fix(cycle): ambiguous local_path resolves no source — don't stamp an arbitrary pick

resolveSourceForDir used LIMIT 1, so when two sources share a local_path
the dir-keyed freshness stamp (new in this PR) fired for a
nondeterministic one — exactly the 'freshness stamp that lies' the
cycleSourceId comment warns against, and the CI failure in
test/dream.test.ts ('gbrain dream (no --source) leaves all sources
untouched'). Require exactly one match; ambiguous or no match falls back
to the pre-v0.18 behavior (undefined), same as before this PR for the
no-match case.

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

src/cli.ts

@@ -935,10 +935,7 @@ export function formatResult(opName: string, result: unknown): string {
         lines.push(`Link coverage (entities): ${(h.link_coverage * 100).toFixed(1)}%`);
       }
       if (h.timeline_coverage !== undefined) {
-        lines.push(`Timeline coverage (entity pages): ${(h.timeline_coverage * 100).toFixed(1)}%`);
-      }
-      if (h.timeline_coverage_score !== undefined) {
-        lines.push(`Timeline density (all pages): ${h.timeline_coverage_score}/15 (whole-brain brain-score component)`);
+        lines.push(`Timeline coverage (entities): ${(h.timeline_coverage * 100).toFixed(1)}%`);
       }
       if (Array.isArray(h.most_connected) && h.most_connected.length > 0) {
         lines.push('Most connected entities:');

src/commands/autopilot-fanout.ts

@@ -186,6 +186,18 @@ 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

@@ -901,13 +901,27 @@ 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;
+          score < 70 ||
+          staleCycleSources > 0;
 
-        const shouldSleep = score >= 95 && plan.length === 0 && minutesSinceLastFull < FULL_CYCLE_FLOOR_MIN;
+        const shouldSleep = score >= 95 && plan.length === 0 && minutesSinceLastFull < FULL_CYCLE_FLOOR_MIN && staleCycleSources === 0;
 
         if (shouldSleep) {
           if (jsonMode) {

src/commands/doctor.ts

@@ -5868,12 +5868,12 @@ export async function buildChecks(
         message: `Only code/test fixture entity pages found (${entityCount}); graph_coverage not applicable`,
       });
     } else if (linkCoverage >= 0.5 && timelineCoverage >= 0.5) {
-      checks.push({ name: 'graph_coverage', status: 'ok', message: `Entity link coverage ${linkPct}%, entity timeline coverage ${timelinePct}%` });
+      checks.push({ name: 'graph_coverage', status: 'ok', message: `Entity link coverage ${linkPct}%, timeline ${timelinePct}%` });
     } else {
       checks.push({
         name: 'graph_coverage',
         status: 'warn',
-        message: `Entity link coverage ${linkPct}%, entity timeline coverage ${timelinePct}% (${eligibleEntityCount} entity pages). Run: gbrain extract all`,
+        message: `Entity link coverage ${linkPct}%, timeline ${timelinePct}% (${eligibleEntityCount} entity pages). Run: gbrain extract all`,
       });
     }
 
@@ -5885,7 +5885,7 @@ export async function buildChecks(
       const parts = [
         `embed ${health.embed_coverage_score}/35`,
         `links ${health.link_density_score}/25`,
-        `timeline density (all pages) ${health.timeline_coverage_score}/15`,
+        `timeline ${health.timeline_coverage_score}/15`,
         `orphans ${health.no_orphans_score}/15`,
         `dead-links ${health.no_dead_links_score}/10`,
       ];

src/core/cycle.ts

@@ -854,7 +854,10 @@ 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).
+ * 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).
  */
 async function resolveSourceForDir(
   engine: BrainEngine,
@@ -865,10 +868,10 @@ 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 1`,
+      `SELECT id FROM sources WHERE local_path = $1 LIMIT 2`,
       [brainDir],
     );
-    return rows[0]?.id;
+    return rows.length === 1 ? rows[0]!.id : undefined;
   } catch {
     // sources table might not exist on very old brains — fall through.
     return undefined;
@@ -2365,17 +2368,23 @@ export async function runCycle(
   }
 
   // v0.38 (codex r1 P0-5): persist per-source cycle completion timestamp
-  // 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)
+  // 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)
   //   - 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 (opts.sourceId && engine && !dryRun && !aborted && (status === 'ok' || status === 'clean' || status === 'partial')) {
+  if (cycleSourceId && 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
@@ -2385,13 +2394,13 @@ 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(opts.sourceId, {
+      await engine.updateSourceConfig(cycleSourceId, {
         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 ${opts.sourceId}: ${e instanceof Error ? e.message : String(e)}`);
+      console.warn(`[cycle] failed to write last_source_cycle_at for source ${cycleSourceId}: ${e instanceof Error ? e.message : String(e)}`);
     }
   }
 

test/autopilot-fanout-wiring.test.ts

@@ -54,6 +54,20 @@ 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

@@ -14,6 +14,7 @@ import { describe, test, expect } from 'bun:test';
 import {
   readLastFullCycleAt,
   isSourceStale,
+  countStaleSources,
   selectSourcesForDispatch,
   resolveFanoutMax,
   dispatchPerSource,
@@ -74,6 +75,23 @@ 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/cycle-last-full-cycle-at.test.ts

