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/extract.ts

@@ -43,7 +43,7 @@ import {
 } from '../core/link-extraction.ts';
 import { createProgress } from '../core/progress.ts';
 import { getCliOptions, cliOptsToProgressOptions } from '../core/cli-options.ts';
-import { pathToSlug, slugifyPath, pruneDir, isSyncable } from '../core/sync.ts';
+import { pathToSlug, pruneDir, isSyncable } from '../core/sync.ts';
 // v0.41.18.0: withRetry + isRetryableConnError + WithRetryOpts moved to
 // src/core/retry.ts as the canonical primitive. Engine methods
 // (addLinksBatch/addTimelineEntriesBatch/upsertChunks) now self-retry via
@@ -269,24 +269,14 @@ export function extractMarkdownLinks(content: string): { name: string; relTarget
 export function resolveSlug(fileDir: string, relTarget: string, allSlugs: Set<string>): string | null {
   const targetNoExt = relTarget.endsWith('.md') ? relTarget.slice(0, -3) : relTarget;
 
-  // Issue #1964: wikilinks carry raw Obsidian paths (`[[llm-wiki/entities/AI 3.0]]`)
-  // but allSlugs holds sync-slugified slugs (`llm-wiki/entities/ai-3.0`). Try the
-  // raw candidate first (back-compat), then the sync-consistent slugified form.
-  const hit = (candidate: string): string | null => {
-    if (allSlugs.has(candidate)) return candidate;
-    const slugified = slugifyPath(candidate);
-    if (slugified !== candidate && allSlugs.has(slugified)) return slugified;
-    return null;
-  };
-
-  const s1 = hit(join(fileDir, targetNoExt));
-  if (s1) return s1;
+  const s1 = join(fileDir, targetNoExt);
+  if (allSlugs.has(s1)) return s1;
 
   const parts = fileDir.split('/').filter(Boolean);
   for (let strip = 1; strip <= parts.length; strip++) {
     const ancestor = parts.slice(0, parts.length - strip).join('/');
-    const candidate = hit(ancestor ? join(ancestor, targetNoExt) : targetNoExt);
-    if (candidate) return candidate;
+    const candidate = ancestor ? join(ancestor, targetNoExt) : targetNoExt;
+    if (allSlugs.has(candidate)) return candidate;
   }
 
   return null;

src/core/link-extraction.ts

@@ -14,7 +14,6 @@
 import type { BrainEngine } from './engine.ts';
 import type { PageType } from './types.ts';
 import { ensureWellFormed } from './text-safe.ts';
-import { slugifyPath } from './sync.ts';
 
 /**
  * v0.42.7 — link-extraction version stamp. Bump this ISO timestamp whenever the
@@ -483,29 +482,14 @@ export async function extractPageLinks(
     // pre-v0.40.8.2 behavior of dropping bare wikilinks outside
     // DIR_PATTERN.
     if (ref.needsResolution) {
-      if (typeof resolver.resolveBasenameMatches !== 'function') continue;
+      if (!opts.globalBasename || typeof resolver.resolveBasenameMatches !== 'function') {
+        continue;
+      }
       // Issue #972 (codex): resolve by the wikilink TARGET (ref.slug — the
       // text inside `[[...]]` before any `|`), NOT the display alias
       // (ref.name = match[2]). `[[struktura|the project]]` must resolve
       // `struktura`, not "the project". The display text is for context only.
-      //
-      // Issue #1964: a dir-qualified wikilink (`[[llm-wiki/entities/AI 3.0]]`)
-      // carries a raw Obsidian path while page slugs are sync-slugified
-      // (`llm-wiki/entities/ai-3.0`). Slugify the path the same way sync does,
-      // then match by exact slug or path-suffix (wiki-root-relative authoring).
-      // This runs regardless of global_basename — it's dir-qualified, so the
-      // cross-dir false-positive risk the flag guards against doesn't apply.
-      // Mirrors the FS path's resolveSlug ancestor walk. Bare `[[name]]`
-      // wikilinks still require the global_basename flag.
-      let matches: string[] = [];
-      const slugified = ref.slug.includes('/') ? slugifyPath(ref.slug) : '';
-      if (slugified.includes('/')) {
-        const tail = slugified.slice(slugified.lastIndexOf('/') + 1);
-        matches = (await resolver.resolveBasenameMatches(tail))
-          .filter(m => m === slugified || m.endsWith(`/${slugified}`));
-      } else if (opts.globalBasename) {
-        matches = await resolver.resolveBasenameMatches(ref.slug);
-      }
+      const matches = await resolver.resolveBasenameMatches(ref.slug);
       if (matches.length === 0) continue;
       const idx = content.indexOf(ref.slug);
       const context = idx >= 0 ? excerpt(content, idx, 240) : ref.name;

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;
       }
     }
   }

test/extract-fs.test.ts

@@ -389,33 +389,6 @@ describe('resolveSlugAll', () => {
   });
 });
 
