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/autopilot.ts

@@ -686,7 +686,6 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
       try {
         const { MinionQueue } = await import('../core/minions/queue.ts');
         const { computeRecommendations, embeddingProviderConfigured, HOSTED_EMBED_KEY_CONFIG } = await import('../core/brain-score-recommendations.ts');
-        const { countExtractionLag } = await import('../core/remediation/context.ts');
         const queue = new MinionQueue(engine);
         const slotMs = Math.floor(Date.now() / (baseInterval * 1000)) * baseInterval * 1000;
         const slot = new Date(slotMs).toISOString();
@@ -878,9 +877,6 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
             return !!(process.env[envVar] || (cfgField ? embedKeyCfg[cfgField] : undefined));
           }),
           hasChatApiKey: !!(process.env.ANTHROPIC_API_KEY || await engine.getConfig('anthropic_api_key')),
-          // Real extraction-lag gate for sync.repo/extract.all — same counter
-          // loadRecommendationContext uses (replaces the health.stale_pages proxy).
-          extractionLagPages: await countExtractionLag(engine),
         };
         // v0.41.18.0 (A5 + A19 + A22, T15): consult onboard recommendations
         // ALONGSIDE doctor's brain-score recommendations. Onboard's 4 new

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/core/brain-score-recommendations.ts

@@ -146,16 +146,6 @@ export interface RecommendationContext {
   chatModel?: string;
   /** Whether the chat provider has a usable API key. */
   hasChatApiKey?: boolean;
-  /**
-   * Count of pages needing link/timeline extraction — the SAME staleness the
-   * `gbrain extract --stale` walk and doctor's `links_extraction_lag` check use
-   * (`engine.countStalePagesForExtraction`). Gates the sync→extract pipeline
-   * (sync.repo / extract.all). Replaces the old `health.stale_pages` gate, which
-   * counted "pages whose updated_at predates their newest timeline entry" — a
-   * proxy that broke when the updated_at-on-timeline-insert trigger was dropped
-   * (migration v10) and never reflected real extraction work.
-   */
-  extractionLagPages?: number;
 }
 
 /** Triage result for one check. */
@@ -202,28 +192,20 @@ export function computeRecommendations(
   const source = ctx.sourceId ?? 'default';
 
   // ---------------------------------------------------------------------
-  // sync.repo + extract.all — the materialization pipeline, gated on the REAL
-  // extraction lag (pages whose link/timeline edges are stale), NOT on the
-  // legacy `health.stale_pages` proxy. `extractionLagPages` comes from the same
-  // counter the `extract --stale` walk + doctor's `links_extraction_lag` use, so
-  // the recommendation can only fire when running extract will actually reduce
-  // it (and clear the rec). See RecommendationContext.extractionLagPages.
-  // sync.repo is the prerequisite: re-sync so pages are current before extract
-  // materializes their edges.
+  // sync.repo — fires when sync hasn't run recently OR pages are stale
   // ---------------------------------------------------------------------
-  const extractionLag = ctx.extractionLagPages ?? 0;
-  if (ctx.repoPath && extractionLag > 0) {
+  if (ctx.repoPath && health.stale_pages > 0) {
     const params = { repoPath: ctx.repoPath, sourceId: ctx.sourceId, noEmbed: true };
     out.push({
       id: 'sync.repo',
       job: 'sync',
       params,
       idempotency_key: idemKey(source, 'sync', params),
-      severity: extractionLag > 50 ? 'high' : 'medium',
-      est_seconds: Math.min(600, 30 + extractionLag * 0.5),
+      severity: health.stale_pages > 50 ? 'high' : 'medium',
+      est_seconds: Math.min(600, 30 + health.stale_pages * 0.5),
       est_usd_cost: 0,  // sync is fs+DB only
       depends_on: [],
-      rationale: `Sync before extracting ${extractionLag} page${extractionLag === 1 ? '' : 's'} with stale link/timeline edges`,
+      rationale: `${health.stale_pages} stale page${health.stale_pages === 1 ? '' : 's'} on disk`,
       status: 'remediable',
     });
   }
@@ -255,7 +237,7 @@ export function computeRecommendations(
       est_seconds: Math.min(3600, 5 + health.missing_embeddings * 0.05),
       est_usd_cost,
       // sync should run first so embed sees fresh pages.
-      depends_on: ctx.repoPath && extractionLag > 0 ? ['sync.repo'] : [],
+      depends_on: ctx.repoPath && health.stale_pages > 0 ? ['sync.repo'] : [],
       rationale: `${health.missing_embeddings} chunk${health.missing_embeddings === 1 ? '' : 's'} invisible to vector search`,
       status: 'remediable',
     });
@@ -285,7 +267,7 @@ export function computeRecommendations(
   // Triggered when sync.repo fires (because sync was set to noEmbed:true,
   // and noExtract:true after T5 lands → extract job is the materializer).
   // ---------------------------------------------------------------------
-  if (ctx.repoPath && extractionLag > 0) {
+  if (ctx.repoPath && health.stale_pages > 0) {
     const params = { mode: 'all', dir: ctx.repoPath };
     out.push({
       id: 'extract.all',
@@ -296,7 +278,7 @@ export function computeRecommendations(
       est_seconds: Math.min(600, 30 + health.page_count * 0.01),
       est_usd_cost: 0,
       depends_on: ['sync.repo'],
-      rationale: `Materialize link + timeline edges for ${extractionLag} page${extractionLag === 1 ? '' : 's'} with stale extraction`,
+      rationale: 'Materialize link + timeline edges from fresh pages',
       status: 'remediable',
     });
   }

