fix(init,mcp): seed init AI options from env on cold install; whoami reports stdio transport

Two backlog fixes:

- init (#1058): loadConfig() returns null on a cold install (no config.json
  AND no DATABASE_URL), short-circuiting before its env merge — so
  GBRAIN_EMBEDDING_MODEL / GBRAIN_EMBEDDING_DIMENSIONS /
  GBRAIN_EXPANSION_MODEL / GBRAIN_CHAT_MODEL were silently ignored and
  Tier-3 detection auto-picked by API key instead. resolveAIOptions' config
  seed now falls back to those env vars directly when loadConfig() is null
  (new exported helper seedAIOptionsFromConfig, env-injectable for tests).

- whoami (#1061): the stdio MCP dispatch is remote/untrusted by design but
  has no per-token auth (local pipe), so whoami threw unknown_transport on
  the primary stdio surface. The stdio dispatch now marks
  ctx.transport = 'stdio' and whoami returns {transport: 'stdio', scopes: []}
  for it. Trust posture unchanged: remote stays true, the marker is never
  used for trust decisions, and an unmarked auth-less remote context still
  throws (fail-closed preserved).

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

src/commands/extract.ts

@@ -1651,7 +1651,7 @@ async function extractTimelineFromDB(
  * make re-extraction idempotent). EVERY processed page is stamped, including
  * zero-link pages — they WERE processed.
  */
-export async function extractStaleFromDB(
+async function extractStaleFromDB(
   engine: BrainEngine,
   opts: {
     dryRun: boolean;

src/commands/init.ts

@@ -161,7 +161,7 @@ interface ResolveAIOptionsArgs {
   nonInteractive: boolean;       // --non-interactive (forces D3 fail-loud, no picker)
 }
 
-interface ResolvedAIOptions {
+export interface ResolvedAIOptions {
   embedding_model?: string;
   embedding_dimensions?: number;
   expansion_model?: string;
@@ -170,6 +170,41 @@ interface ResolvedAIOptions {
   noEmbedding?: boolean;
 }
 
+/**
+ * Seed init's AI options from persisted config, falling back to the raw env
+ * vars when loadConfig() returned null (#1058). On a cold install (no
+ * config.json AND no DATABASE_URL) loadConfig short-circuits BEFORE its env
+ * merge, so GBRAIN_EMBEDDING_MODEL / GBRAIN_EMBEDDING_DIMENSIONS /
+ * GBRAIN_EXPANSION_MODEL / GBRAIN_CHAT_MODEL were silently ignored by init
+ * and Tier-3 detection auto-picked by API key instead. Exported for unit
+ * tests (env injectable).
+ */
+export function seedAIOptionsFromConfig(
+  cfg: GBrainConfig | null,
+  env: NodeJS.ProcessEnv = process.env,
+): ResolvedAIOptions {
+  const envDims = env.GBRAIN_EMBEDDING_DIMENSIONS
+    ? parseInt(env.GBRAIN_EMBEDDING_DIMENSIONS, 10)
+    : NaN;
+  const seed = cfg ?? {
+    embedding_disabled: undefined,
+    embedding_model: env.GBRAIN_EMBEDDING_MODEL,
+    embedding_dimensions: Number.isFinite(envDims) ? envDims : undefined,
+    expansion_model: env.GBRAIN_EXPANSION_MODEL,
+    chat_model: env.GBRAIN_CHAT_MODEL,
+  };
+  const out: ResolvedAIOptions = {};
+  if (seed.embedding_disabled) {
+    out.noEmbedding = true;
+  } else if (seed.embedding_model) {
+    out.embedding_model = seed.embedding_model;
+    if (seed.embedding_dimensions) out.embedding_dimensions = seed.embedding_dimensions;
+  }
+  if (seed.expansion_model) out.expansion_model = seed.expansion_model;
+  if (seed.chat_model) out.chat_model = seed.chat_model;
+  return out;
+}
+
 /**
  * Resolve AI provider options for `gbrain init`.
  *
@@ -203,18 +238,13 @@ async function resolveAIOptions(opts: ResolveAIOptionsArgs): Promise<ResolvedAIO
   // user already opted into deferred mode.
   try {
     const { loadConfig } = await import('../core/config.ts');
-    const cfg = loadConfig();
-    if (cfg?.embedding_disabled) {
-      out.noEmbedding = true;
-    } else if (cfg?.embedding_model) {
-      out.embedding_model = cfg.embedding_model;
-      if (cfg.embedding_dimensions) out.embedding_dimensions = cfg.embedding_dimensions;
-    }
-    if (cfg?.expansion_model) out.expansion_model = cfg.expansion_model;
-    if (cfg?.chat_model) out.chat_model = cfg.chat_model;
+    // #1058: loadConfig() returns null on a cold install (no config.json AND
+    // no DATABASE_URL) — before it ever reaches its env merge. The seed helper
+    // falls back to the same GBRAIN_* env vars directly in that case.
+    Object.assign(out, seedAIOptionsFromConfig(loadConfig()));
   } catch {
-    // loadConfig throws when no brain configured — first-time install, fall
-    // through to env detection.
+    // loadConfig threw — treat as first-time install, fall through to env
+    // detection.
   }
 
