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/config.ts

@@ -908,10 +908,6 @@ export const KNOWN_CONFIG_KEYS: readonly string[] = [
   'facts.extraction_model',
   // #2113: output-token cap for the per-turn facts extractor (default 4000).
   'facts.extraction_max_tokens',
-  // Owner opt-in: let the local stdio MCP pipe read this owner's private facts
-  // (find_trajectory / recall). Default off; HTTP transport ignores it. See
-  // src/core/facts/reader-trust.ts.
-  'facts.trust_local_reads',
   // Dream cycle config
   'dream.synthesize.session_corpus_dir',
   'dream.synthesize.meeting_transcripts_dir',

src/core/engine.ts

@@ -591,8 +591,6 @@ export interface TrajectoryOpts {
   sourceIds?: string[];
   /** When true, filters to visibility='world' only. Set by MCP layer from ctx.remote. */
   remote?: boolean;
-  /** Owner opt-in: read private facts despite `remote`. See facts/reader-trust.ts. */
-  trustedFactReads?: boolean;
   /** Metric filter. When set, only facts with this canonical metric label participate. */
   metric?: string;
   /**

src/core/facts/meta-hook.ts

@@ -17,7 +17,6 @@
 import type { OperationContext } from './../operations.ts';
 import type { FactRow } from './../engine.ts';
 import { effectiveConfidence } from './decay.ts';
-import { readableFactVisibilities } from './reader-trust.ts';
 
 const DEFAULT_TTL_MS = 30_000;
 const DEFAULT_TOP_K = 10;
@@ -51,13 +50,7 @@ export async function getBrainHotMemoryMeta(
   const sessionId = (ctx as { source_session?: string }).source_session
     ?? null;
   const allowListHash = hashAllowList(ctx.takesHoldersAllowList);
-  // Visibility tier: untrusted remote → world-only; trusted local +
-  // owner-trusted reads → all rows. Folded into the cache key (the header's
-  // "cache entries don't bleed across tiers" invariant): trustedFactReads is
-  // re-read from config per call, so a mid-session opt-out must not keep
-  // serving a private-inclusive cached payload for the TTL window.
-  const visibility = readableFactVisibilities(ctx);
-  const cacheKey = `${sourceId}::${sessionId ?? '_'}::${allowListHash}::${visibility ? 'world' : 'all'}`;
+  const cacheKey = `${sourceId}::${sessionId ?? '_'}::${allowListHash}`;
 
   const ttl = Math.max(1000, opts.ttlMs ?? DEFAULT_TTL_MS);
   const topK = Math.max(1, Math.min(opts.topK ?? DEFAULT_TOP_K, 25));
@@ -68,6 +61,10 @@ export async function getBrainHotMemoryMeta(
     return cached.payload;
   }
 
+  // Build a fresh payload. Visibility tier: remote → world-only;
+  // local → all rows.
+  const visibility = ctx.remote === false ? undefined : ['world'] as ('world' | 'private')[];
+
   let rows: FactRow[] = [];
   if (sessionId) {
     rows = await ctx.engine.listFactsBySession(sourceId, sessionId, {

