From c595a7a5480caefc9497b02ab3eec48587b38601 Mon Sep 17 00:00:00 2001
From: mohammed <mohammed18200118@gmail.com>
Date: Sun, 10 Aug 2025 06:18:44 +0300
Subject: [PATCH 01/18] getting worktree to work in both lsp and normal cli
 mode

---
 codeflash/cli_cmds/cli.py                    |  1 +
 codeflash/code_utils/coverage_utils.py       | 12 ++-
 codeflash/code_utils/git_utils.py            | 75 ++++++++++++++++++-
 codeflash/lsp/beta.py                        |  6 ++
 codeflash/lsp/server.py                      |  4 +-
 codeflash/optimization/function_optimizer.py | 26 +++++--
 codeflash/optimization/optimizer.py          | 79 +++++++++++++++++++-
 codeflash/telemetry/sentry.py                |  2 +-
 tests/test_code_utils.py                     |  5 +-
 9 files changed, 191 insertions(+), 19 deletions(-)

diff --git a/codeflash/cli_cmds/cli.py b/codeflash/cli_cmds/cli.py
index 34e5ad223..5aa331f36 100644
--- a/codeflash/cli_cmds/cli.py
+++ b/codeflash/cli_cmds/cli.py
@@ -94,6 +94,7 @@ def parse_args() -> Namespace:
         help="Path to the directory of the project, where all the pytest-benchmark tests are located.",
     )
     parser.add_argument("--no-draft", default=False, action="store_true", help="Skip optimization for draft PRs")
+    parser.add_argument("--worktree", default=False, action="store_true", help="Use worktree for optimization")
 
     args, unknown_args = parser.parse_known_args()
     sys.argv[:] = [sys.argv[0], *unknown_args]
diff --git a/codeflash/code_utils/coverage_utils.py b/codeflash/code_utils/coverage_utils.py
index 21aa06ad9..966910630 100644
--- a/codeflash/code_utils/coverage_utils.py
+++ b/codeflash/code_utils/coverage_utils.py
@@ -39,16 +39,20 @@ def build_fully_qualified_name(function_name: str, code_context: CodeOptimizatio
     return full_name
 
 
-def generate_candidates(source_code_path: Path) -> list[str]:
+def generate_candidates(source_code_path: Path) -> set[str]:
     """Generate all the possible candidates for coverage data based on the source code path."""
-    candidates = [source_code_path.name]
+    candidates = set()
+    candidates.add(source_code_path.name)
     current_path = source_code_path.parent
 
+    last_added = source_code_path.name
     while current_path != current_path.parent:
-        candidate_path = str(Path(current_path.name) / candidates[-1])
-        candidates.append(candidate_path)
+        candidate_path = str(Path(current_path.name) / last_added)
+        candidates.add(candidate_path)
+        last_added = candidate_path
         current_path = current_path.parent
 
+    candidates.add(str(source_code_path))
     return candidates
 
 
diff --git a/codeflash/code_utils/git_utils.py b/codeflash/code_utils/git_utils.py
index 00f9f5e28..3374ef32c 100644
--- a/codeflash/code_utils/git_utils.py
+++ b/codeflash/code_utils/git_utils.py
@@ -9,13 +9,14 @@
 from functools import cache
 from io import StringIO
 from pathlib import Path
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, Optional
 
 import git
 from rich.prompt import Confirm
 from unidiff import PatchSet
 
 from codeflash.cli_cmds.console import logger
+from codeflash.code_utils.compat import codeflash_cache_dir
 from codeflash.code_utils.config_consts import N_CANDIDATES
 
 if TYPE_CHECKING:
@@ -192,3 +193,75 @@ def get_last_commit_author_if_pr_exists(repo: Repo | None = None) -> str | None:
         return None
     else:
         return last_commit.author.name
+
+
+worktree_dirs = codeflash_cache_dir / "worktrees"
+patches_dir = codeflash_cache_dir / "patches"
+
+
+def create_worktree_snapshot_commit(worktree_dir: Path, commit_message: str) -> None:
+    repository = git.Repo(worktree_dir, search_parent_directories=True)
+    repository.git.commit("-am", commit_message, "--no-verify")
+
+
+def create_detached_worktree(module_root: Path) -> Optional[Path]:
+    if not check_running_in_git_repo(module_root):
+        logger.warning("Module is not in a git repository. Skipping worktree creation.")
+        return None
+    git_root = git_root_dir()
+    current_time_str = time.strftime("%Y%m%d-%H%M%S")
+    worktree_dir = worktree_dirs / f"{git_root.name}-{current_time_str}"
+
+    result = subprocess.run(["git", "worktree", "add", "-d", str(worktree_dir)], cwd=git_root, check=True)
+    if result.returncode != 0:
+        logger.error(f"Failed to create worktree: {result.stderr}")
+        return None
+
+    print(result.stdout)
+
+    # Get uncommitted diff from the original repo
+    repository = git.Repo(module_root, search_parent_directories=True)
+    uni_diff_text = repository.git.diff(None, "HEAD", ignore_blank_lines=True, ignore_space_at_eol=True)
+
+    if not uni_diff_text.strip():
+        logger.info("No uncommitted changes to copy to worktree.")
+        return worktree_dir
+
+    # Write the diff to a temporary file
+    with tempfile.NamedTemporaryFile(mode="w+", suffix=".codeflash.patch", delete=False) as tmp_patch_file:
+        tmp_patch_file.write(uni_diff_text + "\n")  # the new line here is a must otherwise the last hunk won't be valid
+        tmp_patch_file.flush()
+
+        patch_path = Path(tmp_patch_file.name).resolve()
+
+        # Apply the patch inside the worktree
+        try:
+            subprocess.run(["git", "apply", patch_path], cwd=worktree_dir, check=True)
+            create_worktree_snapshot_commit(worktree_dir, "Initial Snapshot")
+        except subprocess.CalledProcessError as e:
+            logger.error(f"Failed to apply patch to worktree: {e}")
+
+        return worktree_dir
+
+
+def remove_worktree(worktree_dir: Path) -> None:
+    try:
+        repository = git.Repo(worktree_dir, search_parent_directories=True)
+        repository.git.worktree("remove", "--force", worktree_dir)
+    except Exception:
+        logger.exception(f"Failed to remove worktree: {worktree_dir}")
+
+
+def create_diff_from_worktree(worktree_dir: Path, files: list[str], fto_name: str) -> Path:
+    repository = git.Repo(worktree_dir, search_parent_directories=True)
+    uni_diff_text = repository.git.diff(None, "HEAD", *files, ignore_blank_lines=True, ignore_space_at_eol=True)
+    uni_diff_text = uni_diff_text.strip()
+    if not uni_diff_text:
+        logger.warning("No changes found in worktree.")
+        return None
+    # write to patches_dir
+    patches_dir.mkdir(parents=True, exist_ok=True)
+    patch_path = patches_dir / f"{worktree_dir.name}.{fto_name}.patch"
+    with patch_path.open("w", encoding="utf8") as f:
+        f.write(uni_diff_text + "\n")
+    return patch_path
diff --git a/codeflash/lsp/beta.py b/codeflash/lsp/beta.py
index 4ed0b7a62..b99185be7 100644
--- a/codeflash/lsp/beta.py
+++ b/codeflash/lsp/beta.py
@@ -100,6 +100,7 @@ def initialize_function_optimization(
         f"Args set - function: {server.optimizer.args.function}, file: {server.optimizer.args.file}", "Info"
     )
 