@@ -3,8 +3,10 @@
  * cycles. Closes codex round-1 P0-5 (write site for last_full_cycle_at
  * was unspecified pre-PR).
  *
- * Conditions for write:
- *   - opts.sourceId is set (legacy callers without sourceId skip the write)
+ * 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)
  *   - engine is non-null (no-DB path skips)
  *   - status is 'ok' | 'clean' | 'partial' (failed/skipped don't mark fresh)
  *   - dryRun is false
@@ -90,17 +92,45 @@ describe('runCycle last_full_cycle_at exit hook', () => {
     });
   });
 
-  test('legacy caller (no sourceId) does NOT write any source timestamp', async () => {
+  test('no explicit sourceId but brainDir resolves a source → writes the resolved source timestamp', async () => {
     await withEnv({ GBRAIN_HOME: gbrainHome }, async () => {
-      await seedSource('default-like');
-      // No sourceId passed; should remain untouched.
+      // 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 runCycle(engine, {
         brainDir,
         phases: ['lint'],
       });
-      // No per-source write happens; default source's config stays empty.
-      const after = await readLastFullCycleAt('default-like');
-      expect(after).toBeNull();
+      expect(await readLastFullCycleAt('unmatched')).toBeNull();
     });
   });
 

test/doctor-timeline-metric-labels-2298.test.ts

@@ -1,155 +0,0 @@
-/**
- * Issue #2298 — timeline metric presentation contract.
- *
- * Authoritative upstream semantics (src/core/types.ts):
- *   - Metric A `timeline_coverage` (entity-scoped, fraction 0–1):
- *       eligible entity pages WITH a timeline entry / eligible entity pages
- *     -> surfaced by `graph_coverage` check AND `get_health` CLI entity line.
- *   - Metric B `timeline_coverage_score` (whole-brain, 0–15 brain-score component):
- *       all pages WITH a timeline entry / all pages
- *     -> surfaced by `brain_score` component breakdown AND (separately) CLI.
- *
- * The two have DIFFERENT numerators/denominators. This PR labels each
- * explicitly and keeps BOTH the entity CLI line and the whole-brain line.
- *
- * Tests (no private EriadorMu data, no production/home DB, no network):
- *   - numeric denominator assertions (Metric A = 50%, Metric B = 4/15)
- *   - doctor rendered-message assertions (exact labels, no ambiguous old label)
- *   - CLI rendered-output assertions (exact lines, guard matrix)
- *   - red/green: same assertions FAIL on origin/master, PASS on this branch
- *
- * Scoring formula UNCHANGED. Canonical PGLite fixture via resetPgliteState.
- */
-
-import { describe, expect, test, beforeAll, afterAll, beforeEach } from 'bun:test';
-import { PGLiteEngine } from '../src/core/pglite-engine.ts';
-import { sqlQueryForEngine } from '../src/core/sql-query.ts';
-import { resetPgliteState } from './helpers/reset-pglite.ts';
-import { buildChecks } from '../src/commands/doctor.ts';
-import { formatResult } from '../src/cli.ts';
-
-let engine: PGLiteEngine;
-
-async function seedFourPages(eng: PGLiteEngine): Promise<void> {
-  const sql = sqlQueryForEngine(eng);
-  // 2 eligible entity pages, 2 technical/non-entity pages.
-  // Only ONE entity page has a timeline entry; only ONE total page does.
-  await sql`
-    INSERT INTO pages (slug, source_id, type, title, compiled_truth, frontmatter, content_hash, created_at, updated_at)
-    VALUES
-      ('acme-example', 'default', 'company', 'Acme', '', '{}', 'h1', now(), now()),
-      ('alice-example', 'default', 'person', 'Alice', '', '{}', 'h2', now(), now()),
-      ('technical-a', 'default', 'note', 'Tech A', '', '{}', 'h3', now(), now()),
-      ('technical-b', 'default', 'note', 'Tech B', '', '{}', 'h4', now(), now())
-  `;
-  const companyId = (await sql`SELECT id FROM pages WHERE slug='acme-example'`)[0].id as number;
-  await sql`INSERT INTO timeline_entries (page_id, date, source, summary, detail)
-    VALUES (${companyId}, CURRENT_DATE, 'test', 'milestone', '{}')`;
-}
-
-beforeAll(async () => {
-  engine = new PGLiteEngine();
-  await engine.connect({});
-  await engine.initSchema();
-});
-
-afterAll(async () => {
-  await engine.disconnect();
-});
-
-beforeEach(async () => {
-  await resetPgliteState(engine);
-});
-
-describe('issue #2298 — numeric denominator semantics', () => {
-  test('entity timeline coverage = 1/2 = 50% (2 eligible entities, 1 with timeline)', async () => {
-    await seedFourPages(engine);
-    const health = await engine.getHealth();