src/core/facts/reader-trust.ts

@@ -1,48 +0,0 @@
-/**
- * Fact-read visibility trust.
- *
- * Fact rows are tagged `private` | `world`. Remote/untrusted callers
- * (`remote === true`) see only `world` rows — the posture that keeps a
- * published or HTTP-served brain from leaking private claims to strangers.
- *
- * But the stdio MCP server is an unauthenticated LOCAL pipe: on a single-owner
- * machine the caller IS the owner, yet it still defaults `remote: true` for
- * safety, so the owner's own agent is denied the owner's own private facts
- * (e.g. `find_trajectory` returns empty over MCP even though the facts exist).
- *
- * `trustedFactReads` is a narrow, READ-ONLY trust elevation, deliberately
- * DECOUPLED from `remote` so every other remote protection — file_upload
- * confinement, source isolation, fence stripping, takes-holder scoping — stays
- * fully in force. The stdio MCP server sets it ONLY when the brain owner opts
- * in via the `facts.trust_local_reads` config (default off). The HTTP/published
- * transport never sets it, so a served brain stays world-only regardless.
- */
-export interface FactReaderTrust {
-  /**
-   * Mirrors OperationContext.remote. FAIL-CLOSED: anything not strictly
-   * `false` is treated as remote/untrusted (CLAUDE.md trust invariant).
-   */
-  remote?: boolean;
-  /** Owner opt-in: this remote caller may read private facts. */
-  trustedFactReads?: boolean;
-}
-
-/**
- * True when the reader is restricted to `visibility = 'world'` rows.
- * Fail-closed: an unset/undefined `remote` is untrusted — only an explicit
- * `remote: false` (trusted local CLI) or an explicit owner opt-in
- * (`trustedFactReads: true`) reads private rows.
- */
-export function factsWorldOnly(t: FactReaderTrust): boolean {
-  return t.remote !== false && t.trustedFactReads !== true;
-}
-
-/**
- * Visibility filter for list-style fact reads: `['world']` when the reader is
- * world-only, `undefined` (no filter — all rows) when it is trusted.
- */
-export function readableFactVisibilities(
-  t: FactReaderTrust,
-): ('private' | 'world')[] | undefined {
-  return factsWorldOnly(t) ? ['world'] : undefined;
-}

src/core/operations.ts

@@ -18,7 +18,6 @@ import { captureEvalCandidate, isEvalCaptureEnabled, isEvalScrubEnabled } from '
 import type { HybridSearchMeta } from './types.ts';
 import { extractPageLinks, isAutoLinkEnabled, isAutoTimelineEnabled, isGlobalBasenameEnabled, parseTimelineEntries, makeResolver, type UnresolvedFrontmatterRef } from './link-extraction.ts';
 import { isFactsBackstopEligible } from './facts/eligibility.ts';
-import { readableFactVisibilities } from './facts/reader-trust.ts';
 import { stripTakesFence } from './takes-fence.ts';
 import { stripFactsFence } from './facts-fence.ts';
 import { getContentFlag } from './quarantine.ts';
@@ -334,14 +333,14 @@ export interface OperationContext {
    */
   remote: boolean;
   /**
-   * Owner opt-in (`facts.trust_local_reads`): allow this remote caller to read
-   * `private` facts. A NARROW, read-only trust elevation decoupled from
-   * `remote` — every other remote protection (file confinement, source
-   * isolation, fence stripping, takes scoping) stays in force. Set ONLY by the
-   * stdio MCP server when the config is on; the HTTP transport never sets it.
-   * Consulted via `src/core/facts/reader-trust.ts`.
+   * 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.
    */
-  trustedFactReads?: boolean;
+  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
@@ -3639,7 +3638,6 @@ const find_trajectory: Operation = {
       entitySlug: p.entity_slug,
       ...scope,
       remote: ctx.remote === true,
-      trustedFactReads: ctx.trustedFactReads === true,
       metric,
       kind,
       since,
@@ -3724,9 +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) => {
@@ -3738,6 +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',
@@ -4000,9 +4005,13 @@ const recall: Operation = {
     const includeExpired = p.include_expired === true;
     const grep = typeof p.grep === 'string' ? p.grep.toLowerCase() : null;
 
-    // Visibility filter: world-only for untrusted remote callers; all rows for
-    // trusted local CLI and owner-trusted reads (facts.trust_local_reads).
-    const visibility = readableFactVisibilities(ctx);
+    // Visibility filter: remote callers see world-only unless their token
+    // grants elevated visibility (future-proofing; v0.31 ships world-only
+    // for remote, all for local CLI).
+    const visibility =
+      ctx.remote === false
+        ? undefined
+        : ['world'] as ('private' | 'world')[];
 
     let rows: Awaited<ReturnType<typeof ctx.engine.listFactsByEntity>> = [];
 