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/core/remediation/context.ts

@@ -8,7 +8,6 @@
 
 import type { BrainEngine } from '../engine.ts';
 import type { RecommendationContext } from '../brain-score-recommendations.ts';
-import { LINK_EXTRACTOR_VERSION_TS } from '../link-extraction.ts';
 
 // Re-export so consumers can `import { RecommendationContext } from '../remediation'`
 // — the canonical RecommendationContext type still lives in
@@ -69,29 +68,5 @@ export async function loadRecommendationContext(
     embeddingDimensions,
     embeddingProviderConfigured: embeddingConfigured,
     hasChatApiKey: !!(process.env.ANTHROPIC_API_KEY || fileCfg?.anthropic_api_key),
-    extractionLagPages: await countExtractionLag(engine),
   };
 }
-
-/**
- * Real extraction-lag count — the SAME staleness `gbrain extract --stale`
- * processes (engine.countStalePagesForExtraction with
- * versionTs=LINK_EXTRACTOR_VERSION_TS, matching doctor's links_extraction_lag
- * check — without versionTs, pages stamped before an extractor version bump
- * would lag for doctor/extract but never trip this gate). Drives the
- * sync→extract recommendation pipeline; replaces the legacy
- * `health.stale_pages` proxy that no longer reflected real extraction work
- * after the v10 trigger drop.
- *
- * Shared by loadRecommendationContext AND the D7 per-step recheck in
- * runRemediation — the recheck MUST refresh this gate alongside getHealth,
- * or a completed extract step keeps re-firing off the frozen initial count.
- */
-export async function countExtractionLag(engine: BrainEngine): Promise<number> {
-  try {
-    return await engine.countStalePagesForExtraction({ versionTs: LINK_EXTRACTOR_VERSION_TS });
-  } catch {
-    /* counter unavailable (very old brain / mid-migration) — treat as 0 */
-    return 0;
-  }
-}

src/core/remediation/run.ts

@@ -16,7 +16,7 @@ import {
   computeRecommendations,
 } from '../brain-score-recommendations.ts';
 import type { RemediationStep } from '../remediation-step.ts';
-import { countExtractionLag, loadRecommendationContext } from './context.ts';
+import { loadRecommendationContext } from './context.ts';
 import { computeRemediationPlan } from './plan.ts';
 import type {
   RemediationHooks,
@@ -65,7 +65,7 @@ export async function runRemediation(
     clearRemediationCheckpoint,
   } = await import('../remediation-checkpoint.ts');
 
