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

@@ -38,7 +38,6 @@ import { logSelfUpgrade } from '../core/audit/self-upgrade-audit.ts';
 import { detectInstallMethod } from './upgrade.ts';
 import { evaluateQuietHours } from '../core/minions/quiet-hours.ts';
 import { inspectLock } from '../core/db-lock.ts';
-import { registerCleanup } from '../core/process-cleanup.ts';
 
 /**
  * v0.37.7.0 #1162 — classify autopilot reconnect-loop errors.
@@ -434,37 +433,6 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
   let stopping = false;
   let childSupervisor: ChildWorkerSupervisor | null = null;
 
-  // #1872: graceful engine shutdown. On PGLite the cycle steps run INLINE in
-  // this process, so a hard `process.exit` mid-write (systemctl stop →
-  // SIGTERM) kills WASM Postgres with the WAL dirty and can corrupt the
-  // brain. Two exit paths must both close the engine:
-  //   - autopilot's own shutdown() below (owns SIGINT + internal stops like
-  //     max_crashes / cycle-failure-cap), and
-  //   - process-cleanup's SIGTERM handler (installed at cli.ts module load;
-  //     it runs the cleanup registry with a 3s deadline and then exits) —
-  //     which is why closeEngine is ALSO registered there.
-  // closeEngine aborts the in-flight inline cycle (runCycle checks the
-  // signal between phases and threads it into phase sub-work), gives it a
-  // short bounded window to wind down, then disconnects. PGLite's
-  // disconnect() drains the pending query and checkpoints before closing;
-  // a second call is a no-op (disconnect snapshots + nulls the handle), so
-  // both paths firing is safe.
-  const shutdownAbort = new AbortController();
-  let inflightInlineCycle: Promise<unknown> | null = null;
-  const closeEngine = async () => {
-    shutdownAbort.abort(new Error('autopilot shutdown'));
-    if (inflightInlineCycle) {
-      // ponytail: 2s cap keeps us inside process-cleanup's 3s deadline; a
-      // between-phase abort resolves instantly, a mid-phase one may not.
-      await Promise.race([
-        inflightInlineCycle.catch(() => { /* cycle errors already logged by the loop */ }),
-        new Promise((r) => setTimeout(r, 2_000)),
-      ]);
-    }
-    try { await engine.disconnect(); } catch { /* best-effort */ }
-  };
-  const deregisterEngineClose = registerCleanup('autopilot-engine-close', closeEngine);
-
   if (spawnManagedWorker) {
     const cliPath = resolveGbrainCliPath();
     // Cgroup-aware auto-sized RSS watchdog cap (issue #1678). The old flat
@@ -552,10 +520,6 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
         childSupervisor.killChild('SIGKILL');
       }
     }
-    // #1872: abort the in-flight inline cycle and close the engine BEFORE
-    // process.exit — a hard exit mid-write corrupts PGLite's WASM Postgres.
-    await closeEngine();
-    deregisterEngineClose();
     try { unlinkSync(lockPath); } catch { /* already gone */ }
     process.exit(0);
   };
@@ -1044,21 +1008,16 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
       // path's phase set). Now both converge on the same primitive.
       try {
         const { runCycle } = await import('../core/cycle.ts');
-        // #1872: track the promise so closeEngine can drain it on shutdown,
-        // and pass the abort signal so the cycle winds down between phases.
-        const cyclePromise = runCycle(engine, {
+        const report = await runCycle(engine, {
           brainDir: repoPath,
           // Autopilot daemon path: pulls by default (matches
           // pre-v0.17 autopilot behavior). CLI dream defaults false
           // for cron safety; that choice is scoped to dream only.
           pull: true,
-          signal: shutdownAbort.signal,
           yieldBetweenPhases: async () => {
             await new Promise(r => setImmediate(r));
           },
         });
-        inflightInlineCycle = cyclePromise;
-        const report = await cyclePromise.finally(() => { inflightInlineCycle = null; });
         // Only 'failed' (every attempted phase failed) trips the autopilot
         // circuit breaker. 'partial' means at least one phase warned or
         // failed while others ran — that's a soft signal, not a fatal

src/commands/dream.ts

@@ -26,7 +26,6 @@
 import type { BrainEngine } from '../core/engine.ts';
 import {
   runCycle,
-  resolveSourceForDir,
   ALL_PHASES,
   type CyclePhase,
   type CycleReport,
@@ -381,9 +380,9 @@ Options:
 
