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/commands/apply-migrations.ts

@@ -108,7 +108,7 @@ Flags:
 
 Exit codes:
   0  Success (including "nothing to do").
-  1  An orchestrator failed, or schema migrations are pending (re-run with --yes).
+  1  An orchestrator failed.
   2  Invalid arguments.
 `);
 }
@@ -259,41 +259,6 @@ function printDryRun(plan: Plan, installed: string): void {
   }
 }
 
-/**
- * #1530: schema-drift pre-flight resolution. When the schema version is
- * behind, `--yes`/`--non-interactive` runs the schema migrations right there
- * (the engine is already connected); interactive runs warn and return true so
- * the caller exits non-zero instead of claiming "All migrations up to date".
- * All output goes to stderr (migrations never print to stdout).
- *
- * Returns true when the schema is STILL behind after this call.
- */
-async function resolveSchemaBehind(opts: {
-  schemaVer: number;
-  latest: number;
-  autoApply: boolean;
-  run: () => Promise<{ applied: number; current: number }>;
-}): Promise<boolean> {
-  const { schemaVer, latest, autoApply, run } = opts;
-  if (schemaVer >= latest) return false;
-  if (autoApply) {
-    console.error(`Schema version ${schemaVer} is behind latest ${latest}; running schema migrations...`);
-    try {
-      const result = await run();
-      console.error(`Applied ${result.applied} schema migration(s); now at v${result.current}.`);
-      return false;
-    } catch (err) {
-      console.error(`Schema migration failed: ${err instanceof Error ? err.message : String(err)}`);
-      return true;
-    }
-  }
-  console.warn(
-    `\n⚠️  Schema version ${schemaVer} is behind latest ${latest}.\n` +
-    `   Run \`gbrain apply-migrations --yes\` to apply now, or \`gbrain init --migrate-only\`.\n`,
-  );
-  return true;
-}
-
 function orchestratorOptsFrom(cli: ApplyMigrationsArgs): OrchestratorOpts {
   return {
     yes: cli.yes || cli.nonInteractive,
@@ -389,13 +354,10 @@ export async function runApplyMigrations(args: string[]): Promise<void> {
     if (cli.forceAll) return; // both surfaces flushed
   }
 
-  // Pre-flight: detect schema migrations (migrate.ts) being behind.
-  // apply-migrations historically ran orchestrator migrations only; schema
-  // migrations run via connectEngine() / initSchema(). Users expect this CLI
-  // to handle everything (Issue 1 from v0.18.0 field report; #1530). With
-  // --yes/--non-interactive we apply them here; otherwise we warn and make
-  // sure the run does NOT report "All migrations up to date" with exit 0.
-  let schemaBehind = false;
+  // Pre-flight: warn if schema migrations (migrate.ts) are behind.
+  // apply-migrations runs orchestrator migrations only; schema migrations
+  // run via connectEngine() / initSchema(). Users often expect this CLI
+  // to handle everything (Issue 1 from v0.18.0 field report).
   try {
     const { LATEST_VERSION } = await import('../core/migrate.ts');
     const { loadConfig: lc, toEngineConfig } = await import('../core/config.ts');
@@ -415,16 +377,14 @@ export async function runApplyMigrations(args: string[]): Promise<void> {
         await eng.connect(toEngineConfig(cfg));
         const verStr = await eng.getConfig('version');
         const schemaVer = parseInt(verStr || '1', 10);
-        const { runMigrations } = await import('../core/migrate.ts');
-        schemaBehind = await resolveSchemaBehind({
-          schemaVer,
-          latest: LATEST_VERSION,
-          // --list and --dry-run are read-only surfaces: never mutate schema
-          // even when combined with --yes/--non-interactive.
-          autoApply: (cli.yes || cli.nonInteractive) && !cli.dryRun && !cli.list,
-          run: () => runMigrations(eng),
-        });
         await eng.disconnect();
+        if (schemaVer < LATEST_VERSION) {
+          console.warn(
+            `\n⚠️  Schema version ${schemaVer} is behind latest ${LATEST_VERSION}.\n` +
+            `   Schema migrations run automatically on next connectEngine() / initSchema().\n` +
+            `   To run them now: gbrain init --migrate-only\n`,
+          );
+        }
       }
     }
   } catch {
@@ -459,13 +419,6 @@ export async function runApplyMigrations(args: string[]): Promise<void> {
 
