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

@@ -151,100 +151,6 @@ export function shouldSpawnAutopilotWorker(args: string[]): boolean {
   return !args.includes('--no-worker');
 }
 
-/**
- * #1525 — positional subcommand translation.
- *
- * Pre-fix, `gbrain autopilot status` silently fell through to "start daemon"
- * because `runAutopilot()` only branched on flag forms (`--status`, etc.).
- * `status` was treated as a stray positional and ignored.
- *
- * This translator maps known positional subcommands to their flag form so
- * `autopilot status` is equivalent to `autopilot --status`, then rejects
- * any unrecognized positional with a fail-loud error before any side
- * effect (lockfile, daemon spawn, sync dispatch) runs.
- *
- * Scope decisions:
- *   - Known aliases: `status` → `--status`, `install` → `--install`,
- *     `uninstall` → `--uninstall`, `start` → (drop; default daemon launch).
- *   - `stop` is intentionally NOT aliased here. Stopping a running daemon
- *     is a new behavior (read PID from lock, SIGTERM, drain) that deserves
- *     its own design and PR. Users typing `gbrain autopilot stop` today get
- *     the unknown-positional error with the canonical alternatives.
- *   - At most one positional allowed; multiple positionals fail loud.
- */
-// Every flag that consumes the NEXT argv token. Missing one here makes the
-// translator misread the flag's value as a positional subcommand and exit 2
-// (e.g. `--install --target linux-cron`). Keep in sync with parseArg call sites.
-const AUTOPILOT_VALUE_FLAGS = new Set(['--repo', '--interval', '--target']);
-const AUTOPILOT_POSITIONAL_ALIASES: Record<string, string | null> = {
-  status: '--status',
-  install: '--install',
-  uninstall: '--uninstall',
-  start: null, // drop the positional; default behavior is daemon launch
-};
-
-export type PositionalTranslation =
-  | { ok: true; args: string[] }
-  | {
-      ok: false;
-      reason: 'unknown_subcommand' | 'multiple_subcommands';
-      message: string;
-    };
-
-export function translatePositionalSubcommands(args: string[]): PositionalTranslation {
-  const out: string[] = [];
-  let positionalSeen = false;
-  let i = 0;
-  while (i < args.length) {
-    const a = args[i];
-    if (AUTOPILOT_VALUE_FLAGS.has(a)) {
-      // Pass through the flag and its value untouched. If the value is
-      // missing at end-of-argv, fall through so the existing parseArg
-      // path can report the broken usage.
-      out.push(a);
-      if (i + 1 < args.length) {
-        out.push(args[i + 1]);
-        i += 2;
-      } else {
-        i += 1;
-      }
-      continue;
-    }
-    if (a.startsWith('-')) {
-      out.push(a);
-      i += 1;
-      continue;
-    }
-    // Positional subcommand.
-    if (positionalSeen) {
-      const known = Object.keys(AUTOPILOT_POSITIONAL_ALIASES).join(', ');
-      return {
-        ok: false,
-        reason: 'multiple_subcommands',
-        message: `Multiple subcommands given. Use only one of: ${known}.`,
-      };
-    }
-    positionalSeen = true;
-    if (a in AUTOPILOT_POSITIONAL_ALIASES) {
-      const alias = AUTOPILOT_POSITIONAL_ALIASES[a];
-      if (alias) out.push(alias);
-      i += 1;
-      continue;
-    }
-    const known = Object.keys(AUTOPILOT_POSITIONAL_ALIASES).join(', ');
-    return {
-      ok: false,
-      reason: 'unknown_subcommand',
-      message:
-        `Unknown subcommand: \`${a}\`.\n` +
-        `Allowed subcommands: ${known}.\n` +
-        `Or use the flag form: --status, --install, --uninstall.\n` +
-        `Run \`gbrain autopilot --help\` for full usage.`,
-    };
-  }
-  return { ok: true, args: out };
-}
-
 export function isPidAlive(pid: number): boolean {
   if (!Number.isFinite(pid) || pid <= 0) return false;
   try {
@@ -457,11 +363,6 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
       '       gbrain autopilot --install [--repo <path>]\n' +
       '       gbrain autopilot --uninstall\n' +
       '       gbrain autopilot --status [--json]\n\n' +
-      'Subcommand aliases:\n' +
-      '       gbrain autopilot status     → --status\n' +
-      '       gbrain autopilot install    → --install\n' +
-      '       gbrain autopilot uninstall  → --uninstall\n' +
-      '       gbrain autopilot start      → (default daemon launch)\n\n' +
       'Self-maintaining brain daemon. Runs the full maintenance cycle\n' +
       '(lint + backlinks + sync + extract + embed + orphans) on an interval.\n\n' +
       'For a one-shot cron-triggered cycle, see `gbrain dream`.',
@@ -469,16 +370,6 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
     return;
   }
 