-// ─── issue #1964: cross-directory wikilinks — slug/path mismatch ──────────
-
-describe('issue #1964: raw Obsidian wikilink paths resolve to sync-slugified slugs', () => {
-  test('resolveSlug slugifies the candidate (sync-consistent), no flag needed', () => {
-    const all = new Set(['llm-wiki/entities/ai-3.0']);
-    // Wikilink literal `[[llm-wiki/entities/AI 3.0]]` — spaces + uppercase.
-    expect(resolveSlug('llm-wiki/notes', 'llm-wiki/entities/AI 3.0.md', all))
-      .toBe('llm-wiki/entities/ai-3.0');
-  });
-
-  test('resolveSlug slugifies raw (unslugified) fileDir too', () => {
-    const all = new Set(['llm-wiki/entities/ai-3.0']);
-    // fileDir comes from dirname(relPath) — the raw on-disk directory.
-    expect(resolveSlug('LLM Wiki/Notes', 'entities/AI 3.0.md', all))
-      .toBe('llm-wiki/entities/ai-3.0');
-  });
-
-  test('extractLinksFromFile resolves cross-directory wikilink with flag OFF as a typed edge', async () => {
-    const allSlugs = new Set(['llm-wiki/entities/ai-3.0', 'llm-wiki/notes/roadmap']);
-    const content = '---\ntitle: Roadmap\ntype: concept\n---\n\nSee [[llm-wiki/entities/AI 3.0]].\n';
-    const links = await extractLinksFromFile(content, 'llm-wiki/notes/roadmap.md', allSlugs);
-    expect(links.map(l => l.to_slug)).toEqual(['llm-wiki/entities/ai-3.0']);
-    // Dir-qualified path resolution is exact, NOT the basename fallback.
-    expect(links[0].link_type).not.toBe('wikilink_basename');
-  });
-});
-
 describe('issue #972 repro: bare wikilinks resolve when flag is on', () => {
   // End-to-end: reproduces the issue's exact repro inside a tempdir +
   // PGLite, then asserts edge count under both flag states.

test/link-extraction.test.ts

@@ -9,8 +9,6 @@ import {
   parseTimelineEntries,
   isAutoLinkEnabled,
   FRONTMATTER_LINK_MAP,
-  buildBasenameIndex,
-  queryBasenameIndex,
   type SlugResolver,
 } from '../src/core/link-extraction.ts';
 import type { BrainEngine } from '../src/core/engine.ts';
@@ -426,46 +424,6 @@ describe('extractPageLinks', () => {
     expect(strk!.linkType).toBe('wikilink_basename');
   });
 
-  // ─── issue #1964: dir-qualified wikilinks with raw Obsidian paths ────────
-
-  test('#1964: dir-qualified wikilink resolves via sync-consistent slugification (flag OFF)', async () => {
-    // `[[llm-wiki/entities/AI 3.0]]` is a raw Obsidian path; the page slug
-    // is the sync-slugified `llm-wiki/entities/ai-3.0`. Must resolve WITHOUT
-    // global_basename (it's dir-qualified) and must NOT leak to a same-tail
-    // page in a different directory.
-    const resolver: SlugResolver = {
-      resolve: async () => null,
-      resolveBasenameMatches: async (name) =>
-        name === 'ai-3.0' ? ['other/ai-3.0', 'llm-wiki/entities/ai-3.0'] : [],
-    };
-    const { candidates } = await extractPageLinks(
-      'llm-wiki/notes/roadmap',
-      'See [[llm-wiki/entities/AI 3.0]] for the model.',
-      {}, 'concept', resolver,
-      // opts.globalBasename omitted (= false) — path is dir-qualified
-    );
-    expect(candidates.map(c => c.targetSlug)).toEqual(['llm-wiki/entities/ai-3.0']);
-    expect(candidates[0].linkType).toBe('wikilink_basename');
-    expect(candidates[0].linkSource).toBe('wikilink-resolved');
-  });
-
-  test('#1964: path-suffix match resolves wiki-root-relative paths against a real index', async () => {
-    // Author writes `[[llm-wiki/entities/AI 3.0]]` but the brain nests the
-    // wiki under a vault dir. Suffix match rescues it; queried through the
-    // REAL basename index so the tail-key lookup is exercised end to end.
-    const idx = buildBasenameIndex(['vault/llm-wiki/entities/ai-3.0', 'people/ai-3.0']);
-    const resolver: SlugResolver = {
-      resolve: async () => null,
-      resolveBasenameMatches: async (name) => queryBasenameIndex(idx, name),
-    };
-    const { candidates } = await extractPageLinks(
-      'vault/llm-wiki/notes/roadmap',
-      'See [[llm-wiki/entities/AI 3.0]].',
-      {}, 'concept', resolver,
-    );
-    expect(candidates.map(c => c.targetSlug)).toEqual(['vault/llm-wiki/entities/ai-3.0']);
-  });
-
   test('opts.skipFrontmatter suppresses the frontmatter pass', async () => {
     // Real resolver shape that WOULD resolve frontmatter source: too,
     // but skipFrontmatter blocks the path entirely.

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 () => {