   const toRun: Migration[] = [...plan.partial, ...plan.pending];
   if (toRun.length === 0) {
-    if (schemaBehind) {
-      console.error(
-        'Orchestrator migrations are up to date, but schema migrations are behind. ' +
-        'Run `gbrain apply-migrations --yes` (or `--force-schema`) to apply them.',
-      );
-      process.exit(1);
-    }
     console.log('All migrations up to date.');
     process.exit(0);
   }
@@ -550,5 +503,4 @@ export const __testing = {
   buildPlan,
   indexCompleted,
   statusForVersion,
-  resolveSchemaBehind,
 };

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/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/apply-migrations.test.ts

@@ -10,7 +10,7 @@ import { describe, test, expect } from 'bun:test';
 import { __testing } from '../src/commands/apply-migrations.ts';
 import type { CompletedMigrationEntry } from '../src/core/preferences.ts';
 
-const { parseArgs, indexCompleted, buildPlan, statusForVersion, resolveSchemaBehind } = __testing;
+const { parseArgs, indexCompleted, buildPlan, statusForVersion } = __testing;
 
 describe('parseArgs', () => {
   test('default flags', () => {
@@ -180,60 +180,3 @@ describe('runApplyMigrations exit codes (v0.36.1.x #1062)', () => {
     expect(src).toMatch(/All migrations up to date[\s\S]{0,80}process\.exit\(0\)/);
   });
 });
-
-// #1530: apply-migrations must not report "All migrations up to date" (exit 0)
-// while the SCHEMA is behind. --yes runs the schema migrations in the
-// pre-flight; interactive runs flag schemaBehind and exit 1.
-describe('resolveSchemaBehind (#1530)', () => {
-  test('schema up to date → false, migrations not run', async () => {
-    let ran = false;
-    const behind = await resolveSchemaBehind({
-      schemaVer: 5,
-      latest: 5,
-      autoApply: true,
-      run: async () => { ran = true; return { applied: 0, current: 5 }; },
-    });
-    expect(behind).toBe(false);
-    expect(ran).toBe(false);
-  });
-
-  test('behind + autoApply → runs schema migrations, no longer behind', async () => {
-    let ran = false;
-    const behind = await resolveSchemaBehind({
-      schemaVer: 3,
-      latest: 5,
-      autoApply: true,
-      run: async () => { ran = true; return { applied: 2, current: 5 }; },
-    });
-    expect(behind).toBe(false);
-    expect(ran).toBe(true);
-  });
-
-  test('behind + interactive → warns and stays behind, migrations not run', async () => {
-    let ran = false;
-    const behind = await resolveSchemaBehind({
-      schemaVer: 3,
-      latest: 5,
-      autoApply: false,
-      run: async () => { ran = true; return { applied: 2, current: 5 }; },
-    });
-    expect(behind).toBe(true);
-    expect(ran).toBe(false);
-  });
-
-  test('behind + autoApply + migration failure → stays behind', async () => {
-    const behind = await resolveSchemaBehind({
-      schemaVer: 3,
-      latest: 5,
-      autoApply: true,
-      run: async () => { throw new Error('boom'); },
-    });
-    expect(behind).toBe(true);
-  });
-
-  test('up-to-date branch exits 1 when schemaBehind (source shape)', async () => {
-    const { readFileSync } = await import('fs');
-    const src = readFileSync('src/commands/apply-migrations.ts', 'utf8');
-    expect(src).toMatch(/if \(schemaBehind\)[\s\S]{0,300}process\.exit\(1\)[\s\S]{0,120}All migrations up to date/);
-  });
-});

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();
     });
   });