   // --- Tier 1+2: explicit flags ---------------------------------------------

src/commands/jobs.ts

@@ -1479,31 +1479,7 @@ export async function registerBuiltinHandlers(
       embedSkipReason = 'auto_embed_disabled';
     }
 
-    // #2849: large-sync extract deferral follow-up. performSync skips inline
-    // link/timeline extraction when totalChanges > 100, leaving
-    // links_extracted_at unstamped. A standalone sync job (webhook push,
-    // sync trigger) has no autopilot extract phase behind it, so the pages
-    // would stay extraction-stale until a manual `gbrain extract --stale`.
-    // Queue a source-scoped stale sweep instead. Best-effort + idempotent:
-    // a duplicate sweep finds 0 stale pages and no-ops.
-    let extractJobId: number | null = null;
-    if (result.extractDeferred) {
-      try {
-        const { MinionQueue } = await import('../core/minions/queue.ts');
-        const queue = new MinionQueue(engine);
-        const followUp = await queue.add(
-          'extract',
-          { stale: true, ...(sourceId ? { sourceId } : {}) },
-          {
-            idempotency_key: `sync-extract-stale:${sourceId ?? 'default'}:${Math.floor(Date.now() / 30_000)}`,
-            maxWaiting: 1,
-          },
-        );
-        extractJobId = followUp.id;
-      } catch { /* best-effort: extract --stale sweeps it later */ }
-    }
-
-    return { ...result, embed_job_id: embedJobId, embed_skip_reason: embedSkipReason, extract_stale_job_id: extractJobId };
+    return { ...result, embed_job_id: embedJobId, embed_skip_reason: embedSkipReason };
   });
 
   registerBuiltinJob(worker, engine, 'embed', async (job) => {
@@ -1676,20 +1652,6 @@ export async function registerBuiltinHandlers(
   });
 
   worker.register('extract', async (job) => {
-    // #2849: stale-sweep mode — the sync handler's large-sync deferral
-    // follow-up. DB-source (reads page content from the DB, so it runs on
-    // checkout-less brains), source-scopable, idempotent. Same core as
-    // `gbrain extract --stale`.
-    if (job.data.stale === true) {
-      const { extractStaleFromDB } = await import('./extract.ts');
-      return await extractStaleFromDB(engine, {
-        dryRun: !!job.data.dryRun,
-        jsonMode: false,
-        includeFrontmatter: false,
-        sourceIdFilter: typeof job.data.sourceId === 'string' ? job.data.sourceId : undefined,
-        catchUp: false,
-      });
-    }
     const { runExtractCore } = await import('./extract.ts');
     const mode = (typeof job.data.mode === 'string' && ['links', 'timeline', 'all'].includes(job.data.mode))
       ? (job.data.mode as 'links' | 'timeline' | 'all')

