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/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/doctor-categories.ts

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

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/doctor-categories.test.ts

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

test/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/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.