-  let ctx = await loadRecommendationContext(engine);
+  const ctx = await loadRecommendationContext(engine);
 
   // Pre-flight ceiling check via the shared plan computation.
   const initialPlan = await computeRemediationPlan(engine, { targetScore });
@@ -305,11 +305,6 @@ export async function runRemediation(
       // steps with bumped retry suffix (D1).
       if (recs.length === 0 || stepCount >= maxJobs) break;
       const freshHealth = await engine.getHealth();
-      // Refresh the extraction-lag gate alongside health: ctx was loaded once
-      // before the loop, and a completed sync/extract step is exactly what
-      // drives the count down. Reusing the frozen initial count would re-fire
-      // sync.repo/extract.all every recheck until maxJobs.
-      ctx = { ...ctx, extractionLagPages: await countExtractionLag(engine) };
       recs = computeRecommendations(freshHealth, ctx).filter((r) => r.status === 'remediable');
     }
   };

src/core/types.ts

@@ -1423,15 +1423,6 @@ export interface BrainStats {
 export interface BrainHealth {
   page_count: number;
   embed_coverage: number;
-  /**
-   * LEGACY proxy: count of pages whose `updated_at` predates their newest
-   * timeline entry. This bumped meaningfully only while a trigger updated
-   * `pages.updated_at` on timeline insert; that trigger was dropped in
-   * migration v10, so the metric no longer reflects real "needs work" state.
-   * NO LONGER gates remediations — the sync→extract pipeline now gates on
-   * `RecommendationContext.extractionLagPages` (the real extraction-lag from
-   * `countStalePagesForExtraction`). Retained for the CLI health line + back-compat.
-   */
   stale_pages: number;
   /**
    * Islanded pages — zero inbound AND zero outbound links. A hub page

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/brain-score-recommendations.test.ts

@@ -119,12 +119,13 @@ describe('computeRecommendations', () => {
     expect(recs.find((r) => r.id === 'embed.stale')).toBeUndefined();
   });
 
-  test('extraction lag + dead links produce sync + backlinks + extract', () => {
+  test('stale pages + dead links produce sync + backlinks + extract', () => {
     const health = makeHealth({
+      stale_pages: 25,
       dead_links: 8,
       brain_score: 70,
     });
-    const recs = computeRecommendations(health, { repoPath: '/brain', embeddingProviderConfigured: true, extractionLagPages: 25 });
+    const recs = computeRecommendations(health, { repoPath: '/brain', embeddingProviderConfigured: true });
     const ids = recs.map((r) => r.id);
     expect(ids).toContain('sync.repo');
     expect(ids).toContain('backlinks.fix');
@@ -132,17 +133,18 @@ describe('computeRecommendations', () => {
   });
 
   test('extract.all depends on sync.repo (D14: stable ids)', () => {
-    const health = makeHealth();
-    const recs = computeRecommendations(health, { repoPath: '/brain', embeddingProviderConfigured: true, extractionLagPages: 10 });
+    const health = makeHealth({ stale_pages: 10 });
+    const recs = computeRecommendations(health, { repoPath: '/brain', embeddingProviderConfigured: true });
     const extract = recs.find((r) => r.id === 'extract.all');
     expect(extract?.depends_on).toContain('sync.repo');
   });
 