   --source <id>       Scope the cycle to one source so doctor's
                       cycle_freshness check sees a fresh stamp on
-                      completion. When omitted, gbrain derives the
-                      source from --dir / the configured checkout
-                      when it matches a source's local_path (#1869).
+                      completion. Without this, gbrain dream's
+                      timestamp never lands and federated brains
+                      see "stale cycle" forever.
   --source-id <id>    Alias for --source. Matches the v0.37.7.0+
                       naming used by import/extract/graph-query.
 
@@ -635,25 +634,6 @@ export async function runDream(engine: BrainEngine | null, args: string[]): Prom
     );
     process.exit(1);
   }
-
-  // #1869: a path-scoped run (--dir, or the configured sync.repo_path) whose
-  // directory matches a registered source's local_path IS that source's cycle
-  // — derive the source id so runCycle writes last_source_cycle_at /
-  // last_full_cycle_at on success and doctor's cycle_freshness check stops
-  // reading perpetually stale. Explicit --source still wins (resolved above).
-  // Fixed here at the command level, NOT in runCycle's stamp gate, so legacy
-  // global callers (autopilot-global-maintenance runs GLOBAL_PHASES with a
-  // brainDir and no sourceId) can't falsely stamp per-source freshness.
-  // A derived match on an archived source is skipped silently (falls back to
-  // legacy unscoped behavior) — stamping it would mask staleness on restore,
-  // mirroring the explicit --source archived guard above.
-  if (resolvedSourceId === undefined && engine !== null && brainDir !== null) {
-    const derived = await resolveSourceForDir(engine, brainDir);
-    if (derived !== undefined) {
-      const src = await fetchSource(engine, derived);
-      if (src?.archived !== true) resolvedSourceId = derived;
-    }
-  }
   // ─── issue #1678: bounded single-hold extract_atoms drain ──────────
   if (opts.drain) {
     if (engine === null) {

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/cycle.ts

@@ -855,16 +855,8 @@ interface SyncPhaseResult extends PhaseResult {
  * Resolve the source id for a brain directory by looking up the sources
  * table. Returns undefined when no registered source matches (falls back
  * to pre-v0.18 global config.sync.* keys).
- *
- * Exported for dream.ts (#1869): a `gbrain dream --dir <path>` run whose
- * path matches a registered source's local_path is a per-source cycle in
- * everything but name, so dream derives the source id up front and passes
- * it as opts.sourceId — landing the freshness stamp without changing
- * runCycle's stamp/lock semantics for legacy global callers (the
- * autopilot-global-maintenance handler runs GLOBAL_PHASES with a brainDir
- * and MUST NOT stamp per-source freshness; see rejected PR #2549).
  */
-export async function resolveSourceForDir(
+async function resolveSourceForDir(
   engine: BrainEngine,
   brainDir: string | null,
 ): Promise<string | undefined> {

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-shutdown-engine-close.test.ts