src/commands/serve-http.ts

@@ -2146,13 +2146,8 @@ export async function runServeHttp(engine: BrainEngine, options: ServeHttpOption
   //     Other event types (ping, pull_request, etc.) return 202 'ignored'
   //     so GitHub doesn't retry.
   // D15.5: HMAC compare uses the shared safeHexEqual helper.
-  // D18: submits 'sync' job with extraction + auto_embed_backfill enabled and
-  //     priority -10 (above autopilot's 0). noExtract:false opts normal
-  //     incremental pushes into sync's inline link/timeline extraction (#2849
-  //     — the standalone sync handler defaults noExtract to TRUE, which left
-  //     webhook-imported pages permanently stale). Large (>100 file) pushes
-  //     defer inline extract; the sync handler queues an extract --stale
-  //     follow-up job for that branch.
+  // D18: submits 'sync' job with auto_embed_backfill=true and priority -10
+  //     (above autopilot's 0).
   // ---------------------------------------------------------------------------
   const githubWebhookLimiter = rateLimit({
     windowMs: 60_000,
@@ -2272,7 +2267,6 @@ export async function runServeHttp(engine: BrainEngine, options: ServeHttpOption
           'sync',
           {
             sourceId: source.id,
-            noExtract: false,
             auto_embed_backfill: true,
             embed_reason: 'webhook',
           },

src/commands/sync.ts

@@ -222,14 +222,6 @@ export interface SyncResult {
    * everything," the exact misdiagnosis in the #1794 recurrence report.
    */
   bankedFiles?: number;
-  /**
-   * #2849: true when extraction was REQUESTED (noExtract false) but this sync
-   * skipped inline link/timeline extraction because totalChanges > 100 (the
-   * #1794 large-sync deferral). links_extracted_at stays unstamped for the
-   * imported pages. The standalone `sync` job handler queues a source-scoped
-   * `extract --stale` follow-up when set; CLI runs print the manual hint.
-   */
-  extractDeferred?: boolean;
 }
 
 /**
@@ -1387,10 +1379,6 @@ See also:
     {
       sourceId: sourceIdArg,
       repoPath: source.local_path,
-      // #2849: opt in to inline extraction — the standalone sync handler
-      // defaults noExtract to TRUE (dedupe for doctor's [sync, extract]
-      // remediation plan), which would leave triggered syncs extraction-stale.
-      noExtract: false,
       auto_embed_backfill: true,
       embed_reason: 'sync_trigger',
     },
@@ -3299,16 +3287,11 @@ async function performSyncInner(engine: BrainEngine, opts: SyncOpts): Promise<Sy
   // the stale sweep scans the whole source, so banked-across-runs pages are
   // covered regardless.
   const extractOpts = opts.sourceId ? { sourceId: opts.sourceId } : undefined;
-  let extractDeferred = false;
   if (!opts.noExtract && totalChanges > 100 && pagesAffected.length > 0) {
-    // #2849: surface the deferral to callers. A standalone sync job (webhook
-    // push, sync trigger) has no autopilot extract phase behind it, so the
-    // job handler queues an `extract --stale` follow-up off this flag.
-    extractDeferred = true;
     slog(
       `  Large sync: deferring link/timeline extraction. ` +
       `Run 'gbrain extract --stale${opts.sourceId ? ` --source-id ${opts.sourceId}` : ''}' ` +
-      `(sync jobs queue this follow-up automatically).`,
+      `(or let the autopilot cycle's extract phase sweep it).`,
     );
   }
   if (!opts.noExtract && totalChanges <= 100 && pagesAffected.length > 0) {
@@ -3417,7 +3400,6 @@ async function performSyncInner(engine: BrainEngine, opts: SyncOpts): Promise<Sy
     chunksCreated,
     embedded,
     pagesAffected,
-    extractDeferred,
   };
 }
 