-  test('embed.stale depends on sync.repo when extraction also needed', () => {
+  test('embed.stale depends on sync.repo when sync also needed', () => {
     const health = makeHealth({
+      stale_pages: 10,
       missing_embeddings: 100,
     });
-    const recs = computeRecommendations(health, { repoPath: '/brain', embeddingProviderConfigured: true, extractionLagPages: 10 });
+    const recs = computeRecommendations(health, { repoPath: '/brain', embeddingProviderConfigured: true });
     const embed = recs.find((r) => r.id === 'embed.stale');
     expect(embed?.depends_on).toContain('sync.repo');
   });
@@ -157,9 +159,9 @@ describe('computeRecommendations', () => {
   test('severity ordering: critical before high before medium', () => {
     const health = makeHealth({
       missing_embeddings: 100,  // critical
+      stale_pages: 80,          // high
     });
-    // extractionLagPages > 50 → sync.repo fires at 'high' severity.
-    const recs = computeRecommendations(health, { repoPath: '/brain', embeddingProviderConfigured: true, extractionLagPages: 80 });
+    const recs = computeRecommendations(health, { repoPath: '/brain', embeddingProviderConfigured: true });
     const critIdx = recs.findIndex((r) => r.severity === 'critical');
     const highIdx = recs.findIndex((r) => r.severity === 'high');
     expect(critIdx).toBeLessThan(highIdx);
@@ -168,10 +170,11 @@ describe('computeRecommendations', () => {
   // D6 #5 — THE critical regression test for the agent contract.
   test('D6 #5: determinism — same input twice produces identical output', () => {
     const health = makeHealth({
+      stale_pages: 10,
       missing_embeddings: 50,
       dead_links: 3,
     });
-    const ctx = { repoPath: '/brain', embeddingProviderConfigured: true, sourceId: 'default', extractionLagPages: 10 };
+    const ctx = { repoPath: '/brain', embeddingProviderConfigured: true, sourceId: 'default' };
     const run1 = computeRecommendations(health, ctx);
     const run2 = computeRecommendations(health, ctx);
     expect(JSON.stringify(run1)).toBe(JSON.stringify(run2));

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/remediation-context-extraction-lag.test.ts

@@ -1,62 +0,0 @@
-// test/remediation-context-extraction-lag.test.ts
-//
-// Pins the v-next fix: the sync→extract remediation pipeline gates on REAL
-// extraction lag, not the legacy `health.stale_pages` proxy (which counted
-// "updated_at predates newest timeline entry" — meaningless after the v10
-// trigger drop). loadRecommendationContext now populates `extractionLagPages`
-// from `engine.countStalePagesForExtraction` — the SAME counter the
-// `gbrain extract --stale` walk and doctor's `links_extraction_lag` use — so a
-// recommendation can only fire when running extract will actually reduce it.
-
-import { afterAll, beforeAll, describe, expect, it } from 'bun:test';
-import { PGLiteEngine } from '../src/core/pglite-engine.ts';
-import { loadRecommendationContext } from '../src/core/remediation/context.ts';
-
-let engine: PGLiteEngine;
-
-beforeAll(async () => {
-  engine = new PGLiteEngine();
-  await engine.connect({});
-  await engine.initSchema();
-});
-
-afterAll(async () => {
-  await engine.disconnect();
-});
-
-describe('loadRecommendationContext — extractionLagPages wiring', () => {
-  it('is 0 on an empty brain (nothing to extract)', async () => {
-    const ctx = await loadRecommendationContext(engine);
-    expect(ctx.extractionLagPages).toBe(0);
-  });
-
-  it('reflects the real extraction-lag count once a page needs extraction', async () => {
-    // A freshly-imported page has links_extracted_at = NULL, which the canonical
-    // countStalePagesForExtraction predicate counts as stale-for-extraction.
-    await engine.putPage('p0', {
-      title: 'p0',
-      type: 'note' as never,
-      compiled_truth: 'body that is long enough to pass any minimum-length guards in the codebase',
-      timeline: '',
-      frontmatter: {},
-      source_path: 'p0.md',
-    });
-    const ctx = await loadRecommendationContext(engine);
-    expect(ctx.extractionLagPages).toBeGreaterThan(0);
-  });
-
-  it('counts pages stamped before LINK_EXTRACTOR_VERSION_TS (version-bump arm)', async () => {
-    // Backdate p0 so BOTH the NULL arm and the updated_at arm are quiet:
-    // updated_at < links_extracted_at, but links_extracted_at predates the
-    // extractor version stamp. doctor's links_extraction_lag and
-    // `extract --stale` both count this page; the remediation gate must too.
-    await engine.executeRaw(
-      `UPDATE pages SET updated_at = '2020-01-01T00:00:00Z'::timestamptz,
-                        links_extracted_at = '2020-01-02T00:00:00Z'::timestamptz
-        WHERE slug = 'p0'`,
-      [],
-    );
-    const ctx = await loadRecommendationContext(engine);
-    expect(ctx.extractionLagPages).toBeGreaterThan(0);
-  });
-});

