test(dream): conform dream-dir-source-stamp to canonical PGLite isolation pattern

check:test-isolation R3/R4 flagged the new test file: engine was created
in beforeEach (outside beforeAll) and never disconnected in afterAll.
Switch to the canonical shared-engine pattern (beforeAll create,
beforeEach resetPgliteState, afterAll disconnect) per
test/helpers/reset-pglite.ts.

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

docs/tutorials/company-brain.md

@@ -223,16 +223,14 @@ export GBRAIN_REMOTE_CLIENT_ID=<Alice's client_id>
 export GBRAIN_REMOTE_CLIENT_SECRET=<Alice's client_secret>
 export GBRAIN_REMOTE_MCP_URL=https://brain.acme-co.com/mcp
 
-gbrain search "performance review"
+gbrain search "performance review" --remote
 ```
 
-(On a thin-client install every shared op routes through the remote MCP server automatically — no flag needed. The env vars select whose credentials the call uses.)
-
 Alice should see results only from `customers` and `shared`. The performance-review notes live in `internal`, which she's not scoped to read. She shouldn't see them.
 
 ```bash
 # Terminal 2, as Bob (export his credentials similarly)
-gbrain search "performance review"
+gbrain search "performance review" --remote
 ```
 
 Bob should see the performance-review notes from `internal`, plus anything related from `shared`. He shouldn't see anything that lives only in `customers`.
@@ -516,7 +514,7 @@ The first sync embeds every page, which takes time. Check `gbrain sources status
 
 ### "I see a page I shouldn't see"
 
-This shouldn't happen, but if you suspect it, run `gbrain search <query> --json` as the constrained client (thin-client install, with the client's `GBRAIN_REMOTE_*` env exported) and inspect the `source_id` field on every returned result. Every row should be in the client's `--federated-read` set. If one isn't, file an issue with the exact slug and source IDs.
+This shouldn't happen, but if you suspect it, run `gbrain search <query> --remote --json` as the constrained client and inspect the `source_id` field on every returned result. Every row should be in the client's `--federated-read` set. If one isn't, file an issue with the exact slug and source IDs.
 
 ### "The synthesized answer is wrong"
 

src/cli.ts

@@ -464,11 +464,7 @@ async function main() {
     // routed path. Date → ISO string; bigint → string (postgres.js shape);
     // Buffer → object. Microsecond-cost; eliminates a whole drift bug class.
     const result = JSON.parse(JSON.stringify(rawResult, bigintToStringReplacer));
-    // #380 pass-through: `--json` (undeclared on most ops, promised by docs)
-    // emits the raw op result instead of the human formatter.
-    const output = params.json === true
-      ? JSON.stringify(result, null, 2) + '\n'
-      : formatResult(op.name, result);
+    const output = formatResult(op.name, result);
     if (output) process.stdout.write(output);
   } catch (e: unknown) {
     // v0.42.20.0 (codex D4): on error, set exitCode + return so the `finally`
@@ -551,10 +547,7 @@ async function runThinClientRouted(
       signal: sigintController.signal,
     });
     const result = unpackToolResult(raw);
-    // #380: same --json seam as the local-engine path (renderer parity).
-    const output = params.json === true
-      ? JSON.stringify(result, null, 2) + '\n'
-      : formatResult(op.name, result);
+    const output = formatResult(op.name, result);
     if (output) process.stdout.write(output);
   } catch (e: unknown) {
     if (e instanceof RemoteMcpError) {
@@ -764,28 +757,10 @@ export function resolveQueryImage(
   return { path: imagePath, base64, mime };
 }
 
-/**
- * #380: undeclared flags that are honored DOWNSTREAM of parseOpArgs and must
- * keep passing through when unknown flags become hard errors:
- *   - source     → makeContext's resolveSourceId (the --source axis)
- *   - brain      → the mount/brain routing axis (docs promise the flag)
- *   - dry_run    → makeContext's ctx.dryRun (ops without a declared dry_run)
- *   - json       → raw-JSON output seam (local + thin-client paths)
- */
-const PASSTHROUGH_VALUE_FLAGS = new Set(['source', 'brain']);
-const PASSTHROUGH_BOOL_FLAGS = new Set(['dry_run', 'json']);
-
 export function parseOpArgs(op: Operation, args: string[]): Record<string, unknown> {
   const params: Record<string, unknown> = {};
   const positional = op.cliHints?.positional || [];
   let posIdx = 0;
-  const cliName = op.cliHints?.name || op.name;
-  const MAX_STDIN = 5_000_000; // 5MB cap, shared by stdin and --file
-  // #380: `--file <path>` fills the op's declared stdin param (put's `content`)
-  // from a file. Driven by cliHints.stdin — no per-op hard-coding — and
-  // disabled when the op declares a real `file` param of its own.
