fix(rerank): classify missing auth before fallback (#2059)

Missing ZEROENTROPY_API_KEY threw AIConfigError from auth resolution, which
rerank.ts recorded as reason 'unknown' — and doctor's reranker_health had no
unknown bucket, so it reported ok while every rerank silently failed open.

- gateway.rerank wraps AIConfigError from applyResolveAuth as
  RerankError(reason: 'auth') before any HTTP call.
- checkRerankerHealth warns on >=3 'unknown' failures in the 7-day window
  (covers historical pre-fix audit rows), with a ZEROENTROPY_API_KEY setup
  hint when the error summary points at a missing key.
- Tests: RerankError(auth) classification, applyReranker fail-open + audit
  reason, doctor warn on repeated unknowns.

Takeover of #2070.

Co-authored-by: maxpetrusenkoagent <maxpetrusenkoagent@users.noreply.github.com>
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

src/commands/doctor.ts

@@ -1551,6 +1551,24 @@ export async function checkRerankerHealth(engine: BrainEngine): Promise<Check> {
       };
     }
 
+    // Historical #2059 rows were logged as `unknown` before missing reranker
+    // auth was classified at the gateway. Surface repeated unknowns instead of
+    // reporting "ok" while every rerank fails open.
+    const unknownFails = failures.filter((f) => f.reason === 'unknown');
+    if (unknownFails.length >= 3) {
+      const setupHint = unknownFails.some((f) => {
+        const summary = String(f.error_summary ?? '');
+        return summary.includes('ZEROENTROPY_API_KEY') || summary.toLowerCase().includes('api key');
+      })
+        ? ' Fix: verify ZEROENTROPY_API_KEY and run `gbrain models doctor`.'
+        : '';
+      return {
+        name: 'reranker_health',
+        status: 'warn',
+        message: `${unknownFails.length} unknown reranker failure(s) in last 7 days.${setupHint}`,
+      };
+    }
+
     return {
       name: 'reranker_health',
       status: 'ok',

src/commands/init.ts

@@ -161,7 +161,7 @@ interface ResolveAIOptionsArgs {
   nonInteractive: boolean;       // --non-interactive (forces D3 fail-loud, no picker)
 }
 
-export interface ResolvedAIOptions {
+interface ResolvedAIOptions {
   embedding_model?: string;
   embedding_dimensions?: number;
   expansion_model?: string;
@@ -170,41 +170,6 @@ export 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`.
  *
@@ -238,13 +203,18 @@ async function resolveAIOptions(opts: ResolveAIOptionsArgs): Promise<ResolvedAIO
   // user already opted into deferred mode.
   try {
     const { loadConfig } = await import('../core/config.ts');
-    // #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()));
+    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;
   } catch {
-    // loadConfig threw — treat as first-time install, fall through to env
-    // detection.
+    // loadConfig throws when no brain configured — first-time install, fall
+    // through to env detection.
   }
 
   // --- Tier 1+2: explicit flags ---------------------------------------------

src/core/ai/gateway.ts

@@ -3656,7 +3656,15 @@ export async function rerank(input: RerankInput): Promise<RerankResult[]> {
   // whose request/response shape differs from ZE/llama.cpp (e.g. Voyage with
   // `top_k` / `data[]`) needs separate adapter hooks in a follow-up plan.
   const url = `${compat.baseURL.replace(/\/$/, '')}${tp.path ?? '/models/rerank'}`;
-  const auth = applyResolveAuth(recipe, cfg, 'reranker');
+  let auth: { apiKey?: string; headers?: Record<string, string> };
+  try {
+    auth = applyResolveAuth(recipe, cfg, 'reranker');
+  } catch (err) {
+    if (err instanceof AIConfigError) {
+      throw new RerankError(err.message, 'auth');
+    }
+    throw err;
+  }
   // applyResolveAuth returns { apiKey } for Bearer-style auth (SDK's native
   // path) or { headers } for custom-header providers (Azure). v0.37.6.0:
   // recipes can ALSO declare default_headers (attribution etc.) which flow

src/core/operations.ts

@@ -332,15 +332,6 @@ 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
@@ -3722,10 +3713,9 @@ 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: []}, 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.',
+    '{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.',
   params: {},
   scope: 'read',
   handler: async (ctx) => {
@@ -3737,12 +3727,6 @@ 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

@@ -32,12 +32,6 @@ 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`.
@@ -209,7 +203,6 @@ 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

@@ -42,10 +42,6 @@ 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/rerank.test.ts

@@ -154,6 +154,28 @@ describe('gateway.rerank() — happy path', () => {
 describe('gateway.rerank() — error classification', () => {
   beforeEach(() => configureZE());
 