-  // #1525: translate positional subcommands to their flag form BEFORE any
-  // side effect (lockfile, daemon spawn, sync dispatch). Unknown positionals
-  // fail loud here rather than silently starting the daemon.
-  const translated = translatePositionalSubcommands(args);
-  if (!translated.ok) {
-    console.error(translated.message);
-    process.exit(2);
-  }
-  args = translated.args;
-
   if (args.includes('--install')) {
     await installDaemon(engine, args);
     return;

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/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/autopilot-positional-subcommands.test.ts

@@ -1,197 +0,0 @@
-/**
- * Tests for translatePositionalSubcommands() — the v0.41.x #1525 fix that
- * prevents `gbrain autopilot status` from silently starting the daemon.
- *
- * IRON RULE regression guard: the exact ticket repro (`gbrain autopilot
- * status`) MUST translate to `--status`, not fall through to the default
- * daemon launch. Verified by the "ticket-exact repro" case below.
- */
-
-import { describe, test, expect } from 'bun:test';
-import { translatePositionalSubcommands } from '../src/commands/autopilot.ts';
-
-describe('translatePositionalSubcommands — known aliases', () => {
-  test('IRON RULE — `autopilot status` translates to `--status` (ticket #1525 repro)', () => {
-    const r = translatePositionalSubcommands(['status']);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual(['--status']);
-  });
-
-  test('`install` translates to `--install`', () => {
-    const r = translatePositionalSubcommands(['install']);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual(['--install']);
-  });
-
-  test('`uninstall` translates to `--uninstall`', () => {
-    const r = translatePositionalSubcommands(['uninstall']);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual(['--uninstall']);
-  });
-
-  test('`start` drops the positional (default daemon launch)', () => {
-    const r = translatePositionalSubcommands(['start']);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual([]);
-  });
-
-  test('`start --json` drops only the positional, keeps the flag', () => {
-    const r = translatePositionalSubcommands(['start', '--json']);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual(['--json']);
-  });
-});
-
-describe('translatePositionalSubcommands — flag/positional interleaving', () => {
-  test('`status --json` preserves the trailing flag', () => {
-    const r = translatePositionalSubcommands(['status', '--json']);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual(['--status', '--json']);
-  });
-
-  test('`--json status` preserves the leading flag', () => {
-    const r = translatePositionalSubcommands(['--json', 'status']);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual(['--json', '--status']);
-  });
-
-  test('`--repo /foo status` does not mis-classify the path as positional', () => {
-    const r = translatePositionalSubcommands(['--repo', '/foo', 'status']);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual(['--repo', '/foo', '--status']);
-  });
-
-  test('`--interval 300 install` does not mis-classify the number as positional', () => {
-    const r = translatePositionalSubcommands(['--interval', '300', 'install']);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual(['--interval', '300', '--install']);
-  });
-
-  test('`--install --target linux-cron` does not mis-classify the target as positional', () => {
-    // --target is installDaemon's value flag; its value must never be read
-    // as a positional subcommand (regression guard for the review fix).
-    const r = translatePositionalSubcommands(['--install', '--target', 'linux-cron']);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual(['--install', '--target', 'linux-cron']);
-  });
-
-  test('`install --target macos` keeps the alias translation and the target value', () => {
-    const r = translatePositionalSubcommands(['install', '--target', 'macos']);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual(['--install', '--target', 'macos']);
-  });
-
-  test('value-flag at end of argv with missing value passes through (so parseArg can report it)', () => {
-    const r = translatePositionalSubcommands(['--repo']);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual(['--repo']);
-  });
-
-  test('value-flag whose value looks like an alias is NOT translated', () => {
