diff --git a/.github/workflows/sync-branches.lock.yml b/.github/workflows/sync-branches.lock.yml
index 7da366b..8541123 100644
--- a/.github/workflows/sync-branches.lock.yml
+++ b/.github/workflows/sync-branches.lock.yml
@@ -276,7 +276,7 @@ jobs:
           DEFAULT_BRANCH: ${{ github.event.repository.default_branch }}
           GITHUB_REPOSITORY: ${{ github.repository }}
         name: Merge default branch into all autoloop program branches
-        run: "python3 - << 'PYEOF'\nimport os, subprocess, sys\n\ntoken = os.environ.get(\"GITHUB_TOKEN\", \"\")\nrepo = os.environ.get(\"GITHUB_REPOSITORY\", \"\")\ndefault_branch = os.environ.get(\"DEFAULT_BRANCH\", \"main\")\n\n# List all remote branches matching the autoloop/* pattern\nresult = subprocess.run(\n    [\"git\", \"branch\", \"-r\", \"--list\", \"origin/autoloop/*\"],\n    capture_output=True, text=True\n)\nif result.returncode != 0:\n    print(f\"Failed to list remote branches: {result.stderr}\")\n    sys.exit(0)\n\nbranches = [b.strip().replace(\"origin/\", \"\") for b in result.stdout.strip().split(\"\\n\") if b.strip()]\n\nif not branches:\n    print(\"No autoloop/* branches found. Nothing to sync.\")\n    sys.exit(0)\n\nprint(f\"Found {len(branches)} autoloop branch(es) to sync: {branches}\")\n\nfailed = []\nfor branch in branches:\n    print(f\"\\n--- Syncing {branch} with {default_branch} ---\")\n\n    # Fetch both branches\n    subprocess.run([\"git\", \"fetch\", \"origin\", branch], capture_output=True)\n    subprocess.run([\"git\", \"fetch\", \"origin\", default_branch], capture_output=True)\n\n    # Check out the program branch\n    checkout = subprocess.run(\n        [\"git\", \"checkout\", branch],\n        capture_output=True, text=True\n    )\n    if checkout.returncode != 0:\n        # Try creating a local tracking branch\n        checkout = subprocess.run(\n            [\"git\", \"checkout\", \"-b\", branch, f\"origin/{branch}\"],\n            capture_output=True, text=True\n        )\n    if checkout.returncode != 0:\n        print(f\"  Failed to checkout {branch}: {checkout.stderr}\")\n        failed.append(branch)\n        continue\n\n    # Merge the default branch into the program branch\n    merge = subprocess.run(\n        [\"git\", \"merge\", f\"origin/{default_branch}\", \"--no-edit\",\n         \"-m\", f\"Merge {default_branch} into {branch}\"],\n        capture_output=True, text=True\n    )\n    if merge.returncode != 0:\n        print(f\"  Merge conflict or failure for {branch}: {merge.stderr}\")\n        # Abort the merge to leave a clean state\n        subprocess.run([\"git\", \"merge\", \"--abort\"], capture_output=True)\n        failed.append(branch)\n        continue\n\n    # Push the updated branch\n    push = subprocess.run(\n        [\"git\", \"push\", \"origin\", branch],\n        capture_output=True, text=True\n    )\n    if push.returncode != 0:\n        print(f\"  Failed to push {branch}: {push.stderr}\")\n        failed.append(branch)\n        continue\n\n    print(f\"  Successfully synced {branch}\")\n\n# Return to default branch\nsubprocess.run([\"git\", \"checkout\", default_branch], capture_output=True)\n\nif failed:\n    print(f\"\\n⚠️ Failed to sync {len(failed)} branch(es): {failed}\")\n    print(\"These branches may need manual conflict resolution.\")\n    # Don't fail the workflow — log the issue but continue\nelse:\n    print(f\"\\n✅ All {len(branches)} branch(es) synced successfully.\")\nPYEOF"
+        run: "python3 - << 'PYEOF'\nimport os, subprocess, sys\n\ntoken = os.environ.get(\"GITHUB_TOKEN\", \"\")\nrepo = os.environ.get(\"GITHUB_REPOSITORY\", \"\")\ndefault_branch = os.environ.get(\"DEFAULT_BRANCH\", \"main\")\n\n# Discover all remote branches matching the autoloop/* pattern.\n# Use ls-remote instead of 'git branch -r' so we don't depend on\n# pre-fetched remote-tracking refs (shallow checkouts won't have them).\nresult = subprocess.run(\n    [\"git\", \"ls-remote\", \"--heads\", \"origin\", \"autoloop/*\"],\n    capture_output=True, text=True\n)\nif result.returncode != 0:\n    print(f\"Failed to list remote branches: {result.stderr}\")\n    sys.exit(0)\n\nimport re as _re\nbranches = [_re.sub(r\"^.*refs/heads/\", \"\", b.strip()) for b in result.stdout.strip().split(\"\\n\") if b.strip()]\n\nif not branches:\n    print(\"No autoloop/* branches found. Nothing to sync.\")\n    sys.exit(0)\n\nprint(f\"Found {len(branches)} autoloop branch(es) to sync: {branches}\")\n\nfailed = []\nfor branch in branches:\n    print(f\"\\n--- Syncing {branch} with {default_branch} ---\")\n\n    # Fetch both branches\n    subprocess.run([\"git\", \"fetch\", \"origin\", branch], capture_output=True)\n    subprocess.run([\"git\", \"fetch\", \"origin\", default_branch], capture_output=True)\n\n    # Check out the program branch\n    checkout = subprocess.run(\n        [\"git\", \"checkout\", branch],\n        capture_output=True, text=True\n    )\n    if checkout.returncode != 0:\n        # Try creating a local tracking branch\n        checkout = subprocess.run(\n            [\"git\", \"checkout\", \"-b\", branch, f\"origin/{branch}\"],\n            capture_output=True, text=True\n        )\n    if checkout.returncode != 0:\n        print(f\"  Failed to checkout {branch}: {checkout.stderr}\")\n        failed.append(branch)\n        continue\n\n    # Merge the default branch into the program branch\n    merge = subprocess.run(\n        [\"git\", \"merge\", f\"origin/{default_branch}\", \"--no-edit\",\n         \"-m\", f\"Merge {default_branch} into {branch}\"],\n        capture_output=True, text=True\n    )\n    if merge.returncode != 0:\n        print(f\"  Merge conflict or failure for {branch}: {merge.stderr}\")\n        # Abort the merge to leave a clean state\n        subprocess.run([\"git\", \"merge\", \"--abort\"], capture_output=True)\n        failed.append(branch)\n        continue\n\n    # Push the updated branch\n    push = subprocess.run(\n        [\"git\", \"push\", \"origin\", branch],\n        capture_output=True, text=True\n    )\n    if push.returncode != 0:\n        print(f\"  Failed to push {branch}: {push.stderr}\")\n        failed.append(branch)\n        continue\n\n    print(f\"  Successfully synced {branch}\")\n\n# Return to default branch\nsubprocess.run([\"git\", \"checkout\", default_branch], capture_output=True)\n\nif failed:\n    print(f\"\\n⚠️ Failed to sync {len(failed)} branch(es): {failed}\")\n    print(\"These branches may need manual conflict resolution.\")\n    # Don't fail the workflow — log the issue but continue\nelse:\n    print(f\"\\n✅ All {len(branches)} branch(es) synced successfully.\")\nPYEOF"
 