+  test('missing required reranker API key → RerankError(auth) before HTTP call', async () => {
+    configureGateway({
+      reranker_model: 'zeroentropyai:zerank-2',
+      env: {},
+    });
+    let called = false;
+    __setRerankTransportForTests(async () => {
+      called = true;
+      return mockResp({ results: [{ index: 0, relevance_score: 0.5 }] });
+    });
+
+    try {
+      await rerank({ query: 'q', documents: ['d'] });
+      throw new Error('should have thrown');
+    } catch (err) {
+      expect(err).toBeInstanceOf(RerankError);
+      expect((err as RerankError).reason).toBe('auth');
+      expect((err as Error).message).toContain('ZEROENTROPY_API_KEY');
+      expect(called).toBe(false);
+    }
+  });
+
   test('401 → auth', async () => {
     __setRerankTransportForTests(async () => new Response('Unauthorized', { status: 401 }));
     try {

test/doctor.test.ts

@@ -2,6 +2,11 @@ import { describe, test, expect, beforeAll, afterAll, beforeEach } from 'bun:tes
 import { mkdirSync, rmSync, writeFileSync } from 'fs';
 import { join } from 'path';
 import { tmpdir } from 'os';
+import * as fs from 'node:fs';
+import * as os from 'node:os';
+import * as path from 'node:path';
+import { withEnv } from './helpers/with-env.ts';
+import { logRerankFailure } from '../src/core/rerank-audit.ts';
 
 describe('doctor command', () => {
   test('doctor module exports runDoctor', async () => {
@@ -47,6 +52,34 @@ describe('doctor command', () => {
     expect(check.issues![0].action).toContain('trigger');
   });
 
+  test('reranker_health warns on repeated unknown rerank failures', async () => {
+    const { checkRerankerHealth } = await import('../src/commands/doctor.ts');
+    const tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'gbrain-rerank-doctor-'));
+    try {
+      await withEnv({ GBRAIN_AUDIT_DIR: tmpDir }, async () => {
+        for (let i = 0; i < 3; i++) {
+          logRerankFailure({
+            model: 'zeroentropyai:zerank-2',
+            reason: 'unknown',
+            query_hash: `unknown${i}`,
+            doc_count: 30,
+            error_summary: 'ZeroEntropy reranker requires ZEROENTROPY_API_KEY.',
+          });
+        }
+        const check = await checkRerankerHealth({
+          async getConfig(key: string): Promise<string | null> {
+            return key === 'search.reranker.enabled' ? 'true' : null;
+          },
+        } as any);
+        expect(check.status).toBe('warn');
+        expect(check.message).toContain('unknown');
+        expect(check.message).toContain('ZEROENTROPY_API_KEY');
+      });
+    } finally {
+      fs.rmSync(tmpDir, { recursive: true, force: true });
+    }
+  });
+
   test('runDoctor accepts null engine for filesystem-only mode', async () => {
     const { runDoctor } = await import('../src/commands/doctor.ts');
     // runDoctor should accept null engine — it runs filesystem checks only.

test/init-env-detection.test.ts

@@ -12,7 +12,7 @@
  */
 
 import { describe, test, expect } from 'bun:test';
-import { groupReadyByProvider, findEnvKeyTypos, seedAIOptionsFromConfig } from '../src/commands/init.ts';
+import { groupReadyByProvider, findEnvKeyTypos } from '../src/commands/init.ts';
 
 describe('groupReadyByProvider — embedding touchpoint', () => {
   test('OPENAI_API_KEY alone → openai is ready', async () => {
@@ -149,47 +149,3 @@ 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/search/rerank.test.ts

@@ -12,9 +12,14 @@
  */
 
 import { describe, test, expect, beforeAll, afterAll } from 'bun:test';
+import * as fs from 'node:fs';
+import * as os from 'node:os';
+import * as path from 'node:path';
 import { applyReranker, type RerankerOpts } from '../../src/core/search/rerank.ts';
 import { RerankError, type RerankResult } from '../../src/core/ai/gateway.ts';
+import { readRecentRerankFailures } from '../../src/core/rerank-audit.ts';
 import type { SearchResult } from '../../src/core/types.ts';
+import { withEnv } from '../helpers/with-env.ts';
 
 function makeResult(slug: string, score: number, chunk: string): SearchResult {
   return {
@@ -160,6 +165,36 @@ describe('applyReranker — fail-open on every RerankError reason', () => {
     expect(out).toEqual(results);
   });
 
+  test('missing gateway reranker API key fail-opens and audits auth', async () => {
+    const { configureGateway } = await import('../../src/core/ai/gateway.ts');
+    const tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'gbrain-rerank-search-'));
+    try {
+      await withEnv({ GBRAIN_AUDIT_DIR: tmpDir }, async () => {
+        configureGateway({
+          reranker_model: 'zeroentropyai:zerank-2',
+          env: {},
+        });
+
+        const results = [makeResult('a', 1.0, 'doc a')];
+        const out = await applyReranker('q', results, {
+          enabled: true,
+          topNIn: 1,
+          topNOut: null,
+          model: 'zeroentropyai:zerank-2',
+        });
+
+        expect(out).toEqual(results);
+        const failures = readRecentRerankFailures(1);
+        expect(failures).toHaveLength(1);
+        expect(failures[0]!.reason).toBe('auth');
+        expect(failures[0]!.error_summary).toContain('ZEROENTROPY_API_KEY');
+      });
+    } finally {
+      fs.rmSync(tmpDir, { recursive: true, force: true });
+      configureGateway({ env: { ZEROENTROPY_API_KEY: 'test-key' } });
+    }
+  });
+
   test('fail-open on non-RerankError throw too', async () => {
     const results = [makeResult('a', 1.0, 'a')];
     const opts: RerankerOpts = {

test/whoami.test.ts

@@ -94,35 +94,6 @@ 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.