src/core/pglite-engine.ts

@@ -18,7 +18,6 @@ import type {
 } from './engine.ts';
 import { MAX_SEARCH_LIMIT, clampSearchLimit } from './engine.ts';
 import { withRetry, BULK_RETRY_OPTS, resolveBulkRetryOpts, computeNextDelay, type BatchAuditSite } from './retry.ts';
-import { factsWorldOnly } from './facts/reader-trust.ts';
 import { logBatchRetry as auditLogBatchRetry, logBatchExhausted as auditLogBatchExhausted } from './audit/batch-retry-audit.ts';
 import { runMigrations } from './migrate.ts';
 import { PGLITE_SCHEMA_SQL, getPGLiteSchema } from './pglite-schema.ts';
@@ -4319,10 +4318,7 @@ export class PGLiteEngine implements BrainEngine {
     const useArray = Array.isArray(opts.sourceIds) && opts.sourceIds.length > 0;
     const sourceIds = useArray ? opts.sourceIds! : null;
     const sourceId = opts.sourceId ?? 'default';
-    // Direct-engine contract: unset `remote` here means a trusted in-process
-    // caller (CLI/tests) — the fail-closed default lives in the op layer, which
-    // always passes explicit booleans. Normalize before the fail-closed helper.
-    const remoteFilter = factsWorldOnly({ remote: opts.remote === true, trustedFactReads: opts.trustedFactReads === true });
+    const remoteFilter = opts.remote === true;
 
     // Build SQL dynamically. PGLite uses $N positional params; we
     // assemble the WHERE clauses + params array in tandem to keep them

src/core/postgres-engine.ts

@@ -14,7 +14,6 @@ import type {
   SourceRow,
 } from './engine.ts';
 import { withRetry, BULK_RETRY_OPTS, resolveBulkRetryOpts, computeNextDelay, type BatchAuditSite } from './retry.ts';
-import { factsWorldOnly } from './facts/reader-trust.ts';
 import { logBatchRetry as auditLogBatchRetry, logBatchExhausted as auditLogBatchExhausted } from './audit/batch-retry-audit.ts';
 import type {
   DomainBankSampleOpts, CorpusSampleOpts, DomainBankRow,
@@ -4533,10 +4532,7 @@ export class PostgresEngine implements BrainEngine {
     const useArray = Array.isArray(opts.sourceIds) && opts.sourceIds.length > 0;
     const sourceIds = useArray ? opts.sourceIds! : null;
     const sourceId = opts.sourceId ?? 'default';
-    // Direct-engine contract: unset `remote` here means a trusted in-process
-    // caller (CLI/tests) — the fail-closed default lives in the op layer, which
-    // always passes explicit booleans. Normalize before the fail-closed helper.
-    const remoteFilter = factsWorldOnly({ remote: opts.remote === true, trustedFactReads: opts.trustedFactReads === true });
+    const remoteFilter = opts.remote === true;
 
     // Source-scope predicate: array path (federated) wins over scalar.
     // Engine.ts contract: returns chronological points; regressions +

src/mcp/dispatch.ts

@@ -30,15 +30,14 @@ export interface ToolResult {
 export interface DispatchOpts {
   /** Defaults to true (remote/untrusted). Local CLI callers (`gbrain call`) pass false. */
   remote?: boolean;
-  /**
-   * Owner opt-in (`facts.trust_local_reads`): let this remote caller read
-   * `private` facts. Set ONLY by the stdio MCP server; the HTTP transport
-   * leaves it unset so a served brain stays world-only. See
-   * `src/core/facts/reader-trust.ts`.
-   */
-  trustedFactReads?: 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`.
@@ -210,7 +209,7 @@ export function buildOperationContext(
     logger: opts.logger || stderrLogger,
     dryRun: !!params.dry_run,
     remote: opts.remote ?? true,
-    trustedFactReads: opts.trustedFactReads === 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