-  const fileParam = op.cliHints?.stdin && !op.params.file ? op.cliHints.stdin : undefined;
-  let filePath: string | undefined;
 
   for (let i = 0; i < args.length; i++) {
     const arg = args[i];
@@ -799,42 +774,12 @@ export function parseOpArgs(op: Operation, args: string[]): Record<string, unkno
         }
       }
       const key = arg.slice(2).replace(/-/g, '_');
-      if (fileParam && key === 'file') {
-        if (i + 1 >= args.length) {
-          console.error(`Error: ${arg} requires a value.`);
-          process.exit(1);
-        }
-        filePath = args[++i];
-        continue;
-      }
       const paramDef = op.params[key];
-      if (!paramDef) {
-        if (PASSTHROUGH_BOOL_FLAGS.has(key)) {
-          params[key] = true;
-          continue;
-        }
-        if (PASSTHROUGH_VALUE_FLAGS.has(key)) {
-          if (i + 1 >= args.length) {
-            console.error(`Error: ${arg} requires a value.`);
-            process.exit(1);
-          }
-          params[key] = args[++i];
-          continue;
-        }
-        // #380: unknown flags were silently swallowed into params, so typos
-        // like `put --file` created empty pages instead of erroring.
-        console.error(`Unknown option for gbrain ${cliName}: ${arg}`);
-        console.error(`Run 'gbrain ${cliName} --help' for valid flags.`);
-        process.exit(1);
-      }
-      if (paramDef.type === 'boolean') {
+      if (paramDef?.type === 'boolean') {
         params[key] = true;
       } else if (i + 1 < args.length) {
         params[key] = args[++i];
-        if (paramDef.type === 'number') params[key] = Number(params[key]);
-      } else {
-        console.error(`Error: ${arg} requires a value.`);
-        process.exit(1);
+        if (paramDef?.type === 'number') params[key] = Number(params[key]);
       }
     } else if (posIdx < positional.length) {
       const key = positional[posIdx++];
@@ -843,30 +788,10 @@ export function parseOpArgs(op: Operation, args: string[]): Record<string, unkno
     }
   }
 
-  // #380: resolve --file AFTER the loop so --file/--content conflicts are
-  // caught in either order.
-  if (filePath !== undefined && fileParam) {
-    if (params[fileParam] !== undefined) {
-      console.error(`Error: use only one of --file, --${fileParam}, or stdin for gbrain ${cliName}.`);
-      process.exit(1);
-    }
-    let fileContent: string;
-    try {
-      fileContent = readFileSync(filePath, 'utf-8');
-    } catch (e) {
-      console.error(`Error: cannot read --file ${filePath}: ${e instanceof Error ? e.message : String(e)}`);
-      process.exit(1);
-    }
-    if (Buffer.byteLength(fileContent, 'utf-8') > MAX_STDIN) {
-      console.error(`Error: file content exceeds ${MAX_STDIN} bytes. Split into smaller inputs.`);
-      process.exit(1);
-    }
-    params[fileParam] = fileContent;
-  }
-
   // Read stdin for content params
   if (op.cliHints?.stdin && !params[op.cliHints.stdin] && !process.stdin.isTTY) {
     const stdinContent = readFileSync(0, 'utf-8');
+    const MAX_STDIN = 5_000_000; // 5MB
     if (Buffer.byteLength(stdinContent, 'utf-8') > MAX_STDIN) {
       console.error(`Error: stdin content exceeds ${MAX_STDIN} bytes. Split into smaller inputs.`);
       process.exit(1);
@@ -2328,10 +2253,6 @@ export function printOpHelp(op: Operation, invokedName?: string) {
       const prefix = isPos ? `  <${key}>` : `  --${key.replace(/_/g, '-')}`;
       console.log(`${prefix.padEnd(28)} ${def.description || ''}${req}`);
     }
-    // #380: ops that read stdin also accept --file <path> (parseOpArgs).