-    // `--repo status` means "use repo path 'status'", not "show status".
-    // Translator must not destructure the value of --repo.
-    const r = translatePositionalSubcommands(['--repo', 'status']);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual(['--repo', 'status']);
-  });
-});
-
-describe('translatePositionalSubcommands — pass-through cases', () => {
-  test('empty args returns empty args', () => {
-    const r = translatePositionalSubcommands([]);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual([]);
-  });
-
-  test('flag-only invocation passes through unchanged', () => {
-    const r = translatePositionalSubcommands(['--status', '--json']);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual(['--status', '--json']);
-  });
-
-  test('short flag `-h` passes through unchanged', () => {
-    const r = translatePositionalSubcommands(['-h']);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual(['-h']);
-  });
-
-  test('all known bare flags pass through unchanged', () => {
-    const flags = ['--help', '--install', '--uninstall', '--status', '--json', '--inline', '--no-worker'];
-    const r = translatePositionalSubcommands(flags);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual(flags);
-  });
-});
-
-describe('translatePositionalSubcommands — rejection of unknown positionals', () => {
-  test('unknown positional `foo` fails with reason=unknown_subcommand + structured message', () => {
-    const r = translatePositionalSubcommands(['foo']);
-    expect(r.ok).toBe(false);
-    if (!r.ok) {
-      expect(r.reason).toBe('unknown_subcommand');
-      expect(r.message).toContain('Unknown subcommand: `foo`');
-      expect(r.message).toContain('status');
-      expect(r.message).toContain('install');
-      expect(r.message).toContain('uninstall');
-      expect(r.message).toContain('--help');
-    }
-  });
-
-  test('unknown positional `stop` fails with reason=unknown_subcommand (NOT silently aliased)', () => {
-    // Stop is mentioned in the ticket but deliberately NOT aliased in this
-    // PR — stopping a running daemon is a new behavior, not just an alias.
-    // Until that feature lands separately, `stop` must fail loud rather
-    // than starting the daemon (the bug we're fixing).
-    const r = translatePositionalSubcommands(['stop']);
-    expect(r.ok).toBe(false);
-    if (!r.ok) {
-      expect(r.reason).toBe('unknown_subcommand');
-      expect(r.message).toContain('Unknown subcommand: `stop`');
-    }
-  });
-
-  test('unknown positional `status-detail` (close-but-not-matching) fails', () => {
-    const r = translatePositionalSubcommands(['status-detail']);
-    expect(r.ok).toBe(false);
-    if (!r.ok) {
-      expect(r.reason).toBe('unknown_subcommand');
-      expect(r.message).toContain('Unknown subcommand: `status-detail`');
-    }
-  });
-
-  test('multiple positionals fail with reason=multiple_subcommands (`start install`)', () => {
-    const r = translatePositionalSubcommands(['start', 'install']);
-    expect(r.ok).toBe(false);
-    if (!r.ok) {
-      expect(r.reason).toBe('multiple_subcommands');
-      expect(r.message).toContain('Multiple subcommands');
-    }
-  });
-
-  test('multiple positionals fail even when both are known aliases (`status install`)', () => {
-    const r = translatePositionalSubcommands(['status', 'install']);
-    expect(r.ok).toBe(false);
-    if (!r.ok) {
-      expect(r.reason).toBe('multiple_subcommands');
-      expect(r.message).toContain('Multiple subcommands');
-    }
-  });
-
-  test('known-then-unknown rejects with multiple_subcommands (first-positional-wins)', () => {
-    // First positional is known, second is not. Rejection comes from the
-    // multiple-positional rule, which fires before the unknown check; the
-    // intent is "only one subcommand allowed."
-    const r = translatePositionalSubcommands(['status', 'garbage']);
-    expect(r.ok).toBe(false);
-    if (!r.ok) expect(r.reason).toBe('multiple_subcommands');
-  });
-
-  test('unknown-then-known rejects on the unknown (unknown fires before second-positional check)', () => {
-    const r = translatePositionalSubcommands(['garbage', 'status']);
-    expect(r.ok).toBe(false);
-    if (!r.ok) {
-      expect(r.reason).toBe('unknown_subcommand');
-      expect(r.message).toContain('garbage');
-    }
-  });
-});

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.