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/commands/migrate-engine.ts

@@ -3,11 +3,7 @@
  *
  * Usage:
  *   gbrain migrate --to supabase [--url <connection_string>]
- *     (--url is persisted to config.json, mode 0600, so the migrated brain
- *      works without env — #1271)
  *   gbrain migrate --to pglite [--path <db_path>]
- *     (an explicit --path destination is bootstrapped with its own
- *      <path>/.gbrain/config.json so GBRAIN_HOME=<path> just works — #1271)
  *   gbrain migrate --to <engine> --force  (overwrite non-empty target)
  */
 
@@ -15,9 +11,9 @@ import { createEngine } from '../core/engine-factory.ts';
 import { loadConfig, saveConfig, toEngineConfig, gbrainPath, effectiveEnvDatabaseUrl, type GBrainConfig } from '../core/config.ts';
 import type { BrainEngine } from '../core/engine.ts';
 import type { EngineConfig } from '../core/types.ts';
-import { writeFileSync, readFileSync, existsSync, unlinkSync, mkdirSync, chmodSync } from 'fs';
+import { writeFileSync, readFileSync, existsSync, unlinkSync } from 'fs';
 import { createHash } from 'crypto';
-import { resolve, join } from 'path';
+import { resolve } from 'path';
 import { createProgress } from '../core/progress.ts';
 import { getCliOptions, cliOptsToProgressOptions } from '../core/cli-options.ts';
 
@@ -63,31 +59,6 @@ export interface MigrateManifest {
   started_at: string;
 }
 
-/**
- * #1271 Finding 1: make an explicit `--to pglite --path P` destination usable
- * as a standalone brain. Writes `P/.gbrain/config.json` (mode 0600, plus a
- * `*` .gitignore) so `GBRAIN_HOME=P` resolves without a manual `gbrain init`.
- * Never clobbers an existing config at the destination. Returns the written
- * config path, or null when skipped.
- */
-export function bootstrapDestinationConfig(dbPath: string): string | null {
-  const abs = resolve(dbPath);
-  const dir = join(abs, '.gbrain');
-  const file = join(dir, 'config.json');
-  if (existsSync(file)) return null;
-  mkdirSync(dir, { recursive: true });
-  const cfg: GBrainConfig = { engine: 'pglite', database_path: abs };
-  writeFileSync(file, JSON.stringify(cfg, null, 2) + '\n', { mode: 0o600 });
-  try { chmodSync(file, 0o600); } catch { /* platform-specific */ }
-  // Same worktree-safety pattern as saveConfig()'s ensureGitignore, scoped
-  // to the destination home. Don't clobber a user-customized .gitignore.
-  const gitignore = join(dir, '.gitignore');
-  if (!existsSync(gitignore)) {
-    writeFileSync(gitignore, '*\n', { mode: 0o600 });
-  }
-  return file;
-}
-
 export function migrationTargetId(config: EngineConfig): string {
   const locator = config.engine === 'postgres'
     ? config.database_url ?? ''
@@ -381,25 +352,6 @@ export async function runMigrateEngine(sourceEngine: BrainEngine, args: string[]
   };
   saveConfig(newConfig);
 
-  // #1271 Finding 2 (by design, but say it out loud): the connection string
-  // is persisted so the migrated brain works without env. Mode 0600.
-  if (opts.targetEngine === 'postgres' && opts.targetUrl) {
-    console.error('Note: the --url connection string (including credentials) is persisted to config.json (mode 0600).');
-  }
-
-  // #1271 Finding 1: an explicit --path destination doubles as a standalone
-  // GBRAIN_HOME. Best-effort — never fail a completed migration over it.
-  if (opts.targetEngine === 'pglite' && opts.targetPath) {
-    try {
-      const written = bootstrapDestinationConfig(opts.targetPath);
-      if (written) {
-        console.log(`Destination bootstrapped: ${written} (usable via GBRAIN_HOME=${resolve(opts.targetPath)})`);
-      }
-    } catch (e) {
-      console.warn(`  WARN could not bootstrap destination config: ${e instanceof Error ? e.message : String(e)}`);
-    }
-  }
-
   // Clean up
   clearManifest();
 

src/core/operations.ts

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

src/mcp/dispatch.ts

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

src/mcp/server.ts

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

test/init-env-detection.test.ts

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

test/migrate-engine-dest-bootstrap.test.ts

@@ -1,40 +0,0 @@
-import { describe, expect, test } from 'bun:test';
-import { mkdtempSync, mkdirSync, readFileSync, statSync, writeFileSync } from 'fs';
-import { tmpdir } from 'os';
-import { join, resolve } from 'path';
-import { bootstrapDestinationConfig } from '../src/commands/migrate-engine.ts';
-import { loadConfigFileOnly } from '../src/core/config.ts';
-import { withEnv } from './helpers/with-env.ts';
-
-describe('migrate --to pglite destination bootstrap (#1271)', () => {
-  test('writes <path>/.gbrain/config.json so GBRAIN_HOME=<path> resolves a brain', async () => {
-    const dest = mkdtempSync(join(tmpdir(), 'gbrain-dest-'));
-    const written = bootstrapDestinationConfig(dest);
-    const file = join(dest, '.gbrain', 'config.json');
-    expect(written).toBe(file);
-
-    const cfg = JSON.parse(readFileSync(file, 'utf-8'));
-    expect(cfg.engine).toBe('pglite');
-    expect(cfg.database_path).toBe(resolve(dest));
-    expect(statSync(file).mode & 0o777).toBe(0o600);
-    // worktree safety: destination home is git-ignored like saveConfig()'s home
-    expect(readFileSync(join(dest, '.gbrain', '.gitignore'), 'utf-8')).toBe('*\n');
-
-    // The exact failure mode from #1271: config resolution under
-    // GBRAIN_HOME=<path> used to find nothing ("No brain configured").
-    await withEnv({ GBRAIN_HOME: dest }, () => {
-      const loaded = loadConfigFileOnly();
-      expect(loaded?.engine).toBe('pglite');
-      expect(loaded?.database_path).toBe(resolve(dest));
-    });
-  });
-
-  test('never clobbers an existing destination config', () => {
-    const dest = mkdtempSync(join(tmpdir(), 'gbrain-dest-'));
-    mkdirSync(join(dest, '.gbrain'), { recursive: true });
-    writeFileSync(join(dest, '.gbrain', 'config.json'), '{"engine":"postgres"}\n');
-
-    expect(bootstrapDestinationConfig(dest)).toBe(null);
-    expect(JSON.parse(readFileSync(join(dest, '.gbrain', 'config.json'), 'utf-8')).engine).toBe('postgres');
-  });
-});

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.