fix(doctor): register onboard check names in doctor-categories to stop unknown-check warnings

doctor.ts pushes runAllOnboardChecks results into the checks list, but the
7 onboard check names (embed_staleness, entity_link_coverage,
timeline_coverage, takes_count, dangling_aliases, pack_upgrade_available,
type_proliferation) were never added to doctor-categories.ts, so every
doctor run emitted an 'unknown check name' stderr warn per onboard check.

Registers the 5 data-quality names under BRAIN and the 2 schema-pack names
under META (alphabetical order preserved), and widens the drift-guard test
to scan src/core/onboard/checks.ts alongside src/commands/doctor.ts so
future onboard checks can't drift uncategorized.

Takeover of #1839, rebased onto master (keeps master's timeline_dedup_index).

Co-authored-by: mvanhorn <mvanhorn@users.noreply.github.com>
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

src/commands/autopilot.ts

@@ -38,7 +38,6 @@ import { logSelfUpgrade } from '../core/audit/self-upgrade-audit.ts';
 import { detectInstallMethod } from './upgrade.ts';
 import { evaluateQuietHours } from '../core/minions/quiet-hours.ts';
 import { inspectLock } from '../core/db-lock.ts';
-import { registerCleanup } from '../core/process-cleanup.ts';
 
 /**
  * v0.37.7.0 #1162 — classify autopilot reconnect-loop errors.
@@ -434,37 +433,6 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
   let stopping = false;
   let childSupervisor: ChildWorkerSupervisor | null = null;
 
-  // #1872: graceful engine shutdown. On PGLite the cycle steps run INLINE in
-  // this process, so a hard `process.exit` mid-write (systemctl stop →
-  // SIGTERM) kills WASM Postgres with the WAL dirty and can corrupt the
-  // brain. Two exit paths must both close the engine:
-  //   - autopilot's own shutdown() below (owns SIGINT + internal stops like
-  //     max_crashes / cycle-failure-cap), and
-  //   - process-cleanup's SIGTERM handler (installed at cli.ts module load;
-  //     it runs the cleanup registry with a 3s deadline and then exits) —
-  //     which is why closeEngine is ALSO registered there.
-  // closeEngine aborts the in-flight inline cycle (runCycle checks the
-  // signal between phases and threads it into phase sub-work), gives it a
-  // short bounded window to wind down, then disconnects. PGLite's
-  // disconnect() drains the pending query and checkpoints before closing;
-  // a second call is a no-op (disconnect snapshots + nulls the handle), so
-  // both paths firing is safe.
-  const shutdownAbort = new AbortController();
-  let inflightInlineCycle: Promise<unknown> | null = null;
-  const closeEngine = async () => {
-    shutdownAbort.abort(new Error('autopilot shutdown'));
-    if (inflightInlineCycle) {
-      // ponytail: 2s cap keeps us inside process-cleanup's 3s deadline; a
-      // between-phase abort resolves instantly, a mid-phase one may not.
-      await Promise.race([
-        inflightInlineCycle.catch(() => { /* cycle errors already logged by the loop */ }),
-        new Promise((r) => setTimeout(r, 2_000)),
-      ]);
-    }
-    try { await engine.disconnect(); } catch { /* best-effort */ }
-  };
-  const deregisterEngineClose = registerCleanup('autopilot-engine-close', closeEngine);
-
   if (spawnManagedWorker) {
     const cliPath = resolveGbrainCliPath();
     // Cgroup-aware auto-sized RSS watchdog cap (issue #1678). The old flat
@@ -552,10 +520,6 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
         childSupervisor.killChild('SIGKILL');
       }
     }
-    // #1872: abort the in-flight inline cycle and close the engine BEFORE
-    // process.exit — a hard exit mid-write corrupts PGLite's WASM Postgres.
-    await closeEngine();
-    deregisterEngineClose();
     try { unlinkSync(lockPath); } catch { /* already gone */ }
     process.exit(0);
   };
@@ -1044,21 +1008,16 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
       // path's phase set). Now both converge on the same primitive.
       try {
         const { runCycle } = await import('../core/cycle.ts');
-        // #1872: track the promise so closeEngine can drain it on shutdown,
-        // and pass the abort signal so the cycle winds down between phases.
-        const cyclePromise = runCycle(engine, {
+        const report = await runCycle(engine, {
           brainDir: repoPath,
           // Autopilot daemon path: pulls by default (matches
           // pre-v0.17 autopilot behavior). CLI dream defaults false
           // for cron safety; that choice is scoped to dream only.
           pull: true,
-          signal: shutdownAbort.signal,
           yieldBetweenPhases: async () => {
             await new Promise(r => setImmediate(r));
           },
         });
-        inflightInlineCycle = cyclePromise;
-        const report = await cyclePromise.finally(() => { inflightInlineCycle = null; });
         // Only 'failed' (every attempted phase failed) trips the autopilot
         // circuit breaker. 'partial' means at least one phase warned or
         // failed while others ran — that's a soft signal, not a fatal

