fresh = (id: string, agoMin: number) =>

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-last-full-cycle-at.test.ts

@@ -3,10 +3,8 @@
  * cycles. Closes codex round-1 P0-5 (write site for last_full_cycle_at
  * was unspecified pre-PR).
  *
- * Conditions for write (keyed off `cycleSourceId` = opts.sourceId ?? the
- * source resolved from brainDir, so the autopilot's inline cycle — brainDir
- * set, no explicit sourceId — also advances the timestamp, #1993):
- *   - a source resolves (explicit sourceId, or brainDir matches a source)
+ * Conditions for write:
+ *   - opts.sourceId is set (legacy callers without sourceId skip the write)
  *   - engine is non-null (no-DB path skips)
  *   - status is 'ok' | 'clean' | 'partial' (failed/skipped don't mark fresh)
  *   - dryRun is false
@@ -92,45 +90,17 @@ describe('runCycle last_full_cycle_at exit hook', () => {
     });
   });
 
-  test('no explicit sourceId but brainDir resolves a source → writes the resolved source timestamp', async () => {
+  test('legacy caller (no sourceId) does NOT write any source timestamp', async () => {
     await withEnv({ GBRAIN_HOME: gbrainHome }, async () => {
-      // The autopilot's inline cycle sets brainDir but passes no sourceId.
-      // runCycle resolves the source from brainDir (local_path match) into
-      // cycleSourceId and stamps last_full_cycle_at for it — otherwise
-      // cycle_freshness reports the brain stale even while the autopilot
-      // cycles every interval (#1993).
-      await seedSource('resolved-from-dir'); // local_path = brainDir
-      expect(await readLastFullCycleAt('resolved-from-dir')).toBeNull();
-
-      const t0 = Date.now();
-      const report = await runCycle(engine, {
-        brainDir,
-        phases: ['lint'],
-      });
-      expect(['ok', 'clean']).toContain(report.status);
-
-      const after = await readLastFullCycleAt('resolved-from-dir');
-      expect(after).not.toBeNull();
-      expect(new Date(after!).getTime()).toBeGreaterThanOrEqual(t0);
-    });
-  });
-
-  test('no sourceId and brainDir matches no source → does not write', async () => {
-    await withEnv({ GBRAIN_HOME: gbrainHome }, async () => {
-      // A source exists but its local_path does NOT match brainDir, so
-      // resolveSourceForDir returns undefined, cycleSourceId is undefined,
-      // and no per-source timestamp is written.
-      await engine.executeRaw(
-        `INSERT INTO sources (id, name, local_path, config, archived, created_at)
-         VALUES ('unmatched', 'unmatched', '/no/such/repo', '{}'::jsonb, false, NOW())
-         ON CONFLICT (id) DO UPDATE SET local_path = EXCLUDED.local_path`,
-        [],
-      );
+      await seedSource('default-like');
+      // No sourceId passed; should remain untouched.
       await runCycle(engine, {
         brainDir,
         phases: ['lint'],
       });
-      expect(await readLastFullCycleAt('unmatched')).toBeNull();
+      // No per-source write happens; default source's config stays empty.
+      const after = await readLastFullCycleAt('default-like');
+      expect(after).toBeNull();
     });
   });
 

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);
+  });
+});