src/core/operations.ts

@@ -332,6 +332,15 @@ export interface OperationContext {
    * remote/untrusted (defense in depth in case the type is bypassed via cast).
    */
   remote: boolean;
+  /**
+   * Transport marker for auth-less remote surfaces (#1061). The stdio MCP
+   * dispatch sets 'stdio' — it is deliberately `remote: true` (agent-facing,
+   * untrusted) but has no per-token auth (local pipe), so identity ops like
+   * whoami need a way to distinguish "known auth-less transport" from "a
+   * transport bug forgot to thread ctx.auth". Trust decisions MUST NOT key
+   * off this field — only `ctx.remote === false` grants trust.
+   */
+  transport?: 'stdio';
   /**
    * Subagent runtime context (v0.16+). Set by the subagent tool dispatcher when
    * dispatching an op as a tool call from an LLM loop. Used to enforce per-op
@@ -3713,9 +3722,10 @@ const whoami: Operation = {
     'Introspect the calling identity. Returns one of three transport shapes: ' +
     '{transport: "oauth", client_id, client_name, scopes, expires_at}, ' +
     '{transport: "legacy", token_name, scopes, expires_at: null}, or ' +
-    '{transport: "local", scopes: []}. Throws unknown_transport when the ' +
-    'context is ambiguous (remote=true without auth) — fail-closed posture ' +
-    'mirroring the v0.26.9 trust-boundary contract.',
+    '{transport: "local", scopes: []}, or {transport: "stdio", scopes: []} ' +
+    'for the auth-less stdio MCP pipe. Throws unknown_transport when the ' +
+    'context is ambiguous (remote=true without auth and no transport marker) ' +
+    '— fail-closed posture mirroring the v0.26.9 trust-boundary contract.',
   params: {},
   scope: 'read',
   handler: async (ctx) => {
@@ -3727,6 +3737,12 @@ const whoami: Operation = {
     if (ctx.remote === false) {
       return { transport: 'local', scopes: [] };
     }
+    // #1061: stdio MCP is remote/untrusted by design but has no per-token
+    // auth (local pipe) — a known transport, not a bug. Report it instead of
+    // throwing. Empty scopes: nothing here may be used to gate anything.
+    if (!ctx.auth && ctx.transport === 'stdio') {
+      return { transport: 'stdio', scopes: [] };
+    }
     if (!ctx.auth) {
       throw new OperationError(
         'unknown_transport',

src/mcp/dispatch.ts

@@ -32,6 +32,12 @@ export interface DispatchOpts {
   remote?: boolean;
   /** Override the default stderr logger (e.g. CLI uses console.* directly). */
   logger?: OperationContext['logger'];
+  /**
+   * #1061: transport marker for auth-less remote surfaces. The stdio MCP
+   * server passes 'stdio' so identity ops (whoami) can report the transport
+   * instead of throwing unknown_transport. Never used for trust decisions.
+   */
+  transport?: OperationContext['transport'];
   /**
    * v0.28: per-token allow-list for the takes.holder field. Threaded by
    * the HTTP/stdio transport from `access_tokens.permissions.takes_holders`.
@@ -203,6 +209,7 @@ export function buildOperationContext(
     logger: opts.logger || stderrLogger,
     dryRun: !!params.dry_run,
     remote: opts.remote ?? true,
+    transport: opts.transport,
     takesHoldersAllowList: opts.takesHoldersAllowList,
     // v0.34 D4: sourceId is REQUIRED at the type level. Auto-fill 'default'
     // for single-source brains and any caller who didn't resolve a sourceId.

src/mcp/server.ts

@@ -42,6 +42,10 @@ export async function startMcpServer(engine: BrainEngine) {
     // `gbrain call <op>` (sets remote=false in src/cli.ts).
     return dispatchToolCall(engine, name, params, {
       remote: true,
+      // #1061: mark the transport so whoami can report {transport: 'stdio'}
+      // instead of throwing unknown_transport. Trust posture unchanged —
+      // stdio stays remote/untrusted.
+      transport: 'stdio',
       takesHoldersAllowList: ['world'],
       // v0.31: source defaults to 'default' for stdio (no per-token scope).
       // Operators who want a different source on stdio MCP should set

test/init-env-detection.test.ts

@@ -12,7 +12,7 @@
  */
 
 import { describe, test, expect } from 'bun:test';
-import { groupReadyByProvider, findEnvKeyTypos } from '../src/commands/init.ts';
+import { groupReadyByProvider, findEnvKeyTypos, seedAIOptionsFromConfig } from '../src/commands/init.ts';
 