src/commands/dream.ts

@@ -26,7 +26,6 @@
 import type { BrainEngine } from '../core/engine.ts';
 import {
   runCycle,
-  resolveSourceForDir,
   ALL_PHASES,
   type CyclePhase,
   type CycleReport,
@@ -381,9 +380,9 @@ Options:
 
   --source <id>       Scope the cycle to one source so doctor's
                       cycle_freshness check sees a fresh stamp on
-                      completion. When omitted, gbrain derives the
-                      source from --dir / the configured checkout
-                      when it matches a source's local_path (#1869).
+                      completion. Without this, gbrain dream's
+                      timestamp never lands and federated brains
+                      see "stale cycle" forever.
   --source-id <id>    Alias for --source. Matches the v0.37.7.0+
                       naming used by import/extract/graph-query.
 
@@ -635,25 +634,6 @@ export async function runDream(engine: BrainEngine | null, args: string[]): Prom
     );
     process.exit(1);
   }
-
-  // #1869: a path-scoped run (--dir, or the configured sync.repo_path) whose
-  // directory matches a registered source's local_path IS that source's cycle
-  // — derive the source id so runCycle writes last_source_cycle_at /
-  // last_full_cycle_at on success and doctor's cycle_freshness check stops
-  // reading perpetually stale. Explicit --source still wins (resolved above).
-  // Fixed here at the command level, NOT in runCycle's stamp gate, so legacy
-  // global callers (autopilot-global-maintenance runs GLOBAL_PHASES with a
-  // brainDir and no sourceId) can't falsely stamp per-source freshness.
-  // A derived match on an archived source is skipped silently (falls back to
-  // legacy unscoped behavior) — stamping it would mask staleness on restore,
-  // mirroring the explicit --source archived guard above.
-  if (resolvedSourceId === undefined && engine !== null && brainDir !== null) {
-    const derived = await resolveSourceForDir(engine, brainDir);
-    if (derived !== undefined) {
-      const src = await fetchSource(engine, derived);
-      if (src?.archived !== true) resolvedSourceId = derived;
-    }
-  }
   // ─── issue #1678: bounded single-hold extract_atoms drain ──────────
   if (opts.drain) {
     if (engine === null) {

src/core/cycle.ts

@@ -855,16 +855,8 @@ 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).
- *
- * Exported for dream.ts (#1869): a `gbrain dream --dir <path>` run whose
- * path matches a registered source's local_path is a per-source cycle in
- * everything but name, so dream derives the source id up front and passes
- * it as opts.sourceId — landing the freshness stamp without changing
- * runCycle's stamp/lock semantics for legacy global callers (the
- * autopilot-global-maintenance handler runs GLOBAL_PHASES with a brainDir
- * and MUST NOT stamp per-source freshness; see rejected PR #2549).
  */
-export async function resolveSourceForDir(
+async function resolveSourceForDir(
   engine: BrainEngine,
   brainDir: string | null,
 ): Promise<string | undefined> {