test/remediation-run-d7-refresh.serial.test.ts

@@ -1,81 +0,0 @@
-// test/remediation-run-d7-refresh.serial.test.ts
-//
-// Pins the D7-recheck half of the extraction-lag gate fix: runRemediation
-// loads RecommendationContext ONCE before the step loop, and the per-step
-// recheck (D7) must REFRESH ctx.extractionLagPages alongside getHealth.
-// Without the refresh, a completed sync/extract step keeps re-firing off
-// the frozen initial count — the plan never converges and the loop burns
-// steps until maxJobs.
-//
-// SERIAL (R2): uses top-level mock.module for the minion queue +
-// wait-for-completion so no real worker is needed — mocks leak across
-// files in a shard process, so this file must run in its own process.
-
-import { describe, expect, mock, test } from 'bun:test';
-
-// The fake brain: sync.repo clears the extraction lag when it "runs"
-// (today's sync materializes link/timeline edges; extract.all is the
-// explicit re-materializer). The frozen-ctx bug makes runRemediation
-// ignore that and resubmit sync.repo on every D7 recheck.
-let extractionLag = 25;
-const submittedJobs: string[] = [];
-
-mock.module('../src/core/minions/queue.ts', () => ({
-  MinionQueue: class {
-    constructor(_engine: unknown) {}
-    async add(job: string): Promise<{ id: number }> {
-      submittedJobs.push(job);
-      if (job === 'sync' || job === 'extract') extractionLag = 0;
-      return { id: submittedJobs.length };
-    }
-  },
-}));
-
-mock.module('../src/core/minions/wait-for-completion.ts', () => ({
-  waitForCompletion: async () => ({ status: 'completed' }),
-}));
-
-const health = () => ({
-  page_count: 100,
-  embed_coverage: 1.0,
-  stale_pages: 0, // legacy proxy stays 0 — the real counter drives the gate
-  orphan_pages: 0,
-  missing_embeddings: 0,
-  brain_score: 70,
-  dead_links: 0,
-  link_coverage: 1.0,
-  timeline_coverage: 1.0,
-  most_connected: [],
-  embed_coverage_score: 35,
-  link_density_score: 25,
-  timeline_coverage_score: 15,
-  no_orphans_score: 15,
-  no_dead_links_score: 10,
-});
-
-const fakeEngine = {
-  kind: 'pglite' as const,
-  getHealth: async () => health(),
-  getConfig: async (key: string) =>
-    key === 'sync.repo_path' ? '/tmp/brain-example' : null,
-  countStalePagesForExtraction: async () => extractionLag,
-};
-
-describe('runRemediation D7 recheck — extraction-lag gate refresh', () => {
-  test('a completed materializer step clears the gate; the pipeline is not resubmitted', async () => {
-    const { runRemediation } = await import('../src/core/remediation/run.ts');
-    const result = await runRemediation(
-      // Only the methods the orchestrator touches are needed.
-      fakeEngine as never,
-      { targetScore: 0, maxJobs: 6 },
-    );
-    // Frozen-ctx bug: extractionLagPages stays 25 forever, so every D7
-    // recheck re-introduces the sync/extract pipeline and the loop burns
-    // all 6 maxJobs. With the refresh, the plan converges after the first
-    // completed step: no step id is ever submitted twice.
-    const ids = result.submitted.map((s) => s.id);
-    expect(new Set(ids).size).toBe(ids.length);
-    expect(submittedJobs.length).toBeLessThan(3);
-    expect(extractionLag).toBe(0);
-  });
-});

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.