 describe('groupReadyByProvider — embedding touchpoint', () => {
   test('OPENAI_API_KEY alone → openai is ready', async () => {
@@ -149,3 +149,47 @@ describe('findEnvKeyTypos', () => {
     expect(got.find(t => t.userSet === 'COMPLETELY_UNRELATED_KEY')).toBeUndefined();
   });
 });
+
+describe('seedAIOptionsFromConfig — #1058 cold-install env fallback', () => {
+  test('null config (no config.json, no DATABASE_URL) falls back to GBRAIN_* env vars', () => {
+    const got = seedAIOptionsFromConfig(null, {
+      GBRAIN_EMBEDDING_MODEL: 'voyage:voyage-3-large',
+      GBRAIN_EMBEDDING_DIMENSIONS: '1024',
+      GBRAIN_EXPANSION_MODEL: 'openai:gpt-5-mini',
+      GBRAIN_CHAT_MODEL: 'anthropic:claude-sonnet-4-6',
+    });
+    expect(got.embedding_model).toBe('voyage:voyage-3-large');
+    expect(got.embedding_dimensions).toBe(1024);
+    expect(got.expansion_model).toBe('openai:gpt-5-mini');
+    expect(got.chat_model).toBe('anthropic:claude-sonnet-4-6');
+  });
+
+  test('null config + no env vars → empty seed (Tier-3 detection takes over)', () => {
+    const got = seedAIOptionsFromConfig(null, {});
+    expect(got).toEqual({});
+  });
+
+  test('persisted config wins (loadConfig already merged env when non-null)', () => {
+    const got = seedAIOptionsFromConfig(
+      { engine: 'pglite', embedding_model: 'openai:text-embedding-3-small', embedding_dimensions: 1536 } as any,
+      { GBRAIN_EMBEDDING_MODEL: 'voyage:voyage-3-large' },
+    );
+    expect(got.embedding_model).toBe('openai:text-embedding-3-small');
+    expect(got.embedding_dimensions).toBe(1536);
+  });
+
+  test('embedding_disabled sentinel honored on re-init', () => {
+    const got = seedAIOptionsFromConfig({ engine: 'pglite', embedding_disabled: true } as any, {});
+    expect(got.noEmbedding).toBe(true);
+    expect(got.embedding_model).toBeUndefined();
+  });
+
+  test('non-numeric GBRAIN_EMBEDDING_DIMENSIONS ignored, model still seeds', () => {
+    const got = seedAIOptionsFromConfig(null, {
+      GBRAIN_EMBEDDING_MODEL: 'voyage:voyage-3-large',
+      GBRAIN_EMBEDDING_DIMENSIONS: 'not-a-number',
+    });
+    expect(got.embedding_model).toBe('voyage:voyage-3-large');
+    expect(got.embedding_dimensions).toBeUndefined();
+  });
+});

test/sources-webhook.test.ts

@@ -16,7 +16,6 @@
  */
 import { describe, test, expect } from 'bun:test';
 import { createHmac } from 'node:crypto';
-import { readFileSync } from 'node:fs';
 import { safeHexEqual } from '../src/core/timing-safe.ts';
 
 const GITHUB_SECRET = 'super-secret-webhook-key';
@@ -124,25 +123,3 @@ describe('Branch ref construction (D5)', () => {
     expect(pushedRef === `refs/heads/${trackedBranch}`).toBe(false);
   });
 });
-
-describe('Webhook sync job extraction contract (#2849)', () => {
-  test('opts into extraction before the pushed commit is consumed', () => {
-    const serveSource = readFileSync(
-      new URL('../src/commands/serve-http.ts', import.meta.url),
-      'utf8',
-    );
-    const routeStart = serveSource.indexOf("'/webhooks/github'");
-    const queueStart = serveSource.indexOf('const job = await queue.add(', routeStart);
-    const responseStart = serveSource.indexOf('res.status(202)', queueStart);
-    expect(routeStart).toBeGreaterThanOrEqual(0);
-    expect(queueStart).toBeGreaterThan(routeStart);
-    expect(responseStart).toBeGreaterThan(queueStart);
-
-    const routeSource = serveSource.slice(queueStart, responseStart);
-    const payload = routeSource.match(
-      /queue\.add\(\s*'sync',\s*\{([\s\S]*?)\}\s*,\s*\{/,
-    );
-    expect(payload).not.toBeNull();
-    expect(payload?.[1]).toMatch(/\bnoExtract:\s*false\b/);
-  });
-});