src/core/doctor-categories.ts

@@ -35,10 +35,11 @@
  *
  * The doctor renders both side by side.
  *
- * Drift contract: every check name that ships in doctor.ts MUST appear in
+ * Drift contract: every check name that ships through doctor MUST appear in
  * exactly one set below. The drift-guard test in
- * `test/doctor-categories.test.ts` enforces this by reading doctor.ts source
- * via a tagged-string scan and asserting set membership exactly.
+ * `test/doctor-categories.test.ts` enforces this by reading doctor check
+ * emitter sources via a tagged-string scan and asserting set membership
+ * exactly.
  *
  * If you add a new doctor check, you MUST add its name to the appropriate
  * set here. The categorize step in `src/commands/doctor.ts` falls through
@@ -67,12 +68,15 @@ export const BRAIN_CHECK_NAMES: ReadonlySet<string> = new Set([
   'conversation_parser_probe_health',
   'cross_modal_modality_backfill',
   'cycle_freshness',
+  'dangling_aliases',
   'effective_date_health',
+  'embed_staleness',
   'embedding_column_registry',
   'embedding_env_override',
   'embedding_provider',
   'embedding_width_consistency',
   'embeddings',
+  'entity_link_coverage',
   'eval_drift',
   'extract_atoms_backlog',
   'extract_health',
@@ -102,7 +106,9 @@ export const BRAIN_CHECK_NAMES: ReadonlySet<string> = new Set([
   'stub_guard_24h',
   'sync_failures',
   'sync_freshness',
+  'takes_count',
   'takes_weight_grid',
+  'timeline_coverage',
   'unified_multimodal_coverage',
   'voice_gate_health',
 ]);
@@ -170,12 +176,14 @@ export const META_CHECK_NAMES: ReadonlySet<string> = new Set([
   'eval_capture',
   'minions_migration',
   'multi_source_drift',
+  'pack_upgrade_available',
   'schema_pack_active',
   'schema_pack_consistency',
   'schema_pack_source_drift',
   'schema_version',
   'slug_fallback_audit',
   'timeline_dedup_index',
+  'type_proliferation',
   'upgrade_errors',
 ]);
 

test/autopilot-shutdown-engine-close.test.ts

@@ -1,63 +0,0 @@
-/**
- * #1872 — autopilot SIGTERM/SIGINT must close the engine before exit.
- *
- * On PGLite the cycle steps run INLINE in the autopilot process, so a hard
- * `process.exit` mid-write (systemctl stop → SIGTERM) kills WASM Postgres
- * with the WAL dirty and can corrupt the brain. Two exit paths must both
- * close the engine:
- *
- *   - autopilot's own shutdown() (owns SIGINT + internal stops like
- *     max_crashes / cycle-failure-cap), and
- *   - process-cleanup's SIGTERM handler (installed at cli.ts module load,
- *     which exits within its 3s cleanup deadline) — reached via the
- *     registered 'autopilot-engine-close' cleanup callback.
- *
- * Because the shutdown path is deep inside `runAutopilot()` (a long-running
- * daemon loop that ends in process.exit), a behavioral test would have to
- * spawn + signal a real daemon. Following the established precedent
- * (test/autopilot-supervisor-wiring.test.ts, test/autopilot-fanout-wiring.test.ts),
- * these static-shape regressions pin the load-bearing wiring instead.
- */
-import { describe, expect, it } from 'bun:test';
-import { readFileSync } from 'fs';
-import { join } from 'path';
-
-const AUTOPILOT_SRC = readFileSync(
-  join(import.meta.dir, '..', 'src', 'commands', 'autopilot.ts'),
-  'utf8',
-);
-
-describe('autopilot.ts graceful engine shutdown (#1872)', () => {
-  it('registers an engine-close callback in the process-cleanup registry (SIGTERM path)', () => {
-    // process-cleanup owns SIGTERM (installed at cli.ts:10) and hard-exits
-    // after its cleanup pass; without this registration the engine is never
-    // closed on `systemctl stop`.
-    expect(AUTOPILOT_SRC).toContain(
-      "import { registerCleanup } from '../core/process-cleanup.ts';",
-    );
-    expect(AUTOPILOT_SRC).toContain(
-      "registerCleanup('autopilot-engine-close', closeEngine)",
-    );
-  });
-
-  it('closeEngine aborts the in-flight inline cycle then disconnects the engine', () => {
-    // Abort first (runCycle checks the signal between phases and threads it
-    // into phase sub-work), bounded drain, then disconnect.
-    expect(AUTOPILOT_SRC).toMatch(
-      /const closeEngine = async \(\) => \{[\s\S]{0,900}shutdownAbort\.abort\([\s\S]{0,900}engine\.disconnect\(\)/,
-    );
-  });
-
-  it('the inline runCycle call carries the shutdown abort signal and is tracked as in-flight', () => {
-    // PGLite / --inline path: the cycle runs in-process, so shutdown must be
-    // able to (a) signal it to wind down and (b) await it before closing.
-    expect(AUTOPILOT_SRC).toMatch(/signal:\s*shutdownAbort\.signal/);
-    expect(AUTOPILOT_SRC).toMatch(/inflightInlineCycle\s*=\s*cyclePromise/);
-  });
-
-  it('shutdown() awaits closeEngine() before process.exit(0) (SIGINT + internal-stop path)', () => {
-    expect(AUTOPILOT_SRC).toMatch(
-      /await closeEngine\(\);[\s\S]{0,400}process\.exit\(0\)/,
-    );
-  });
-});