-    expect(health.timeline_coverage).toBeDefined();
-    expect(Math.round((health.timeline_coverage ?? 0) * 100)).toBe(50);
-  });
-
-  test('whole-brain timeline density = 1/4 -> score 4/15 (4 total pages, 1 with timeline)', async () => {
-    await seedFourPages(engine);
-    const health = await engine.getHealth();
-    expect(health.timeline_coverage_score).toBeDefined();
-    expect(health.timeline_coverage_score).toBe(4);
-  });
-
-  test('the two metrics use independent denominators', async () => {
-    await seedFourPages(engine);
-    const health = await engine.getHealth();
-    expect(Math.round((health.timeline_coverage ?? 0) * 100)).toBe(50);
-    expect(health.timeline_coverage_score ?? 0).toBe(4);
-    // 50% (entity, /2) != 26.7% (whole-brain, /4). Provably distinct.
-    expect(Math.round(((health.timeline_coverage_score ?? 0) / 15) * 100)).not.toBe(50);
-  });
-});
-
-describe('issue #2298 — doctor rendered-message contract', () => {
-  test('graph_coverage renders entity-scoped label with 50%', async () => {
-    await seedFourPages(engine);
-    const checks = await buildChecks(engine, [], null);
-    const graph = checks.find((c) => c.name === 'graph_coverage');
-    expect(graph, 'graph_coverage check must be present').toBeDefined();
-    expect(graph!.message).toContain('entity timeline coverage 50%');
-    // ambiguous old label must NOT be present
-    expect(graph!.message).not.toMatch(/timeline 50%/);
-    expect(graph!.message).not.toMatch(/timeline \(entity, brain score\)/);
-  });
-
-  test('brain_score renders whole-brain density label 4/15', async () => {
-    await seedFourPages(engine);
-    const checks = await buildChecks(engine, [], null);
-    const brain = checks.find((c) => c.name === 'brain_score');
-    expect(brain, 'brain_score check must be present').toBeDefined();
-    expect(brain!.message).toContain('timeline density (all pages) 4/15');
-    // wrong labels must NOT be present
-    expect(brain!.message).not.toMatch(/timeline 4\/15/);
-    expect(brain!.message).not.toMatch(/timeline \(entity, brain score\)/);
-    // brain-score component must NOT carry the word "entity" (it is whole-brain)
-    const timelinePart = brain!.message.split('timeline density (all pages) 4/15')[0] + 'timeline density (all pages) 4/15';
-    expect(timelinePart).not.toMatch(/entity/);
-  });
-});
-
-describe('issue #2298 — CLI get_health rendered-output contract', () => {
-  function fakeHealth(overrides: Record<string, unknown>): any {
-    return {
-      embed_coverage: 1, missing_embeddings: 0, stale_pages: 0, orphan_pages: 0,
-      link_coverage: 1, timeline_coverage: 0.5, timeline_coverage_score: 4,
-      most_connected: [], ...overrides,
-    };
-  }
-
-  test('both entity and whole-brain lines render, no undefined/15', () => {
-    const out = formatResult('get_health', fakeHealth({}));
-    expect(out).toContain('Timeline coverage (entity pages): 50.0%');
-    expect(out).toContain('Timeline density (all pages): 4/15');
-    expect(out).not.toContain('undefined/15');
-    expect(out).not.toContain('Timeline coverage (entities)');
-    expect(out).not.toMatch(/timeline \(entity, brain score\)/);
-    expect(out).not.toMatch(/bare "timeline 4\/15"/);
-  });
-
-  test('guard matrix: entity present, whole-brain absent -> only entity line', () => {
-    const out = formatResult('get_health', fakeHealth({ timeline_coverage_score: undefined }));
-    expect(out).toContain('Timeline coverage (entity pages): 50.0%');
-    expect(out).not.toContain('Timeline density (all pages)');
-    expect(out).not.toContain('undefined/15');
-  });
-
-  test('guard matrix: whole-brain present, entity absent -> only whole-brain line', () => {
-    const out = formatResult('get_health', fakeHealth({ timeline_coverage: undefined }));
-    expect(out).toContain('Timeline density (all pages): 4/15');
-    expect(out).not.toContain('Timeline coverage (entity pages)');
-    expect(out).not.toContain('undefined/15');
-  });
-
-  test('guard matrix: both absent -> neither timeline line, never undefined/15', () => {
-    const out = formatResult('get_health', fakeHealth({ timeline_coverage: undefined, timeline_coverage_score: undefined }));
-    expect(out).not.toContain('Timeline coverage (entity pages)');
-    expect(out).not.toContain('Timeline density (all pages)');
-    expect(out).not.toContain('undefined/15');
-  });
-});