@@ -1,63 +0,0 @@
-/**
- * #1872 — autopilot SIGTERM/SIGINT must close the engine before exit.
- *
- * On PGLite the cycle steps run INLINE in the autopilot process, so a hard
- * `process.exit` mid-write (systemctl stop → SIGTERM) kills WASM Postgres
- * with the WAL dirty and can corrupt the brain. Two exit paths must both
- * close the engine:
- *
- *   - autopilot's own shutdown() (owns SIGINT + internal stops like
- *     max_crashes / cycle-failure-cap), and
- *   - process-cleanup's SIGTERM handler (installed at cli.ts module load,
- *     which exits within its 3s cleanup deadline) — reached via the
- *     registered 'autopilot-engine-close' cleanup callback.
- *
- * Because the shutdown path is deep inside `runAutopilot()` (a long-running
- * daemon loop that ends in process.exit), a behavioral test would have to
- * spawn + signal a real daemon. Following the established precedent
- * (test/autopilot-supervisor-wiring.test.ts, test/autopilot-fanout-wiring.test.ts),
- * these static-shape regressions pin the load-bearing wiring instead.
- */
-import { describe, expect, it } from 'bun:test';
-import { readFileSync } from 'fs';
-import { join } from 'path';
-
-const AUTOPILOT_SRC = readFileSync(
-  join(import.meta.dir, '..', 'src', 'commands', 'autopilot.ts'),
-  'utf8',
-);
-
-describe('autopilot.ts graceful engine shutdown (#1872)', () => {
-  it('registers an engine-close callback in the process-cleanup registry (SIGTERM path)', () => {
-    // process-cleanup owns SIGTERM (installed at cli.ts:10) and hard-exits
-    // after its cleanup pass; without this registration the engine is never
-    // closed on `systemctl stop`.
-    expect(AUTOPILOT_SRC).toContain(
-      "import { registerCleanup } from '../core/process-cleanup.ts';",
-    );
-    expect(AUTOPILOT_SRC).toContain(
-      "registerCleanup('autopilot-engine-close', closeEngine)",
-    );
-  });
-
-  it('closeEngine aborts the in-flight inline cycle then disconnects the engine', () => {
-    // Abort first (runCycle checks the signal between phases and threads it
-    // into phase sub-work), bounded drain, then disconnect.
-    expect(AUTOPILOT_SRC).toMatch(
-      /const closeEngine = async \(\) => \{[\s\S]{0,900}shutdownAbort\.abort\([\s\S]{0,900}engine\.disconnect\(\)/,
-    );
-  });
-
-  it('the inline runCycle call carries the shutdown abort signal and is tracked as in-flight', () => {
-    // PGLite / --inline path: the cycle runs in-process, so shutdown must be
-    // able to (a) signal it to wind down and (b) await it before closing.
-    expect(AUTOPILOT_SRC).toMatch(/signal:\s*shutdownAbort\.signal/);
-    expect(AUTOPILOT_SRC).toMatch(/inflightInlineCycle\s*=\s*cyclePromise/);
-  });
-
-  it('shutdown() awaits closeEngine() before process.exit(0) (SIGINT + internal-stop path)', () => {
-    expect(AUTOPILOT_SRC).toMatch(
-      /await closeEngine\(\);[\s\S]{0,400}process\.exit\(0\)/,
-    );
-  });
-});