test/doctor-categories.test.ts

@@ -1,10 +1,10 @@
 /**
  * Drift guard for src/core/doctor-categories.ts.
  *
- * Reads src/commands/doctor.ts source via a literal-string scan, enumerates
- * every `name: '<...>'` Check name, and asserts each appears in exactly ONE
- * category set. The union of the four sets must equal the discovered names
- * exactly — no orphans, no extras.
+ * Reads doctor check emitter source via a literal-string scan, enumerates every
+ * `name: '<...>'` Check name, and asserts each appears in exactly ONE category
+ * set. The union of the four sets must equal the discovered names exactly —
+ * no orphans, no extras.
  *
  * This is the structural failure the v0.41.19.0 plan-eng-review caught:
  * doctor.ts grows new checks regularly; without this guard, the
@@ -25,26 +25,30 @@ import {
 } from '../src/core/doctor-categories.ts';
 
 const DOCTOR_TS_PATH = join(import.meta.dir, '..', 'src', 'commands', 'doctor.ts');
+const ONBOARD_CHECKS_TS_PATH = join(import.meta.dir, '..', 'src', 'core', 'onboard', 'checks.ts');
+const CHECK_SOURCE_PATHS = [DOCTOR_TS_PATH, ONBOARD_CHECKS_TS_PATH];
 
 function enumerateCheckNames(): Set<string> {
-  const source = readFileSync(DOCTOR_TS_PATH, 'utf-8');
   const names = new Set<string>();
-  // 1) Inline object-literal form: `{ name: 'foo', ... }`.
-  for (const m of source.matchAll(/name:\s*['"]([a-z][a-z0-9_]+)['"]/g)) {
-    names.add(m[1]);
-  }
-  // 2) Helper-function form: `const name = 'foo';` inside a check helper.
-  //    Catches checks like `nightly_quality_probe_health` and
-  //    `conversation_facts_backlog` that build the Check from a captured
-  //    name constant.
-  for (const m of source.matchAll(/const\s+name\s*=\s*['"]([a-z][a-z0-9_]+)['"]/g)) {
-    names.add(m[1]);
+  for (const path of CHECK_SOURCE_PATHS) {
+    const source = readFileSync(path, 'utf-8');
+    // 1) Inline object-literal form: `{ name: 'foo', ... }`.
+    for (const m of source.matchAll(/name:\s*['"]([a-z][a-z0-9_]+)['"]/g)) {
+      names.add(m[1]);
+    }
+    // 2) Helper-function form: `const name = 'foo';` inside a check helper.
+    //    Catches checks like `nightly_quality_probe_health` and
+    //    `conversation_facts_backlog` that build the Check from a captured
+    //    name constant.
+    for (const m of source.matchAll(/const\s+name\s*=\s*['"]([a-z][a-z0-9_]+)['"]/g)) {
+      names.add(m[1]);
+    }
   }
   return names;
 }
 
 describe('doctor-categories drift guard', () => {
-  test('every check name in doctor.ts source belongs to exactly one category set', () => {
+  test('every doctor-emitted check name belongs to exactly one category set', () => {
     const discovered = enumerateCheckNames();
     const allCategorized = new Set<string>([
       ...BRAIN_CHECK_NAMES,
@@ -59,7 +63,7 @@ describe('doctor-categories drift guard', () => {
     }
     if (missing.length > 0) {
       throw new Error(
-        `These check names appear in doctor.ts but are not categorized in ` +
+        `These check names appear in doctor check emitters but are not categorized in ` +
           `src/core/doctor-categories.ts: ${missing.sort().join(', ')}. ` +
           `Add each to BRAIN/SKILL/OPS/META_CHECK_NAMES.`,
       );
@@ -86,7 +90,7 @@ describe('doctor-categories drift guard', () => {
     expect(dupes).toEqual([]);
   });
 