-    if (op.cliHints?.stdin && !op.params.file) {
-      console.log(`${'  --file <path>'.padEnd(28)} Read ${op.cliHints.stdin} from a file (alternative to --${op.cliHints.stdin} or stdin)`);
-    }
   }
 }
 

src/commands/autopilot.ts

@@ -38,6 +38,7 @@ 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.
@@ -433,6 +434,37 @@ 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
@@ -520,6 +552,10 @@ 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);
   };
@@ -1008,16 +1044,21 @@ 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');
-        const report = await runCycle(engine, {
+        // #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, {
           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

@@ -26,6 +26,7 @@
 import type { BrainEngine } from '../core/engine.ts';
 import {
   runCycle,
+  resolveSourceForDir,
   ALL_PHASES,
   type CyclePhase,
   type CycleReport,
@@ -380,9 +381,9 @@ Options:
 
   --source <id>       Scope the cycle to one source so doctor's
                       cycle_freshness check sees a fresh stamp on
-                      completion. Without this, gbrain dream's
-                      timestamp never lands and federated brains
-                      see "stale cycle" forever.
+                      completion. When omitted, gbrain derives the
+                      source from --dir / the configured checkout
+                      when it matches a source's local_path (#1869).
   --source-id <id>    Alias for --source. Matches the v0.37.7.0+
                       naming used by import/extract/graph-query.
 
@@ -634,6 +635,25 @@ 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

@@ -855,8 +855,16 @@ 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).
  */
-async function resolveSourceForDir(
+export async function resolveSourceForDir(
   engine: BrainEngine,
   brainDir: string | null,
 ): Promise<string | undefined> {

src/core/operations.ts

@@ -769,7 +769,7 @@ const get_page: Operation = {
 
 const put_page: Operation = {
   name: 'put_page',
-  description: 'Write/update a page (markdown with frontmatter). Chunks, embeds, reconciles tags, and (when auto_link/auto_timeline are enabled) extracts + reconciles graph links and timeline entries. On the CLI, `gbrain put SLUG --file PATH` reads content from a file (also `--content` or stdin). For provenance write-through and a binary-NUL guard, prefer `gbrain capture --file PATH --slug SLUG` (v0.39.3.0).',
+  description: 'Write/update a page (markdown with frontmatter). Chunks, embeds, reconciles tags, and (when auto_link/auto_timeline are enabled) extracts + reconciles graph links and timeline entries. For large content on Windows (pipe-buffer limit ~45KB) or any file-as-input workflow, use `gbrain capture --file PATH --slug SLUG` — capture reads the file as a Buffer with a binary-NUL guard and adds provenance write-through (v0.39.3.0).',
   params: {
     slug: { type: 'string', required: true, description: 'Page slug' },
     content: { type: 'string', required: true, description: 'Full markdown content with YAML frontmatter' },
@@ -1384,10 +1384,7 @@ const list_pages: Operation = {
   params: {
     type: { type: 'string', description: 'Filter by page type' },
     tag: { type: 'string', description: 'Filter by tag' },
-    limit: { type: 'number', description: 'Max results (default 50, capped at 100 — use offset to paginate beyond)' },
-    // #2876: the 100-row cap was silent and there was no way past it even
-    // though both engines already support OFFSET on listPages.
-    offset: { type: 'number', description: 'Skip first N results (pagination; pair with limit)' },
+    limit: { type: 'number', description: 'Max results (default 50)' },
     // v0.29 — surface filter that already exists on PageFilters.
     updated_after: {
       type: 'string',
@@ -1418,10 +1415,6 @@ const list_pages: Operation = {
       type: p.type as any,
       tag: p.tag as string,
       limit: clampSearchLimit(p.limit as number | undefined, 50, 100),
-      // #2876: thread pagination through (engines already honor offset).
-      offset: Number.isFinite(p.offset as number) && (p.offset as number) > 0
-        ? Math.floor(p.offset as number)
-        : undefined,
       includeDeleted: (p.include_deleted as boolean) === true,
       updated_after: typeof p.updated_after === 'string' ? p.updated_after : undefined,
       sort,

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

@@ -0,0 +1,63 @@
+/**
+ * #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/cli-args.test.ts

@@ -1,41 +1,8 @@
 import { describe, expect, test } from 'bun:test';
-import { mkdtempSync, rmSync, writeFileSync } from 'fs';
-import { tmpdir } from 'os';
-import { join } from 'path';
 import { parseOpArgs } from '../src/cli.ts';
 import { operationsByName } from '../src/core/operations.ts';
 
 describe('parseOpArgs', () => {
-  // #380: `gbrain put SLUG --file PATH` reads content from the file instead
-  // of silently swallowing the flag and creating an empty page.
