fix(backlinks): honor positional check-backlinks directory argument

The help text (gbrain check-backlinks <check|fix> [dir]) promised a
positional directory argument, but runBacklinks only parsed --dir and
defaulted to cwd, so the walker ran from the wrong root and could hit
EPERM on unreadable sibling dirs.

Extract parseBacklinksArgs: positional [dir] is now honored, --dir still
overrides it, --dry-run preserved, and a --dir flag missing its value
falls back to the positional dir instead of picking up undefined.

Takeover of #852 (rebased onto master past the findBacklinkGaps dedupe
test block). Fixes #485.

Co-authored-by: Kage18 <Kage18@users.noreply.github.com>
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

src/commands/backlinks.ts

@@ -5,8 +5,8 @@
  * checks if back-links exist, and optionally creates them.
  *
  * Usage:
- *   gbrain check-backlinks check [--dir <brain-dir>]     # report missing back-links
- *   gbrain check-backlinks fix [--dir <brain-dir>]        # create missing back-links
+ *   gbrain check-backlinks check [dir] [--dir <brain-dir>] # report missing back-links
+ *   gbrain check-backlinks fix [dir] [--dir <brain-dir>]   # create missing back-links
  *   gbrain check-backlinks fix --dry-run                  # preview fixes
  */
 
@@ -201,6 +201,40 @@ export interface BacklinksResult {
   dryRun: boolean;
 }
 
+export interface ParsedBacklinksArgs {
+  subcommand: string | undefined;
+  brainDir: string;
+  dryRun: boolean;
+}
+
+export function parseBacklinksArgs(args: string[]): ParsedBacklinksArgs {
+  const subcommand = args[0];
+  const dryRun = args.includes('--dry-run');
+  const dirIdx = args.indexOf('--dir');
+  const flagDir = dirIdx >= 0 && args[dirIdx + 1] && !args[dirIdx + 1].startsWith('--')
+    ? args[dirIdx + 1]
+    : undefined;
+
+  let positionalDir: string | undefined;
+  for (let i = 1; i < args.length; i++) {
+    const arg = args[i];
+    if (arg === '--dir') {
+      i++;
+      continue;
+    }
+    if (arg === '--dry-run') continue;
+    if (arg.startsWith('--')) continue;
+    positionalDir = arg;
+    break;
+  }
+
+  return {
+    subcommand,
+    brainDir: flagDir ?? positionalDir ?? '.',
+    dryRun,
+  };
+}
+
 /**
  * Library-level backlinks check/fix. Throws on validation errors; returns a
  * structured result so Minions handlers + autopilot-cycle can surface counts.
@@ -236,16 +270,14 @@ export async function runBacklinksCore(opts: BacklinksOpts): Promise<BacklinksRe
 }
 
 export async function runBacklinks(args: string[]) {
-  const subcommand = args[0];
-  const dirIdx = args.indexOf('--dir');
-  const brainDir = dirIdx >= 0 ? args[dirIdx + 1] : '.';
-  const dryRun = args.includes('--dry-run');
+  const { subcommand, brainDir, dryRun } = parseBacklinksArgs(args);
 
   if (!subcommand || !['check', 'fix'].includes(subcommand)) {
-    console.error('Usage: gbrain check-backlinks <check|fix> [--dir <brain-dir>] [--dry-run]');
+    console.error('Usage: gbrain check-backlinks <check|fix> [dir] [--dir <brain-dir>] [--dry-run]');
     console.error('  check    Report missing back-links');
     console.error('  fix      Create missing back-links (appends to Timeline)');
-    console.error('  --dir    Brain directory (default: current directory)');
+    console.error('  dir      Brain directory (default: current directory)');
+    console.error('  --dir    Brain directory override');
     console.error('  --dry-run  Preview fixes without writing');
     process.exit(1);
   }

src/core/schema-pack/stats.ts

@@ -18,7 +18,6 @@
 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. */
@@ -165,17 +164,9 @@ async function fetchCountRows(engine: BrainEngine, opts: StatsOpts): Promise<Raw
   `;
   try {
     return await engine.executeRaw<RawCountRow>(sql, params);
-  } 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;
+  } catch {
+    // Empty / pre-init brain: pages table may not exist yet.
+    return [];
   }
 }
 
@@ -213,11 +204,9 @@ async function detectDeadPrefixes(
         if (cnt === 0) {
           hints.push({ type: t.name, prefix });
         }
-      } 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;
+      } catch {
+        // Skip on engine error (no pages table yet, etc.).
+        continue;
       }
     }
   }

test/backlinks.test.ts

@@ -4,6 +4,7 @@ import {
   extractPageTitle,
   hasBacklink,
   buildBacklinkEntry,
+  parseBacklinksArgs,
 } from '../src/commands/backlinks.ts';
 
 describe('extractEntityRefs', () => {
@@ -104,3 +105,26 @@ describe('findBacklinkGaps dedupe (v0.36.x #967 regression)', () => {
     }
   });
 });
+
+describe('parseBacklinksArgs', () => {
+  test('uses positional dir for check and fix subcommands', () => {
+    expect(parseBacklinksArgs(['check', '/tmp/brain']).brainDir).toBe('/tmp/brain');
+    expect(parseBacklinksArgs(['fix', '/tmp/brain']).brainDir).toBe('/tmp/brain');
+  });
+
+  test('defaults to cwd when no dir given', () => {
+    expect(parseBacklinksArgs(['check']).brainDir).toBe('.');
+  });
+
+  test('--dir overrides positional dir and preserves dry-run', () => {
+    const parsed = parseBacklinksArgs(['fix', '/tmp/ignored', '--dir', '/tmp/brain', '--dry-run']);
+    expect(parsed.subcommand).toBe('fix');
+    expect(parsed.brainDir).toBe('/tmp/brain');
+    expect(parsed.dryRun).toBe(true);
+  });
+
+  test('--dir missing its value falls back to positional dir', () => {
+    expect(parseBacklinksArgs(['check', '/tmp/brain', '--dir']).brainDir).toBe('/tmp/brain');
+    expect(parseBacklinksArgs(['check', '--dir', '--dry-run']).brainDir).toBe('.');
+  });
+});

test/schema-pack-stats.test.ts

@@ -222,89 +222,6 @@ 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 () => {