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/ai/recipes/litellm-proxy.ts

@@ -56,36 +56,6 @@ export const litellmProxy: Recipe = {
       cost_per_1m_output_usd: undefined,
       price_last_verified: '2026-06-14',
     },
-    // LiteLLM normalizes Cohere / Voyage / Jina / etc. rerank backends to the
-    // same wire shape gbrain's gateway.rerank() already speaks (the
-    // ZeroEntropy/llama.cpp contract):
-    //   { model, query, documents, top_n } → { results: [{ index, relevance_score }] }
-    // So any rerank model the user registers in their LiteLLM config is
-    // reachable via `gbrain config set search.reranker.model litellm:<model>`
-    // with no request/response adapter — same as embeddings ride the proxy.
-    reranker: {
-      models: [], // user-provided; whatever rerank models the proxy serves
-      // No canonical default — the proxy defines its own model ids. The user
-      // sets search.reranker.model explicitly (mirrors the embedding
-      // touchpoint's user_provided_models contract).
-      default_model: '',
-      // The proxied backend bills (Cohere/Voyage/…); pricing-unknown is the
-      // honest state — same stance as this recipe's embedding/chat
-      // touchpoints and budget-tracker's deliberate litellm exclusion from
-      // the free-provider sets.
-      cost_per_1m_tokens_usd: undefined,
-      price_last_verified: '2026-06-27',
-      max_payload_bytes: 5_000_000,
-      // LEAF path only (matches llama-server-reranker's convention). LiteLLM
-      // serves both `/rerank` and `/v1/rerank`, and LITELLM_BASE_URL may be
-      // set with or without the `/v1` suffix (the setup_hint allows both), so
-      // the leaf form yields a valid route either way:
-      //   http://localhost:4000    + /rerank → /rerank        ✓
-      //   http://localhost:4000/v1 + /rerank → /v1/rerank     ✓
-      // Pinning '/v1/rerank' here would double to /v1/v1/rerank → 404 on
-      // /v1-suffixed bases.
-      path: '/rerank',
-    },
   },
-  setup_hint: 'Run LiteLLM (https://docs.litellm.ai) in front of any provider; set LITELLM_BASE_URL (include the /v1 suffix if your proxy serves the OpenAI route there, e.g. http://localhost:4000/v1) + pass --embedding-model litellm:<model> and --embedding-dimensions <N>. For rerank: register a rerank model in LiteLLM and set search.reranker.model litellm:<model-name>.',
+  setup_hint: 'Run LiteLLM (https://docs.litellm.ai) in front of any provider; set LITELLM_BASE_URL (include the /v1 suffix if your proxy serves the OpenAI route there, e.g. http://localhost:4000/v1) + pass --embedding-model litellm:<model> and --embedding-dimensions <N>.',
 };

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/ai/recipe-litellm-reranker.test.ts

@@ -1,88 +0,0 @@
-/**
- * litellm-proxy reranker touchpoint smoke.
- *
- * Sibling of recipe-llama-server-reranker.test.ts. Pins the reranker
- * touchpoint on the LiteLLM proxy recipe so:
- *  - the touchpoint exists with the LEAF '/rerank' path (LiteLLM serves both
- *    /rerank and /v1/rerank, so the leaf form is valid whether or not the
- *    user's LITELLM_BASE_URL carries the /v1 suffix the setup_hint allows)
- *  - a /v1-suffixed base URL does NOT produce /v1/v1/rerank (the original
- *    community PR pinned '/v1/rerank' which 404s on /v1-suffixed bases)
- *  - models: [] (user-provided; proxy defines the model ids)
- *  - pricing stays undefined (proxy can front a paid provider — same honest
- *    pricing-unknown stance as the embedding/chat touchpoints)
- *
- * The gateway.rerank() URL tests drive the real URL builder via the stubbed
- * transport (same seam as test/ai/rerank.test.ts).
- */
-
-import { describe, expect, test, afterEach } from 'bun:test';
-import { getRecipe } from '../../src/core/ai/recipes/index.ts';
-import {
-  configureGateway,
-  resetGateway,
-  rerank,
-  __setRerankTransportForTests,
-} from '../../src/core/ai/gateway.ts';
-
-afterEach(() => {
-  __setRerankTransportForTests(null);
-  resetGateway();
-});
-
-describe('recipe: litellm reranker touchpoint', () => {
-  test('declares reranker touchpoint with leaf /rerank path', () => {
-    const r = getRecipe('litellm')!;
-    const tp = r.touchpoints.reranker;
-    expect(tp).toBeDefined();
-    expect(tp!.path).toBe('/rerank');
-    expect(tp!.max_payload_bytes).toBe(5_000_000);
-  });
-
-  test('reranker touchpoint uses empty models[] for user-provided model ids', () => {
-    const r = getRecipe('litellm')!;
-    expect(r.touchpoints.reranker!.models).toEqual([]);
-  });
-
-  test('pricing stays undefined — proxy can front a paid provider', () => {
-    const r = getRecipe('litellm')!;
-    expect(r.touchpoints.reranker!.cost_per_1m_tokens_usd).toBeUndefined();
-  });
-
-  test('setup_hint keeps the /v1-suffix guidance AND mentions rerank', () => {
-    const r = getRecipe('litellm')!;
-    expect(r.setup_hint).toMatch(/\/v1 suffix/);
-    expect(r.setup_hint).toMatch(/search\.reranker\.model litellm:/);
-  });
-});
-
-describe('gateway.rerank() URL via litellm recipe', () => {
-  async function capturedRerankUrl(baseUrl?: string): Promise<string> {
-    configureGateway({
-      reranker_model: 'litellm:my-reranker',
-      env: {},
-      ...(baseUrl ? { base_urls: { litellm: baseUrl } } : {}),
-    });
-    let capturedUrl = '';
-    __setRerankTransportForTests(async (url) => {
-      capturedUrl = url;
-      return new Response(
-        JSON.stringify({ results: [{ index: 0, relevance_score: 0.9 }] }),
-        { status: 200, headers: { 'content-type': 'application/json' } },
-      );
-    });
-    await rerank({ query: 'q', documents: ['d'] });
-    return capturedUrl;
-  }
-
-  test('default base (no /v1 suffix) → /rerank', async () => {
-    const url = await capturedRerankUrl();
-    expect(url).toBe('http://localhost:4000/rerank');
-  });
-
-  test('/v1-suffixed base → /v1/rerank, NOT /v1/v1/rerank', async () => {
-    const url = await capturedRerankUrl('http://localhost:4000/v1');
-    expect(url).toBe('http://localhost:4000/v1/rerank');
-    expect(url).not.toContain('/v1/v1/');
-  });
-});

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.