fix(embed): handle absolute file paths from native engine

The native engine stores absolute file paths in the DB. buildEmbeddings
unconditionally joined rootDir + file, doubling the path and causing
ENOENT for every symbol — producing 0 embeddings silently.

Check path.isAbsolute() before joining, and add a regression test that
inserts nodes with absolute paths to prevent recurrence.

Closes #760

Author: carlos-alm

src/domain/search/generator.ts

@@ -100,7 +100,7 @@ export async function buildEmbeddings(
   let overflowCount = 0;
 
   for (const [file, fileNodes] of byFile) {
-    const fullPath = path.join(rootDir, file);
+    const fullPath = path.isAbsolute(file) ? file : path.join(rootDir, file);
     let lines: string[];
     try {
       lines = fs.readFileSync(fullPath, 'utf-8').split('\n');

tests/search/embedding-strategy.test.ts

@@ -289,6 +289,47 @@ describe('FTS5 index built alongside embeddings', () => {
   });
 });
 
+describe('absolute file paths in DB (#760)', () => {
+  let absDir: string, absDbPath: string;
+
+  beforeAll(() => {
+    absDir = fs.mkdtempSync(path.join(os.tmpdir(), 'codegraph-abspath-test-'));
+    fs.writeFileSync(
+      path.join(absDir, 'math.js'),
+      'export function add(a, b) { return a + b; }\n',
+    );
+
+    const absDbDir = path.join(absDir, '.codegraph');
+    fs.mkdirSync(absDbDir, { recursive: true });
+    absDbPath = path.join(absDbDir, 'graph.db');
+
+    const db = new Database(absDbPath);
+    db.pragma('journal_mode = WAL');
+    initSchema(db);
+
+    // Insert node with an absolute file path (as the native engine does)
+    const absFile = path.join(absDir, 'math.js');
+    insertNode(db, 'add', 'function', absFile, 1, 1);
+    db.close();
+  });
+
+  afterAll(() => {
+    if (absDir) fs.rmSync(absDir, { recursive: true, force: true });
+  });
+
+  test('produces embeddings when DB stores absolute paths', async () => {
+    EMBEDDED_TEXTS.length = 0;
+    await buildEmbeddings(absDir, 'minilm', absDbPath);
+
+    expect(EMBEDDED_TEXTS.length).toBe(1);
+
+    const db = new Database(absDbPath, { readonly: true });
+    const count = db.prepare('SELECT COUNT(*) as c FROM embeddings').get().c;
+    db.close();
+    expect(count).toBe(1);
+  });
+});
+
 describe('context window overflow detection', () => {
   let bigDir: string, bigDbPath: string;