fix(extract): resolve cross-directory wikilinks via sync-consistent slugification (#1964)

Raw Obsidian wikilink paths ([[llm-wiki/entities/AI 3.0]]) never matched
sync-slugified slugs (llm-wiki/entities/ai-3.0) on either extraction path.

- FS path: resolveSlug now slugifies each candidate (slugifyPath, the same
  function sync uses) when the raw path-equality check misses, in both the
  direct join and the ancestor walk. Dir-qualified wikilinks resolve as
  typed edges without the global_basename flag.
- DB path: extractPageLinks resolves dir-qualified generic wikilinks by
  slugifying the path and matching by exact slug or path suffix against
  the basename index — regardless of global_basename (the flag guards
  bare-name cross-dir ambiguity, which doesn't apply to dir-qualified
  paths). A same-tail page in a different directory can no longer be the
  only candidate and is filtered out.

Fixes #1964

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

src/commands/doctor.ts

@@ -1551,24 +1551,6 @@ 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/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, pruneDir, isSyncable } from '../core/sync.ts';
+import { pathToSlug, slugifyPath, 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
@@ -269,14 +269,24 @@ 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;
 
-  const s1 = join(fileDir, targetNoExt);
-  if (allSlugs.has(s1)) return s1;
+  // 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 parts = fileDir.split('/').filter(Boolean);
   for (let strip = 1; strip <= parts.length; strip++) {
     const ancestor = parts.slice(0, parts.length - strip).join('/');
-    const candidate = ancestor ? join(ancestor, targetNoExt) : targetNoExt;
-    if (allSlugs.has(candidate)) return candidate;
+    const candidate = hit(ancestor ? join(ancestor, targetNoExt) : targetNoExt);
+    if (candidate) return candidate;
   }
 
   return null;

src/core/ai/gateway.ts

@@ -3656,15 +3656,7 @@ 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'}`;
-  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;
-  }
+  const auth = applyResolveAuth(recipe, cfg, 'reranker');
   // 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/link-extraction.ts

@@ -14,6 +14,7 @@
 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
@@ -482,14 +483,29 @@ export async function extractPageLinks(
     // pre-v0.40.8.2 behavior of dropping bare wikilinks outside
     // DIR_PATTERN.
     if (ref.needsResolution) {
-      if (!opts.globalBasename || typeof resolver.resolveBasenameMatches !== 'function') {
-        continue;
-      }
+      if (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.
-      const matches = await resolver.resolveBasenameMatches(ref.slug);
+      //
+      // 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);
+      }
       if (matches.length === 0) continue;
       const idx = content.indexOf(ref.slug);
       const context = idx >= 0 ? excerpt(content, idx, 240) : ref.name;

test/ai/rerank.test.ts

@@ -154,28 +154,6 @@ 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

@@ -2,11 +2,6 @@ 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 () => {
@@ -52,34 +47,6 @@ 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/extract-fs.test.ts

@@ -389,6 +389,33 @@ 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

@@ -9,6 +9,8 @@ import {
   parseTimelineEntries,
   isAutoLinkEnabled,
   FRONTMATTER_LINK_MAP,
+  buildBasenameIndex,
+  queryBasenameIndex,
   type SlugResolver,
 } from '../src/core/link-extraction.ts';
 import type { BrainEngine } from '../src/core/engine.ts';
@@ -424,6 +426,46 @@ 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/search/rerank.test.ts

@@ -12,14 +12,9 @@
  */
 
 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 {
@@ -165,36 +160,6 @@ 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 = {