fix: mirror sync files before commit

app/git.js

@@ -65,19 +65,32 @@ export async function commitAndPush(workspace, repoDir, _spawnSync = spawnSync)
       run(['config', 'user.email', 'ai-review[bot]@gitea'], repoDir);
       run(['config', 'user.name', 'AI Review Bot'], repoDir);
 
-      // Always copy source files over the repo copy so skill files stay in sync.
+      const existingSyncPaths = [];
+      const missingSyncPaths = [];
+
+      // Mirror sync files from workspace into the repo copy.
       for (const relPath of SYNC_PATHS) {
         const src = path.join(workspace, relPath);
         const dest = path.join(repoDir, relPath);
-        if (!fs.existsSync(src)) continue;
+        if (fs.existsSync(src)) {
-        fs.mkdirSync(path.dirname(dest), { recursive: true });
+          fs.mkdirSync(path.dirname(dest), { recursive: true });
-        fs.copyFileSync(src, dest);
+          fs.copyFileSync(src, dest);
+          existingSyncPaths.push(relPath);
+          continue;
+        }
+
+        if (fs.existsSync(dest)) {
+          fs.rmSync(dest, { force: true });
+        }
+        missingSyncPaths.push(relPath);
       }
 
-      const existingSyncPaths = SYNC_PATHS.filter(relPath => fs.existsSync(path.join(repoDir, relPath)));
       if (existingSyncPaths.length > 0) {
         run(['add', ...existingSyncPaths], repoDir);
       }
+      if (missingSyncPaths.length > 0) {
+        run(['rm', '--cached', '--ignore-unmatch', '--', ...missingSyncPaths], repoDir);
+      }
 
       const status = run(['status', '--porcelain'], repoDir);
       if (!status) {

app/git.test.js

@@ -101,7 +101,7 @@ describe('commitAndPush', () => {
     assert.ok(!addCall.args.includes('README.md'));
   });
 
-  it('does not add missing sync paths', async () => {
+  it('removes missing sync paths from the repo copy', async () => {
     const missingPath = path.join(workspace, '.amazonq/rules/triage-findings.md');
     fs.rmSync(missingPath, { force: true });
     fs.rmSync(path.join(workspace, 'repo', '.amazonq/rules/triage-findings.md'), { force: true });
@@ -109,9 +109,10 @@ describe('commitAndPush', () => {
 
     await commitAndPush(workspace, path.join(workspace, 'repo'), spawn);
 
-    const addCall = spawn.calls.find(c => c.args[0] === 'add');
+    const rmCall = spawn.calls.find(c => c.args[0] === 'rm');
-    assert.ok(addCall, 'expected git add to run');
+    assert.ok(rmCall, 'expected git rm to run');
-    assert.ok(!addCall.args.includes('.amazonq/rules/triage-findings.md'));
+    assert.ok(rmCall.args.includes('.amazonq/rules/triage-findings.md'));
+    assert.equal(fs.existsSync(path.join(workspace, 'repo', '.amazonq/rules/triage-findings.md')), false);
   });
 
   it('overwrites existing repo copies with workspace files', async () => {