-  test('every categorized name is currently used in doctor.ts source (no stale entries)', () => {
+  test('every categorized name is currently used in doctor check emitters (no stale entries)', () => {
     const discovered = enumerateCheckNames();
     const allCategorized = new Set<string>([
       ...BRAIN_CHECK_NAMES,
@@ -124,6 +128,14 @@ describe('categorizeCheck', () => {
     expect(categorizeCheck('sync_freshness')).toBe('brain');
   });
 
+  test('returns the right category for onboard data-quality check names', () => {
+    expect(categorizeCheck('embed_staleness')).toBe('brain');
+    expect(categorizeCheck('entity_link_coverage')).toBe('brain');
+    expect(categorizeCheck('timeline_coverage')).toBe('brain');
+    expect(categorizeCheck('takes_count')).toBe('brain');
+    expect(categorizeCheck('dangling_aliases')).toBe('brain');
+  });
+
   test('returns the right category for a known skill name', () => {
     expect(categorizeCheck('resolver_health')).toBe('skill');
     expect(categorizeCheck('skill_conformance')).toBe('skill');
@@ -140,6 +152,24 @@ describe('categorizeCheck', () => {
     expect(categorizeCheck('upgrade_errors')).toBe('meta');
   });
 
+  test('returns the right category for onboard schema-pack check names without warning', () => {
+    const originalWrite = process.stderr.write.bind(process.stderr);
+    const captured: string[] = [];
+    (process.stderr as { write: typeof process.stderr.write }).write = ((
+      chunk: string | Uint8Array,
+    ) => {
+      captured.push(typeof chunk === 'string' ? chunk : Buffer.from(chunk).toString());
+      return true;
+    }) as typeof process.stderr.write;
+    try {
+      expect(categorizeCheck('pack_upgrade_available')).toBe('meta');
+      expect(categorizeCheck('type_proliferation')).toBe('meta');
+      expect(captured.filter((c) => c.includes('[doctor-categories]'))).toEqual([]);
+    } finally {
+      (process.stderr as { write: typeof process.stderr.write }).write = originalWrite;
+    }
+  });
+
   test('unknown check name falls through to meta with a stderr warn (once per process)', () => {
     const originalWrite = process.stderr.write.bind(process.stderr);
     const captured: string[] = [];