test/sync-large-deferral-extract.serial.test.ts

@@ -1,130 +0,0 @@
-/**
- * #2849 — large-sync extract deferral queues an `extract --stale` follow-up.
- *
- * performSync's incremental path skips inline link/timeline extraction when
- * totalChanges > 100 (the #1794 large-sync deferral), leaving
- * links_extracted_at unstamped. Pre-fix, a standalone sync job (webhook push,
- * `gbrain sync trigger`) had NOTHING behind it to sweep those pages — the
- * autopilot cycle's extract phase only walks that cycle's changedSlugs — so a
- * large webhook push left extraction permanently stale until a manual
- * `gbrain extract --stale`.
- *
- * Pins:
- *   (a) performSync surfaces `extractDeferred: true` on the >100 branch and
- *       leaves the pages unstamped/unlinked.
- *   (b) the `sync` job handler queues an `extract` job with
- *       { stale: true, sourceId? } when extractDeferred is set.
- *   (c) the `extract` handler's stale mode actually sweeps: links created +
- *       watermark stamped (end-to-end recovery, no manual step).
- *
- * Marked .serial.test.ts — spawns git subprocesses + shares one PGLite engine.
- */
-
-import { describe, test, expect, beforeAll, afterAll } from 'bun:test';
-import { mkdtempSync, writeFileSync, rmSync, mkdirSync } from 'fs';
-import { execSync } from 'child_process';
-import { tmpdir } from 'os';
-import { join } from 'path';
-import { PGLiteEngine } from '../src/core/pglite-engine.ts';
-import { MinionWorker } from '../src/core/minions/worker.ts';
-import { MinionQueue } from '../src/core/minions/queue.ts';
-import { registerBuiltinHandlers } from '../src/commands/jobs.ts';
-
-let engine: PGLiteEngine;
-let worker: MinionWorker;
-let repoPath: string;
-
-function git(cmd: string): void { execSync(cmd, { cwd: repoPath, stdio: 'pipe' }); }
-
-describe('#2849 — large sync defers extract and queues a stale sweep', () => {
-  beforeAll(async () => {
-    engine = new PGLiteEngine();
-    await engine.connect({});
-    await engine.initSchema();
-    worker = new MinionWorker(engine, { queue: 'test' });
-    await registerBuiltinHandlers(worker, engine, { quiet: true });
-
-    repoPath = mkdtempSync(join(tmpdir(), 'gbrain-large-defer-'));
-    git('git init');
-    git('git config user.email "t@t.com"');
-    git('git config user.name "T"');
-    mkdirSync(join(repoPath, 'people'), { recursive: true });
-    mkdirSync(join(repoPath, 'notes'), { recursive: true });
-    writeFileSync(join(repoPath, 'people/alice.md'), [
-      '---', 'type: person', 'title: Alice', '---', '', 'Alice is a founder.',
-    ].join('\n'));
-    git('git add -A && git commit -m "initial"');
-
-    // Seed: full first sync imports the anchor page + sets last_commit.
-    const { performSync } = await import('../src/commands/sync.ts');
-    await performSync(engine, { repoPath, full: true, noPull: true, noEmbed: true });
-
-    // Second commit: 101 new pages → incremental totalChanges > 100.
-    for (let i = 0; i < 101; i++) {
-      writeFileSync(join(repoPath, `notes/n${i}.md`), [
-        '---', 'type: note', `title: Note ${i}`, '---', '',
-        `[Alice](people/alice) appears in note ${i}.`,
-      ].join('\n'));
-    }
-    git('git add -A && git commit -m "add 101 pages"');
-  }, 120_000);
-
-  afterAll(async () => {
-    if (repoPath) rmSync(repoPath, { recursive: true, force: true });
-    if (engine) await engine.disconnect();
-  }, 60_000);
-
-  test('sync handler defers inline extract and queues extract{stale} follow-up; stale sweep recovers', async () => {
-    const syncHandler = (worker as unknown as { handlers: Map<string, (job: unknown) => Promise<unknown>> })
-      .handlers.get('sync');
-    expect(syncHandler).toBeDefined();
-
-    // Same payload shape the webhook submits (minus embed backfill noise).
-    const result = await syncHandler!({
-      data: { repoPath, noExtract: false, noPull: true, auto_embed_backfill: false },
-      signal: { aborted: false },
-      updateProgress: async () => {},
-    }) as { status: string; extractDeferred?: boolean; extract_stale_job_id?: number | null };
-
-    expect(result.status).toBe('synced');
-    // (a) inline extract was deferred, pages left stale.
-    expect(result.extractDeferred).toBe(true);
-    const staleBefore = await engine.countStalePagesForExtraction();
-    expect(staleBefore).toBeGreaterThan(100);
-    expect(await engine.getLinks('notes/n0')).toHaveLength(0);
-
-    // (b) a follow-up extract job with stale:true was queued.
-    expect(result.extract_stale_job_id).toBeGreaterThan(0);
-    const queue = new MinionQueue(engine);
-    const extractJobs = await queue.getJobs({ name: 'extract', limit: 5 });
-    expect(extractJobs.length).toBe(1);
-    expect((extractJobs[0].data as { stale: boolean }).stale).toBe(true);
-
-    // (c) running the extract handler's stale mode recovers: links + stamps.
-    const extractHandler = (worker as unknown as { handlers: Map<string, (job: unknown) => Promise<unknown>> })
-      .handlers.get('extract');
-    await extractHandler!({
-      data: extractJobs[0].data,
-      signal: { aborted: false },
-      updateProgress: async () => {},
-    });
-    const links = await engine.getLinks('notes/n0');
-    expect(links.some(l => l.to_slug === 'people/alice')).toBe(true);
-    const rows = await engine.executeRaw<{ links_extracted_at: string | null }>(
-      `SELECT links_extracted_at FROM pages WHERE slug = 'notes/n0'`,
-    );
-    expect(rows[0]?.links_extracted_at).not.toBeNull();
-  }, 180_000);
-
-  test('sub-threshold sync does NOT set extractDeferred (no spurious follow-up)', async () => {
-    // One more small commit → inline extract path, no deferral.
-    writeFileSync(join(repoPath, 'notes/small.md'), [
-      '---', 'type: note', 'title: Small', '---', '', 'No big deal.',
-    ].join('\n'));
-    git('git add -A && git commit -m "one small page"');
-    const { performSync } = await import('../src/commands/sync.ts');
-    const result = await performSync(engine, { repoPath, noPull: true, noEmbed: true });
-    expect(result.status).toBe('synced');
-    expect(result.extractDeferred).toBeFalsy();
-  }, 60_000);
-});

