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/doctor-categories.ts

@@ -35,11 +35,10 @@
  *
  * The doctor renders both side by side.
  *
- * Drift contract: every check name that ships through doctor MUST appear in
+ * Drift contract: every check name that ships in doctor.ts MUST appear in
  * exactly one set below. The drift-guard test in
- * `test/doctor-categories.test.ts` enforces this by reading doctor check
- * emitter sources via a tagged-string scan and asserting set membership
- * exactly.
+ * `test/doctor-categories.test.ts` enforces this by reading doctor.ts source
+ * via a tagged-string scan and asserting set membership exactly.
  *
  * If you add a new doctor check, you MUST add its name to the appropriate
  * set here. The categorize step in `src/commands/doctor.ts` falls through
@@ -68,15 +67,12 @@ export const BRAIN_CHECK_NAMES: ReadonlySet<string> = new Set([
   'conversation_parser_probe_health',
   'cross_modal_modality_backfill',
   'cycle_freshness',
-  'dangling_aliases',
   'effective_date_health',
-  'embed_staleness',
   'embedding_column_registry',
   'embedding_env_override',
   'embedding_provider',
   'embedding_width_consistency',
   'embeddings',
-  'entity_link_coverage',
   'eval_drift',
   'extract_atoms_backlog',
   'extract_health',
@@ -106,9 +102,7 @@ export const BRAIN_CHECK_NAMES: ReadonlySet<string> = new Set([
   'stub_guard_24h',
   'sync_failures',
   'sync_freshness',
-  'takes_count',
   'takes_weight_grid',
-  'timeline_coverage',
   'unified_multimodal_coverage',
   'voice_gate_health',
 ]);
@@ -176,14 +170,12 @@ export const META_CHECK_NAMES: ReadonlySet<string> = new Set([
   'eval_capture',
   'minions_migration',
   'multi_source_drift',
-  'pack_upgrade_available',
   'schema_pack_active',
   'schema_pack_consistency',
   'schema_pack_source_drift',
   'schema_version',
   'slug_fallback_audit',
   'timeline_dedup_index',
-  'type_proliferation',
   'upgrade_errors',
 ]);
 

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/doctor-categories.test.ts

@@ -1,10 +1,10 @@
 /**
  * Drift guard for src/core/doctor-categories.ts.
  *
- * Reads doctor check emitter source via a literal-string scan, enumerates every
- * `name: '<...>'` Check name, and asserts each appears in exactly ONE category
- * set. The union of the four sets must equal the discovered names exactly —
- * no orphans, no extras.
+ * Reads src/commands/doctor.ts source via a literal-string scan, enumerates
+ * every `name: '<...>'` Check name, and asserts each appears in exactly ONE
+ * category set. The union of the four sets must equal the discovered names
+ * exactly — no orphans, no extras.
  *
  * This is the structural failure the v0.41.19.0 plan-eng-review caught:
  * doctor.ts grows new checks regularly; without this guard, the
@@ -25,30 +25,26 @@ import {
 } from '../src/core/doctor-categories.ts';
 
 const DOCTOR_TS_PATH = join(import.meta.dir, '..', 'src', 'commands', 'doctor.ts');
-const ONBOARD_CHECKS_TS_PATH = join(import.meta.dir, '..', 'src', 'core', 'onboard', 'checks.ts');
-const CHECK_SOURCE_PATHS = [DOCTOR_TS_PATH, ONBOARD_CHECKS_TS_PATH];
 