-  test('put --file reads the stdin param (content) from a file', () => {
-    const dir = mkdtempSync(join(tmpdir(), 'gbrain-put-file-'));
-    try {
-      const pagePath = join(dir, 'page.md');
-      writeFileSync(pagePath, '# From file\n\nBody loaded from --file.\n');
-      const params = parseOpArgs(operationsByName.put_page, ['concepts/from-file', '--file', pagePath]);
-      expect(params.slug).toBe('concepts/from-file');
-      expect(params.content).toBe('# From file\n\nBody loaded from --file.\n');
-    } finally {
-      rmSync(dir, { recursive: true, force: true });
-    }
-  });
-
-  // #380 regression guard: undeclared-but-honored flags must keep passing
-  // through when unknown flags become hard errors (--source is read by
-  // makeContext; --json by the output seam; --dry-run by ctx.dryRun).
-  test('pass-through allowlist flags survive on ops that do not declare them', () => {
-    const params = parseOpArgs(operationsByName.get_page, [
-      'people/alice-example', '--source', 'wiki', '--json', '--dry-run',
-    ]);
-    expect(params).toEqual({
-      slug: 'people/alice-example',
-      source: 'wiki',
-      json: true,
-      dry_run: true,
-    });
-  });
-
   test('--no-<boolean> maps to false without consuming the next flag', () => {
     const params = parseOpArgs(operationsByName.query, [
       'freshEmbedSourceScope code source',

test/cli.test.ts

@@ -1,5 +1,5 @@
 import { describe, test, expect } from 'bun:test';
-import { existsSync, mkdtempSync, readFileSync, rmSync, writeFileSync } from 'fs';
+import { existsSync, mkdtempSync, readFileSync, rmSync } from 'fs';
 import { tmpdir } from 'os';
 import { join } from 'path';
 
@@ -120,76 +120,6 @@ describe('CLI dispatch integration', () => {
     expect(exitCode).toBe(0);
   });
 
-  // #380 / PR #856: put --help documents the --file input path.
-  test('put --help documents --file input', async () => {
-    const proc = Bun.spawn(['bun', 'run', 'src/cli.ts', 'put', '--help'], {
-      cwd: repoRoot,
-      stdout: 'pipe',
-      stderr: 'pipe',
-    });
-    const stdout = await new Response(proc.stdout).text();
-    const exitCode = await proc.exited;
-    expect(stdout).toContain('Usage: gbrain put');
-    expect(stdout).toContain('--file <path>');
-    expect(exitCode).toBe(0);
-  });
-
-  // #380: unknown flags on shared ops are a hard error (previously silently
-  // swallowed into params — `put --file` created empty pages). parseOpArgs
-  // runs BEFORE engine connect, so the error must fire without a brain.