test/sync-trigger-cli.test.ts

@@ -100,10 +100,6 @@ describe('runSyncTrigger', () => {
     const job = jobs[0];
     expect(job.priority).toBe(-10);
     expect((job.data as { sourceId: string }).sourceId).toBe('default');
-    // #2849: opt in to inline extraction — the standalone sync handler
-    // defaults noExtract to TRUE, which would leave triggered syncs
-    // extraction-stale.
-    expect((job.data as { noExtract: boolean }).noExtract).toBe(false);
     expect((job.data as { auto_embed_backfill: boolean }).auto_embed_backfill).toBe(true);
   });
 

test/whoami.test.ts

@@ -94,6 +94,35 @@ describe('whoami op contract', () => {
     expect(result.expires_at).toBeNull();
   });
 
+  // #1061: stdio MCP is remote/untrusted by design but has no per-token auth
+  // (local pipe). The stdio dispatch marks ctx.transport='stdio'; whoami
+  // reports it instead of throwing unknown_transport.
+  test('stdio transport (remote=true, no auth, transport marker) reports stdio', async () => {
+    const result = (await whoami.handler(
+      ctxWith({ remote: true, auth: undefined, transport: 'stdio' }),
+      {},
+    )) as any;
+    expect(result.transport).toBe('stdio');
+    expect(result.scopes).toEqual([]);
+  });
+
+  test('stdio marker does not mask real auth (auth still wins)', async () => {
+    const result = (await whoami.handler(
+      ctxWith({
+        remote: true,
+        transport: 'stdio',
+        auth: {
+          token: 'gbrain_at_xxx',
+          clientId: 'gbrain_cl_abc',
+          scopes: ['read'],
+          expiresAt: 1,
+        } as AuthInfo,
+      }),
+      {},
+    )) as any;
+    expect(result.transport).toBe('oauth');
+  });
+
   // Q3: ambiguous transport — fail-closed. The footgun this guards against
   // is a future transport that lands without threading auth, where a buggy
   // caller might trust whoami's output to gate sensitive ops.