 function enumerateCheckNames(): Set<string> {
+  const source = readFileSync(DOCTOR_TS_PATH, 'utf-8');
   const names = new Set<string>();
-  for (const path of CHECK_SOURCE_PATHS) {
-    const source = readFileSync(path, 'utf-8');
-    // 1) Inline object-literal form: `{ name: 'foo', ... }`.
-    for (const m of source.matchAll(/name:\s*['"]([a-z][a-z0-9_]+)['"]/g)) {
-      names.add(m[1]);
-    }
-    // 2) Helper-function form: `const name = 'foo';` inside a check helper.
-    //    Catches checks like `nightly_quality_probe_health` and
-    //    `conversation_facts_backlog` that build the Check from a captured
-    //    name constant.
-    for (const m of source.matchAll(/const\s+name\s*=\s*['"]([a-z][a-z0-9_]+)['"]/g)) {
-      names.add(m[1]);
-    }
+  // 1) Inline object-literal form: `{ name: 'foo', ... }`.
+  for (const m of source.matchAll(/name:\s*['"]([a-z][a-z0-9_]+)['"]/g)) {
+    names.add(m[1]);
+  }
+  // 2) Helper-function form: `const name = 'foo';` inside a check helper.
+  //    Catches checks like `nightly_quality_probe_health` and
+  //    `conversation_facts_backlog` that build the Check from a captured
+  //    name constant.
+  for (const m of source.matchAll(/const\s+name\s*=\s*['"]([a-z][a-z0-9_]+)['"]/g)) {
+    names.add(m[1]);
   }
   return names;
 }
 
 describe('doctor-categories drift guard', () => {
-  test('every doctor-emitted check name belongs to exactly one category set', () => {
+  test('every check name in doctor.ts source belongs to exactly one category set', () => {
     const discovered = enumerateCheckNames();
     const allCategorized = new Set<string>([
       ...BRAIN_CHECK_NAMES,
@@ -63,7 +59,7 @@ describe('doctor-categories drift guard', () => {
     }
     if (missing.length > 0) {
       throw new Error(
-        `These check names appear in doctor check emitters but are not categorized in ` +
+        `These check names appear in doctor.ts but are not categorized in ` +
           `src/core/doctor-categories.ts: ${missing.sort().join(', ')}. ` +
           `Add each to BRAIN/SKILL/OPS/META_CHECK_NAMES.`,
       );
@@ -90,7 +86,7 @@ describe('doctor-categories drift guard', () => {
     expect(dupes).toEqual([]);
   });
 
-  test('every categorized name is currently used in doctor check emitters (no stale entries)', () => {
+  test('every categorized name is currently used in doctor.ts source (no stale entries)', () => {
     const discovered = enumerateCheckNames();
     const allCategorized = new Set<string>([
       ...BRAIN_CHECK_NAMES,
@@ -128,14 +124,6 @@ describe('categorizeCheck', () => {
     expect(categorizeCheck('sync_freshness')).toBe('brain');
   });
 
-  test('returns the right category for onboard data-quality check names', () => {
-    expect(categorizeCheck('embed_staleness')).toBe('brain');
-    expect(categorizeCheck('entity_link_coverage')).toBe('brain');
-    expect(categorizeCheck('timeline_coverage')).toBe('brain');
-    expect(categorizeCheck('takes_count')).toBe('brain');
-    expect(categorizeCheck('dangling_aliases')).toBe('brain');
-  });
-
   test('returns the right category for a known skill name', () => {
     expect(categorizeCheck('resolver_health')).toBe('skill');
     expect(categorizeCheck('skill_conformance')).toBe('skill');
@@ -152,24 +140,6 @@ describe('categorizeCheck', () => {
     expect(categorizeCheck('upgrade_errors')).toBe('meta');
   });
 
-  test('returns the right category for onboard schema-pack check names without warning', () => {
-    const originalWrite = process.stderr.write.bind(process.stderr);
-    const captured: string[] = [];
-    (process.stderr as { write: typeof process.stderr.write }).write = ((
-      chunk: string | Uint8Array,
-    ) => {
-      captured.push(typeof chunk === 'string' ? chunk : Buffer.from(chunk).toString());
-      return true;
-    }) as typeof process.stderr.write;
-    try {
-      expect(categorizeCheck('pack_upgrade_available')).toBe('meta');
-      expect(categorizeCheck('type_proliferation')).toBe('meta');
-      expect(captured.filter((c) => c.includes('[doctor-categories]'))).toEqual([]);
-    } finally {
-      (process.stderr as { write: typeof process.stderr.write }).write = originalWrite;
-    }
-  });
-
   test('unknown check name falls through to meta with a stderr warn (once per process)', () => {
     const originalWrite = process.stderr.write.bind(process.stderr);
     const captured: string[] = [];