test/dream-dir-source-stamp.test.ts

@@ -1,99 +0,0 @@
-/**
- * #1869 — `gbrain dream --dir <path>` stamps cycle freshness when the path
- * matches a registered source's local_path.
- *
- * Pre-fix, only `--source <id>` runs wrote last_source_cycle_at /
- * last_full_cycle_at (runCycle's stamp gate reads opts.sourceId, and dream
- * never derived one from --dir), so a path-scoped brain showed doctor's
- * cycle_freshness as perpetually stale.
- *
- * The fix lives in dream.ts (derive the source id from the resolved brain
- * dir via resolveSourceForDir), NOT in runCycle's stamp gate — a runCycle-
- * wide change would make the autopilot-global-maintenance handler (global
- * phases, brainDir set, no sourceId) falsely stamp per-source freshness
- * (the #2194 poisoning class; see rejected PR #2549).
- *
- * Same real-PGLite/no-mocks discipline as test/dream.test.ts; same
- * GBRAIN_HOME isolation as test/cycle-last-full-cycle-at.test.ts (the
- * cycle's PGLite file lock lives under ~/.gbrain).
- */
-import { describe, test, expect, beforeAll, afterAll, beforeEach, afterEach } from 'bun:test';
-import { mkdtempSync, rmSync } from 'fs';
-import { join } from 'path';
-import { tmpdir } from 'os';
-import { PGLiteEngine } from '../src/core/pglite-engine.ts';
-import { resetPgliteState } from './helpers/reset-pglite.ts';
-import { runDream } from '../src/commands/dream.ts';
-import { withEnv } from './helpers/with-env.ts';
-
-let engine: PGLiteEngine;
-let brainDir: string;
-let gbrainHome: string;
-
-beforeAll(async () => {
-  engine = new PGLiteEngine();
-  await engine.connect({});
-  await engine.initSchema();
-}, 60_000);
-
-afterAll(async () => {
-  await engine.disconnect();
-});
-
-beforeEach(async () => {
-  await resetPgliteState(engine);
-  brainDir = mkdtempSync(join(tmpdir(), 'gbrain-dream-stamp-'));
-  gbrainHome = mkdtempSync(join(tmpdir(), 'gbrain-dream-stamp-home-'));
-}, 60_000);
-
-afterEach(() => {
-  rmSync(brainDir, { recursive: true, force: true });
-  rmSync(gbrainHome, { recursive: true, force: true });
-});
-
-async function seedSource(id: string, archived = false): Promise<void> {
-  await engine.executeRaw(
-    `INSERT INTO sources (id, name, local_path, config, archived, created_at)
-     VALUES ($1, $2, $3, '{}'::jsonb, $4, NOW())`,
-    [id, id, brainDir, archived],
-  );
-}
-
-async function readLastFullCycleAt(sourceId: string): Promise<string | null> {
-  const rows = await engine.executeRaw<{ config: Record<string, unknown> | null }>(
-    `SELECT config FROM sources WHERE id = $1`,
-    [sourceId],
-  );
-  const raw = rows[0]?.config?.last_full_cycle_at;
-  return typeof raw === 'string' ? raw : null;
-}
-
-describe('gbrain dream --dir <path> freshness stamp (#1869)', () => {
-  test('--dir matching a source local_path stamps last_full_cycle_at', async () => {
-    await withEnv({ GBRAIN_HOME: gbrainHome }, async () => {
-      await seedSource('path-scoped');
-      expect(await readLastFullCycleAt('path-scoped')).toBeNull();
-
-      const report = await runDream(engine, ['--dir', brainDir, '--phase', 'lint', '--json']);
-      expect(report).toBeTruthy();
-      if (report) expect(['ok', 'clean']).toContain(report.status);
-
-      // Pre-fix this stays null forever: dream never passed a sourceId, so
-      // runCycle's stamp gate skipped the write.
-      expect(await readLastFullCycleAt('path-scoped')).not.toBeNull();
-    });
-  }, 60_000);
-
-  test('--dir matching an ARCHIVED source does not stamp it', async () => {
-    await withEnv({ GBRAIN_HOME: gbrainHome }, async () => {
-      await seedSource('mothballed', true);
-
-      const report = await runDream(engine, ['--dir', brainDir, '--phase', 'lint', '--json']);
-      expect(report).toBeTruthy();
-
-      // Stamping an archived source would mask data staleness when it is
-      // later restored (mirrors the explicit --source archived guard).
-      expect(await readLastFullCycleAt('mothballed')).toBeNull();
-    });
-  }, 60_000);
-});

test/dream.test.ts

@@ -562,22 +562,12 @@ describe('runDream — --source / --source-id (v0.41.13)', () => {
 
   // ─── Back-compat: bare `gbrain dream` does NOT write per-source stamp ─
 
-  test('gbrain dream (no --source) stamps only the source whose local_path matches --dir (#1869)', async () => {
-    // Pre-#1869 this asserted NO source was ever stamped without an explicit
-    // --source — which is exactly the bug: a path-scoped `gbrain dream --dir`
-    // run never landed a freshness stamp and doctor's cycle_freshness stayed
-    // stale forever. New truth: the source whose local_path matches the
-    // resolved brain dir is derived and stamped; unrelated sources stay
-    // untouched (cross-source isolation).
-    await seedSource('alpha'); // local_path = repo → derived + stamped
-    await engine.executeRaw(
-      `INSERT INTO sources (id, name, local_path, config, archived, created_at)
-       VALUES ($1, $2, $3, '{}'::jsonb, false, NOW())`,
-      ['beta', 'beta', '/somewhere/else'],
-    );
+  test('gbrain dream (no --source) leaves all sources untouched (back-compat regression)', async () => {
+    await seedSource('alpha');
+    await seedSource('beta');
     const report = await runDream(engine, ['--dir', repo, '--phase', 'lint', '--json']);
     expect(report).toBeTruthy();
-    expect(await readLastFullCycleAt('alpha')).not.toBeNull();
+    expect(await readLastFullCycleAt('alpha')).toBeNull();
     expect(await readLastFullCycleAt('beta')).toBeNull();
   }, 60_000);