fix(schema-pack): narrow stats catch-all so masked errors surface, not fake 0 pages (#2466)

fetchCountRows and detectDeadPrefixes in src/core/schema-pack/stats.ts
swallowed EVERY engine error into empty results, so any real failure
printed 'Total pages: 0' + a vacuous 100% coverage on a populated brain.
Both catches now swallow only isUndefinedTableError (pre-init brain,
missing pages table) and rethrow everything else. Four regression tests:
real non-zero count on a populated PGLite brain, rethrow on non-missing-
table errors in both catch sites, and the missing-table degrade path.

Takeover of #2493.

Co-authored-by: javieraldape <javieraldape@users.noreply.github.com>
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)
 }
 
-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/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/core/schema-pack/stats.ts

@@ -18,6 +18,7 @@
 import type { BrainEngine } from '../engine.ts';
 import { loadActivePackBestEffort } from './best-effort.ts';
 import type { OperationContext } from '../operations.ts';
+import { isUndefinedTableError } from '../utils.ts';
 
 export interface StatsOpts {
   /** Single source scope. Omit + omit sourceIds for whole-brain aggregate. */
@@ -164,9 +165,17 @@ async function fetchCountRows(engine: BrainEngine, opts: StatsOpts): Promise<Raw
   `;
   try {
     return await engine.executeRaw<RawCountRow>(sql, params);
-  } catch {
-    // Empty / pre-init brain: pages table may not exist yet.
-    return [];
+  } catch (err) {
+    // ONLY swallow the genuine "pages table doesn't exist yet" case
+    // (empty / pre-init brain). #2466: the old bare `catch {}` masked
+    // EVERY error — so any engine-level failure (connection, version
+    // skew, a query incompatibility) was silently converted to 0 rows,
+    // printing "Total pages: 0" on a populated brain and cascading into
+    // false "100% coverage" + a starved `schema suggest`. Surface
+    // everything that is not a missing-table error so the real failure
+    // is visible instead of hidden behind a fake zero.
+    if (isUndefinedTableError(err)) return [];
+    throw err;
   }
 }
 
@@ -204,9 +213,11 @@ async function detectDeadPrefixes(
         if (cnt === 0) {
           hints.push({ type: t.name, prefix });
         }
-      } catch {
-        // Skip on engine error (no pages table yet, etc.).
-        continue;
+      } catch (err) {
+        // #2466: only skip on the genuine "no pages table yet" case;
+        // rethrow any other engine error so it isn't silently masked.
+        if (isUndefinedTableError(err)) continue;
+        throw err;
       }
     }
   }

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/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/schema-pack-stats.test.ts

@@ -222,6 +222,89 @@ describe('runStatsCore — JSON envelope shape', () => {
   });
 });
 
