diff --git a/.github/workflows/e2e-topological-sort.yaml b/.github/workflows/e2e-topological-sort.yaml
index 9cc7d5174..7bfa74684 100644
--- a/.github/workflows/e2e-topological-sort.yaml
+++ b/.github/workflows/e2e-topological-sort.yaml
@@ -1,4 +1,4 @@
-name: E2E - Topological Sort
+name: E2E - Topological Sort (Worktree)
 
 on:
   pull_request:
@@ -8,7 +8,7 @@ on:
   workflow_dispatch:
 
 jobs:
-  topological-sort-optimization:
+  topological-sort-worktree-optimization:
     # Dynamically determine if environment is needed only when workflow files change and contributor is external
     environment: ${{ (github.event_name == 'workflow_dispatch' || (contains(toJSON(github.event.pull_request.files.*.filename), '.github/workflows/') && github.event.pull_request.user.login != 'misrasaurabh1' && github.event.pull_request.user.login != 'KRRT7')) && 'external-trusted-contributors' || '' }}
     runs-on: ubuntu-latest
@@ -90,4 +90,4 @@ jobs:
       - name: Run Codeflash to optimize code
         id: optimize_code
         run: |
-          uv run python tests/scripts/end_to_end_test_topological_sort.py
+          uv run python tests/scripts/end_to_end_test_topological_sort_worktree.py
diff --git a/codeflash/code_utils/git_worktree_utils.py b/codeflash/code_utils/git_worktree_utils.py
index c41637c8d..5ab160c5e 100644
--- a/codeflash/code_utils/git_worktree_utils.py
+++ b/codeflash/code_utils/git_worktree_utils.py
@@ -34,6 +34,12 @@ def get_git_project_id() -> str:
 
 def create_worktree_snapshot_commit(worktree_dir: Path, commit_message: str) -> None:
     repository = git.Repo(worktree_dir, search_parent_directories=True)
+    with repository.config_writer() as cw:
+        if not cw.has_option("user", "name"):
+            cw.set_value("user", "name", "Codeflash Bot")
+        if not cw.has_option("user", "email"):
+            cw.set_value("user", "email", "bot@codeflash.ai")
+
     repository.git.add(".")
     repository.git.commit("-m", commit_message, "--no-verify")
 
diff --git a/tests/scripts/end_to_end_test_topological_sort.py b/tests/scripts/end_to_end_test_topological_sort.py
deleted file mode 100644
index a5ba2c58c..000000000
--- a/tests/scripts/end_to_end_test_topological_sort.py
+++ /dev/null
@@ -1,29 +0,0 @@
-import os
-import pathlib
-
-from codeflash.code_utils.code_utils import add_addopts_to_pyproject
-from end_to_end_test_utilities import CoverageExpectation, TestConfig, run_codeflash_command, run_with_retries
-
-
-def run_test(expected_improvement_pct: int) -> bool:
-    with add_addopts_to_pyproject():
-        config = TestConfig(
-            file_path="topological_sort.py",
-            function_name="Graph.topologicalSort",
-            test_framework="pytest",
-            min_improvement_x=0.05,
-            coverage_expectations=[
-                CoverageExpectation(
-                    function_name="Graph.topologicalSort",
-                    expected_coverage=100.0,
-                    expected_lines=[25, 26, 27, 28, 29, 30, 31],
-                )
-            ],
-        )
-        cwd = (pathlib.Path(__file__).parent.parent.parent / "code_to_optimize").resolve()
-        return_var = run_codeflash_command(cwd, config, expected_improvement_pct)
-    return return_var
-
-
-if __name__ == "__main__":
-    exit(run_with_retries(run_test, int(os.getenv("EXPECTED_IMPROVEMENT_PCT", 5))))
diff --git a/tests/scripts/end_to_end_test_topological_sort_worktree.py b/tests/scripts/end_to_end_test_topological_sort_worktree.py
new file mode 100644
index 000000000..7d5a3fec5
--- /dev/null
+++ b/tests/scripts/end_to_end_test_topological_sort_worktree.py
@@ -0,0 +1,28 @@
+import os
+import pathlib
+
+from end_to_end_test_utilities import CoverageExpectation, TestConfig, run_codeflash_command, run_with_retries
+
+
+def run_test(expected_improvement_pct: int) -> bool:
+    config = TestConfig(
+        file_path="topological_sort.py",
+        function_name="Graph.topologicalSort",
+        test_framework="pytest",
+        min_improvement_x=0.05,
+        use_worktree=True,
+        coverage_expectations=[
+            CoverageExpectation(
+                function_name="Graph.topologicalSort",
+                expected_coverage=100.0,
+                expected_lines=[25, 26, 27, 28, 29, 30, 31],
+            )
+        ],
+    )
+    cwd = (pathlib.Path(__file__).parent.parent.parent / "code_to_optimize").resolve()
+    return_var = run_codeflash_command(cwd, config, expected_improvement_pct)
+    return return_var
+
+
+if __name__ == "__main__":
+    exit(run_with_retries(run_test, int(os.getenv("EXPECTED_IMPROVEMENT_PCT", 5))))
diff --git a/tests/scripts/end_to_end_test_utilities.py b/tests/scripts/end_to_end_test_utilities.py
index e4c634450..afd74823d 100644
--- a/tests/scripts/end_to_end_test_utilities.py
+++ b/tests/scripts/end_to_end_test_utilities.py
@@ -28,6 +28,7 @@ class TestConfig:
     coverage_expectations: list[CoverageExpectation] = field(default_factory=list)
     benchmarks_root: Optional[pathlib.Path] = None
     enable_async: bool = False
+    use_worktree: bool = False
 
 
 def clear_directory(directory_path: str | pathlib.Path) -> None:
@@ -137,6 +138,8 @@ def build_command(
         base_command.extend(["--benchmark", "--benchmarks-root", str(benchmarks_root)])
     if config.enable_async:
         base_command.append("--async")
+    if config.use_worktree:
+        base_command.append("--worktree")
     return base_command