test/dream-dir-source-stamp.test.ts

@@ -1,99 +0,0 @@
-/**
- * #1869 — `gbrain dream --dir <path>` stamps cycle freshness when the path
- * matches a registered source's local_path.
- *
- * Pre-fix, only `--source <id>` runs wrote last_source_cycle_at /
- * last_full_cycle_at (runCycle's stamp gate reads opts.sourceId, and dream
- * never derived one from --dir), so a path-scoped brain showed doctor's
- * cycle_freshness as perpetually stale.
- *
- * The fix lives in dream.ts (derive the source id from the resolved brain
- * dir via resolveSourceForDir), NOT in runCycle's stamp gate — a runCycle-
- * wide change would make the autopilot-global-maintenance handler (global
- * phases, brainDir set, no sourceId) falsely stamp per-source freshness
- * (the #2194 poisoning class; see rejected PR #2549).
- *
- * Same real-PGLite/no-mocks discipline as test/dream.test.ts; same
- * GBRAIN_HOME isolation as test/cycle-last-full-cycle-at.test.ts (the
- * cycle's PGLite file lock lives under ~/.gbrain).
- */
-import { describe, test, expect, beforeAll, afterAll, beforeEach, afterEach } from 'bun:test';
-import { mkdtempSync, rmSync } from 'fs';
-import { join } from 'path';
-import { tmpdir } from 'os';
-import { PGLiteEngine } from '../src/core/pglite-engine.ts';
-import { resetPgliteState } from './helpers/reset-pglite.ts';
-import { runDream } from '../src/commands/dream.ts';
-import { withEnv } from './helpers/with-env.ts';
-
-let engine: PGLiteEngine;
-let brainDir: string;
-let gbrainHome: string;
-
-beforeAll(async () => {
-  engine = new PGLiteEngine();
-  await engine.connect({});
-  await engine.initSchema();
-}, 60_000);
-
-afterAll(async () => {
-  await engine.disconnect();
-});
-
-beforeEach(async () => {
-  await resetPgliteState(engine);
-  brainDir = mkdtempSync(join(tmpdir(), 'gbrain-dream-stamp-'));
-  gbrainHome = mkdtempSync(join(tmpdir(), 'gbrain-dream-stamp-home-'));
-}, 60_000);
-
-afterEach(() => {
-  rmSync(brainDir, { recursive: true, force: true });
-  rmSync(gbrainHome, { recursive: true, force: true });
-});
-
-async function seedSource(id: string, archived = false): Promise<void> {
-  await engine.executeRaw(
-    `INSERT INTO sources (id, name, local_path, config, archived, created_at)
-     VALUES ($1, $2, $3, '{}'::jsonb, $4, NOW())`,
-    [id, id, brainDir, archived],
-  );
-}
-
-async function readLastFullCycleAt(sourceId: string): Promise<string | null> {
-  const rows = await engine.executeRaw<{ config: Record<string, unknown> | null }>(
-    `SELECT config FROM sources WHERE id = $1`,
-    [sourceId],
-  );
-  const raw = rows[0]?.config?.last_full_cycle_at;
-  return typeof raw === 'string' ? raw : null;
-}
-
-describe('gbrain dream --dir <path> freshness stamp (#1869)', () => {
-  test('--dir matching a source local_path stamps last_full_cycle_at', async () => {
-    await withEnv({ GBRAIN_HOME: gbrainHome }, async () => {
-      await seedSource('path-scoped');
-      expect(await readLastFullCycleAt('path-scoped')).toBeNull();
-
-      const report = await runDream(engine, ['--dir', brainDir, '--phase', 'lint', '--json']);
-      expect(report).toBeTruthy();
-      if (report) expect(['ok', 'clean']).toContain(report.status);
-
-      // Pre-fix this stays null forever: dream never passed a sourceId, so
-      // runCycle's stamp gate skipped the write.
-      expect(await readLastFullCycleAt('path-scoped')).not.toBeNull();
-    });
-  }, 60_000);
-
-  test('--dir matching an ARCHIVED source does not stamp it', async () => {
-    await withEnv({ GBRAIN_HOME: gbrainHome }, async () => {
-      await seedSource('mothballed', true);
-
-      const report = await runDream(engine, ['--dir', brainDir, '--phase', 'lint', '--json']);
-      expect(report).toBeTruthy();
-
-      // Stamping an archived source would mask data staleness when it is
-      // later restored (mirrors the explicit --source archived guard).
-      expect(await readLastFullCycleAt('mothballed')).toBeNull();
-    });
-  }, 60_000);
-});

test/dream.test.ts

@@ -562,22 +562,12 @@ describe('runDream — --source / --source-id (v0.41.13)', () => {
 
   // ─── Back-compat: bare `gbrain dream` does NOT write per-source stamp ─
 
-  test('gbrain dream (no --source) stamps only the source whose local_path matches --dir (#1869)', async () => {
-    // Pre-#1869 this asserted NO source was ever stamped without an explicit
-    // --source — which is exactly the bug: a path-scoped `gbrain dream --dir`
-    // run never landed a freshness stamp and doctor's cycle_freshness stayed
-    // stale forever. New truth: the source whose local_path matches the
-    // resolved brain dir is derived and stamped; unrelated sources stay
-    // untouched (cross-source isolation).
-    await seedSource('alpha'); // local_path = repo → derived + stamped
-    await engine.executeRaw(
-      `INSERT INTO sources (id, name, local_path, config, archived, created_at)
-       VALUES ($1, $2, $3, '{}'::jsonb, false, NOW())`,
-      ['beta', 'beta', '/somewhere/else'],
-    );
+  test('gbrain dream (no --source) leaves all sources untouched (back-compat regression)', async () => {
+    await seedSource('alpha');
+    await seedSource('beta');
     const report = await runDream(engine, ['--dir', repo, '--phase', 'lint', '--json']);
     expect(report).toBeTruthy();
-    expect(await readLastFullCycleAt('alpha')).not.toBeNull();
+    expect(await readLastFullCycleAt('alpha')).toBeNull();
     expect(await readLastFullCycleAt('beta')).toBeNull();
   }, 60_000);
 

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.