       - name: Configure Git credentials
         env:
diff --git a/workflows/sync-branches.md b/workflows/sync-branches.md
index 5111d05..73bfa66 100644
--- a/workflows/sync-branches.md
+++ b/workflows/sync-branches.md
@@ -34,8 +34,10 @@ steps:
           return { returncode: result.status, stdout: result.stdout || '', stderr: result.stderr || '' };
       }
 
-      // List all remote branches matching the autoloop/* pattern
-      const listResult = git('branch', '-r', '--list', 'origin/autoloop/*');
+      // Discover all remote branches matching the autoloop/* pattern.
+      // Use ls-remote instead of 'git branch -r' so we don't depend on
+      // pre-fetched remote-tracking refs (shallow checkouts won't have them).
+      const listResult = git('ls-remote', '--heads', 'origin', 'autoloop/*');
       if (listResult.returncode !== 0) {
           console.log('Failed to list remote branches: ' + listResult.stderr);
           process.exit(0);
@@ -44,7 +46,7 @@ steps:
       const branches = listResult.stdout.trim().split('\n')
           .map(b => b.trim())
           .filter(b => b)
-          .map(b => b.replace('origin/', ''));
+          .map(b => b.replace(/^.*refs\/heads\//, ''));
 
       if (branches.length === 0) {
           console.log('No autoloop/* branches found. Nothing to sync.');