+describe('runStatsCore — #2466 catch-narrowing (real count + error surfacing)', () => {
+  // #2466: `gbrain schema stats` reported "Total pages: 0" on a populated
+  // PGLite brain. The bug was a bare `catch {}` in fetchCountRows (and a
+  // sibling in detectDeadPrefixes) that converted ANY engine error into 0
+  // rows. The COUNT query itself is valid on PGLite (proven below), so the
+  // regression pins two things: (a) a populated brain reports the real,
+  // non-zero count through the full runStatsCore path; (b) a non-missing-
+  // table engine error is rethrown, not masked into a fake zero.
+
+  it('reports the real non-zero count on a populated PGLite brain (no false 0)', async () => {
+    await withEnv({ GBRAIN_SCHEMA_PACK: undefined }, async () => {
+      // Seed a realistic mix: typed, untyped, multiple types — like the
+      // 169-page brain in the bug report (scaled down).
+      for (let i = 0; i < 12; i++) {
+        const type = i % 3 === 0 ? '' : (i % 3 === 1 ? 'person' : 'company');
+        await seedPage(`notes/p${i}`, { type, sourcePath: `notes/p${i}.md` });
+      }
+      const result = await runStatsCore(ctxOf());
+      // The core regression: NOT zero.
+      expect(result.aggregate.total_pages).toBe(12);
+      expect(result.aggregate.typed_pages).toBe(8);
+      expect(result.aggregate.untyped_pages).toBe(4);
+      // And coverage is the honest ratio, not the vacuous 1.0 a 0/0 prints.
+      expect(result.aggregate.coverage).not.toBe(1.0);
+    });
+  });
+
+  it('fetchCountRows rethrows a non-missing-table engine error instead of masking it as 0 pages', async () => {
+    await withEnv({ GBRAIN_SCHEMA_PACK: undefined }, async () => {
+      // No pack → detectDeadPrefixes is skipped, isolating the throw to the
+      // fetchCountRows catch we narrowed. The count query (the GROUP BY one)
+      // throws a column-level error (SQLSTATE 42703) — the exact class the
+      // old bare `catch {}` swallowed into 0 rows; everything else succeeds.
+      __setPackLocatorForTests(() => null);
+      const boom = Object.assign(new Error('column "type" does not exist'), { code: '42703' });
+      const stubEngine = {
+        executeRaw: async (sql: string) => {
+          if (/GROUP BY source_id/.test(sql)) throw boom;  // the fetchCountRows query
+          return [];
+        },
+      } as unknown as PGLiteEngine;
+      const ctx = { ...ctxOf(), engine: stubEngine } as unknown as OperationContext;
+      await expect(runStatsCore(ctx)).rejects.toThrow('column "type" does not exist');
+    });
+  });
+
+  it('fetchCountRows still degrades to empty (no throw) on a genuine missing pages table', async () => {
+    await withEnv({ GBRAIN_SCHEMA_PACK: undefined }, async () => {
+      // Pre-init brain shape: the count query hits a missing pages table
+      // (SQLSTATE 42P01). This is the ONLY case the narrowed catch swallows.
+      __setPackLocatorForTests(() => null);
+      const missing = Object.assign(new Error('relation "pages" does not exist'), { code: '42P01' });
+      const stubEngine = {
+        executeRaw: async (sql: string) => {
+          if (/GROUP BY source_id/.test(sql)) throw missing;
+          return [];
+        },
+      } as unknown as PGLiteEngine;
+      const ctx = { ...ctxOf(), engine: stubEngine } as unknown as OperationContext;
+      const result = await runStatsCore(ctx);
+      expect(result.aggregate.total_pages).toBe(0);
+      expect(result.per_source).toEqual([]);
+    });
+  });
+
+  it('detectDeadPrefixes rethrows a non-missing-table error (sibling catch)', async () => {
+    await withEnv({ GBRAIN_HOME: tmpDir, GBRAIN_SCHEMA_PACK: 'tiny' }, async () => {
+      seedTinyPack('tiny', [{ name: 'person', prefix: 'people/' }]);
+      // fetchCountRows (the GROUP BY query) succeeds → []; the per-prefix
+      // dead-prefix LIKE query then throws a non-missing-table error, which
+      // must surface through the narrowed sibling catch.
+      const stubEngine = {
+        executeRaw: async (sql: string) => {
+          if (/GROUP BY source_id/.test(sql)) return [];        // count query: empty brain, fine
+          throw Object.assign(new Error('division by zero'), { code: '22012' });  // the LIKE query
+        },
+      } as unknown as PGLiteEngine;
+      const ctx = { ...ctxOf(), engine: stubEngine } as unknown as OperationContext;
+      await expect(runStatsCore(ctx)).rejects.toThrow('division by zero');
+    });
+  });
+});
+
 describe('runStatsCore — type/untyped split', () => {
   it('treats empty-string type as untyped (not its own bucket)', async () => {
     await withEnv({ GBRAIN_SCHEMA_PACK: undefined }, async () => {

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.