From c3d6305418a428a36d3585484f926e5d52bae976 Mon Sep 17 00:00:00 2001
From: carlos-alm <127798846+carlos-alm@users.noreply.github.com>
Date: Thu, 2 Apr 2026 22:01:20 -0600
Subject: [PATCH 1/2] fix(embed): handle absolute file paths from native engine
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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
---
 src/domain/search/generator.ts          |  2 +-
 tests/search/embedding-strategy.test.ts | 41 +++++++++++++++++++++++++
 2 files changed, 42 insertions(+), 1 deletion(-)

diff --git a/src/domain/search/generator.ts b/src/domain/search/generator.ts
index af87d5aa..69363367 100644
--- a/src/domain/search/generator.ts
+++ b/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');
diff --git a/tests/search/embedding-strategy.test.ts b/tests/search/embedding-strategy.test.ts
index a8e58828..62c5c0c2 100644
--- a/tests/search/embedding-strategy.test.ts
+++ b/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;
 

From 4a29207519ddfd89d4f0d17d6f2218416c21af48 Mon Sep 17 00:00:00 2001
From: carlos-alm <127798846+carlos-alm@users.noreply.github.com>
Date: Thu, 2 Apr 2026 22:01:36 -0600
Subject: [PATCH 2/2] style: fix biome formatting in test

---
 tests/search/embedding-strategy.test.ts | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/tests/search/embedding-strategy.test.ts b/tests/search/embedding-strategy.test.ts
index 62c5c0c2..58376569 100644
--- a/tests/search/embedding-strategy.test.ts
+++ b/tests/search/embedding-strategy.test.ts
@@ -294,10 +294,7 @@ describe('absolute file paths in DB (#760)', () => {
 
   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',
-    );
+    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 });