@@ -35,16 +35,6 @@ export async function startMcpServer(engine: BrainEngine) {
   // shape and cast through `any` (the SDK accepts it via the ServerResult union).
   server.setRequestHandler(CallToolRequestSchema, async (request: any): Promise<any> => {
     const { name, arguments: params } = request.params;
-    // Owner opt-in: the stdio pipe is local + unauthenticated, so on a
-    // single-owner machine its caller is the owner. When facts.trust_local_reads
-    // is on, let fact reads (find_trajectory / recall) see this owner's own
-    // private facts. Narrow + read-only — every other remote protection stays
-    // on (remote stays true). HTTP transport never sets this. Best-effort: a
-    // config read blip falls back to the safe world-only default.
-    let trustedFactReads = false;
-    try {
-      trustedFactReads = (await engine.getConfig('facts.trust_local_reads')) === 'true';
-    } catch { /* keep world-only default */ }
     // v0.28: stdio MCP has no per-token auth (local pipe). Default the
     // takes-holder allow-list to ['world'] so agent-facing callers don't
     // see private hunches via takes_list / takes_search / query. Operators
@@ -52,7 +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,
-      trustedFactReads,
+      // #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/engine-find-trajectory.test.ts

@@ -165,22 +165,6 @@ describe('findTrajectory — visibility filter (D-CDX-1 / R6)', () => {
     const all = await engine.findTrajectory({ entitySlug: 'traj-vis-default' });
     expect(all.length).toBe(2);
   });
-
-  test('remote=true + trustedFactReads bypasses world-only (owner-trusted reads)', async () => {
-    await insertTyped({ entity_slug: 'traj-vis-trusted', metric: 'mrr', value: 50000, visibility: 'private', valid_from: new Date('2026-01-15') });
-    await insertTyped({ entity_slug: 'traj-vis-trusted', metric: 'mrr', value: 99999, visibility: 'world',   valid_from: new Date('2026-04-12') });
-
-    // Untrusted remote: world only.
-    const untrusted = await engine.findTrajectory({ entitySlug: 'traj-vis-trusted', remote: true });
-    expect(untrusted.length).toBe(1);
-    expect(untrusted[0].value).toBe(99999);
-
-    // Owner-trusted remote: sees the private point too. remote stays true — only
-    // fact-read visibility is elevated.
-    const trusted = await engine.findTrajectory({ entitySlug: 'traj-vis-trusted', remote: true, trustedFactReads: true });
-    expect(trusted.length).toBe(2);
-    expect(trusted.map(p => p.value).sort((a, b) => (a! - b!))).toEqual([50000, 99999]);
-  });
 });
 
 describe('findTrajectory — metric + since + until filters', () => {

test/facts-reader-trust.test.ts

@@ -1,43 +0,0 @@
-import { describe, test, expect } from 'bun:test';
-import {
-  factsWorldOnly,
-  readableFactVisibilities,
-} from '../src/core/facts/reader-trust.ts';
-
-describe('factsWorldOnly', () => {
-  test('FAIL-CLOSED: unset remote is untrusted (world-only)', () => {
-    expect(factsWorldOnly({})).toBe(true);
-    expect(factsWorldOnly({ remote: undefined })).toBe(true);
-    expect(factsWorldOnly({ trustedFactReads: false })).toBe(true);
-  });
-
-  test('explicit remote=false (trusted local CLI) sees all', () => {
-    expect(factsWorldOnly({ remote: false })).toBe(false);
-    expect(factsWorldOnly({ remote: false, trustedFactReads: false })).toBe(false);
-  });
-
-  test('untrusted remote callers are world-only', () => {
-    expect(factsWorldOnly({ remote: true })).toBe(true);
-    expect(factsWorldOnly({ remote: true, trustedFactReads: false })).toBe(true);
-  });
-
-  test('owner-trusted remote reads bypass the world-only filter', () => {
-    expect(factsWorldOnly({ remote: true, trustedFactReads: true })).toBe(false);
-  });
-
-  test('trustedFactReads is a no-op for an already-trusted local caller', () => {
-    expect(factsWorldOnly({ remote: false, trustedFactReads: true })).toBe(false);
-  });
-});
-
-describe('readableFactVisibilities', () => {
-  test("world-only readers get the ['world'] filter (incl. unset remote)", () => {
-    expect(readableFactVisibilities({ remote: true })).toEqual(['world']);
-    expect(readableFactVisibilities({})).toEqual(['world']);
-  });
-
-  test('trusted readers get undefined (no filter — all rows)', () => {
-    expect(readableFactVisibilities({ remote: false })).toBeUndefined();
-    expect(readableFactVisibilities({ remote: true, trustedFactReads: true })).toBeUndefined();
-  });
-});

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.