-  test('unknown shared-op flags fail before DB connection', async () => {
-    const home = mkdtempSync(join(tmpdir(), 'gbrain-cli-unknown-flag-'));
-    try {
-      const proc = Bun.spawn(['bun', 'run', 'src/cli.ts', 'get', 'people/alice', '--bogus'], {
-        cwd: repoRoot,
-        stdout: 'pipe',
-        stderr: 'pipe',
-        env: isolatedEnv(home),
-      });
-      const stderr = await new Response(proc.stderr).text();
-      const exitCode = await proc.exited;
-      expect(stderr).toContain('Unknown option for gbrain get: --bogus');
-      expect(stderr).not.toContain('No brain configured');
-      expect(exitCode).toBe(1);
-    } finally {
-      rmSync(home, { recursive: true, force: true });
-    }
-  });
-
-  test('put rejects combining --file and --content', async () => {
-    const home = mkdtempSync(join(tmpdir(), 'gbrain-cli-put-conflict-'));
-    try {
-      const pagePath = join(home, 'page.md');
-      writeFileSync(pagePath, 'file body\n');
-      const proc = Bun.spawn(
-        ['bun', 'run', 'src/cli.ts', 'put', 'a/b', '--content', 'inline', '--file', pagePath],
-        { cwd: repoRoot, stdout: 'pipe', stderr: 'pipe', env: isolatedEnv(home) },
-      );
-      const stderr = await new Response(proc.stderr).text();
-      const exitCode = await proc.exited;
-      expect(stderr).toContain('use only one of --file, --content, or stdin');
-      expect(exitCode).toBe(1);
-    } finally {
-      rmSync(home, { recursive: true, force: true });
-    }
-  });
-
-  test('put --file with a missing path errors instead of writing an empty page', async () => {
-    const home = mkdtempSync(join(tmpdir(), 'gbrain-cli-put-missing-file-'));
-    try {
-      const proc = Bun.spawn(
-        ['bun', 'run', 'src/cli.ts', 'put', 'a/b', '--file', join(home, 'nope.md')],
-        { cwd: repoRoot, stdout: 'pipe', stderr: 'pipe', env: isolatedEnv(home) },
-      );
-      const stderr = await new Response(proc.stderr).text();
-      const exitCode = await proc.exited;
-      expect(stderr).toContain('cannot read --file');
-      expect(exitCode).toBe(1);
-    } finally {
-      rmSync(home, { recursive: true, force: true });
-    }
-  });
-
   test('upgrade --help prints usage without running upgrade', async () => {
     const proc = Bun.spawn(['bun', 'run', 'src/cli.ts', 'upgrade', '--help'], {
       cwd: repoRoot,

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

@@ -0,0 +1,99 @@
+/**
+ * #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

@@ -562,12 +562,22 @@ describe('runDream — --source / --source-id (v0.41.13)', () => {
 
   // ─── Back-compat: bare `gbrain dream` does NOT write per-source stamp ─
 
-  test('gbrain dream (no --source) leaves all sources untouched (back-compat regression)', async () => {
-    await seedSource('alpha');
-    await seedSource('beta');
+  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'],
+    );
     const report = await runDream(engine, ['--dir', repo, '--phase', 'lint', '--json']);
     expect(report).toBeTruthy();
-    expect(await readLastFullCycleAt('alpha')).toBeNull();
+    expect(await readLastFullCycleAt('alpha')).not.toBeNull();
     expect(await readLastFullCycleAt('beta')).toBeNull();
   }, 60_000);
 

test/list-pages-offset.test.ts

@@ -1,55 +0,0 @@
-import { describe, test, expect } from 'bun:test';
-import { operationsByName } from '../src/core/operations.ts';
-
-/**
- * #2876: `gbrain list --limit` silently clamped at 100 with no pagination.
- * list_pages now declares `offset` (both engines already supported it on
- * PageFilters) and the limit description discloses the 100-row cap.
- */
-describe('list_pages pagination (#2876)', () => {
-  const listPagesOp = operationsByName.list_pages;
-
-  function makeCtx(captured: unknown[]) {
-    return {
-      engine: {
-        listPages: async (filters: unknown) => {
-          captured.push(filters);
-          return [];
-        },
-      },
-      config: { engine: 'pglite' },
-      logger: { info() {}, warn() {}, error() {} },
-      dryRun: false,
-      remote: false,
-      sourceId: 'default',
-    } as any;
-  }
-
-  test('declares offset param and discloses the 100-row cap on limit', () => {
-    expect(listPagesOp.params.offset).toBeDefined();
-    expect(listPagesOp.params.offset.type).toBe('number');
-    expect(listPagesOp.params.limit.description).toContain('100');
-  });
-
-  test('threads offset through to engine.listPages', async () => {
-    const captured: any[] = [];
-    await listPagesOp.handler(makeCtx(captured), { limit: 10, offset: 30 });
-    expect(captured[0].offset).toBe(30);
-    expect(captured[0].limit).toBe(10);
-  });
-
-  test('drops negative, non-finite, and zero offsets', async () => {
-    const captured: any[] = [];
-    const ctx = makeCtx(captured);
-    await listPagesOp.handler(ctx, { offset: -5 });
-    await listPagesOp.handler(ctx, { offset: Infinity });
-    await listPagesOp.handler(ctx, { offset: 0 });
-    for (const f of captured) expect(f.offset).toBeUndefined();
-  });
-
-  test('floors fractional offsets', async () => {
-    const captured: any[] = [];
-    await listPagesOp.handler(makeCtx(captured), { offset: 7.9 });
-    expect(captured[0].offset).toBe(7);
-  });
-});