+    server.optimizer.worktree_mode()
     optimizable_funcs, _, _ = server.optimizer.get_optimizable_functions()
     if not optimizable_funcs:
         server.show_message_log(f"No optimizable functions found for {params.functionName}", "Warning")
@@ -334,9 +335,13 @@ def perform_function_optimization(  # noqa: PLR0911
     speedup = original_code_baseline.runtime / best_optimization.runtime
 
     server.show_message_log(f"Optimization completed for {params.functionName} with {speedup:.2f}x speedup", "Info")
+    diff_patch_files = server.optimizer.patch_files
 
     # CRITICAL: Clear the function filter after optimization to prevent state corruption
     server.optimizer.args.function = None
+    server.optimizer.patch_files = []
+    server.optimizer.current_worktree = None
+    server.optimizer.cleanup_temporary_paths()
     server.show_message_log("Cleared function filter to prevent state corruption", "Info")
 
     return {
@@ -345,4 +350,5 @@ def perform_function_optimization(  # noqa: PLR0911
         "message": "Optimization completed successfully",
         "extra": f"Speedup: {speedup:.2f}x faster",
         "optimization": optimized_source,
+        "diff_patch_files": diff_patch_files,
     }
diff --git a/codeflash/lsp/server.py b/codeflash/lsp/server.py
index 030574a8d..753487f9e 100644
--- a/codeflash/lsp/server.py
+++ b/codeflash/lsp/server.py
@@ -11,6 +11,8 @@
 if TYPE_CHECKING:
     from lsprotocol.types import InitializeParams, InitializeResult
 
+    from codeflash.optimization.optimizer import Optimizer
+
 
 class CodeflashLanguageServerProtocol(LanguageServerProtocol):
     _server: CodeflashLanguageServer
@@ -44,7 +46,7 @@ def _find_pyproject_toml(self, workspace_path: str) -> Path | None:
 class CodeflashLanguageServer(LanguageServer):
     def __init__(self, *args: Any, **kwargs: Any) -> None:  # noqa: ANN401
         super().__init__(*args, **kwargs)
-        self.optimizer = None
+        self.optimizer: Optimizer | None = None
         self.args = None
 
     def prepare_optimizer_arguments(self, config_file: Path) -> None:
diff --git a/codeflash/optimization/function_optimizer.py b/codeflash/optimization/function_optimizer.py
index d009c3b9c..18f356d08 100644
--- a/codeflash/optimization/function_optimizer.py
+++ b/codeflash/optimization/function_optimizer.py
@@ -1239,7 +1239,9 @@ def process_review(
             "coverage_message": coverage_message,
         }
 
-        if not self.args.no_pr and not self.args.staging_review:
+        raise_pr = not self.args.no_pr
+
+        if raise_pr and not self.args.staging_review:
             data["git_remote"] = self.args.git_remote
             check_create_pr(**data)
         elif self.args.staging_review:
@@ -1250,12 +1252,24 @@ def process_review(
                 trace_id=self.function_trace_id, is_optimization_found=best_optimization is not None
             )
 
-        if ((not self.args.no_pr) or not self.args.staging_review) and (
-            self.args.all or env_utils.get_pr_number() or (self.args.file and not self.args.function)
+        if raise_pr and (
+            self.args.all
+            or env_utils.get_pr_number()
+            or self.args.replay_test
+            or (self.args.file and not self.args.function)
         ):
-            self.write_code_and_helpers(
-                self.function_to_optimize_source_code, original_helper_code, self.function_to_optimize.file_path
-            )
+            self.revert_code_and_helpers(original_helper_code)
+            return
+
+        if self.args.staging_review:
+            # always revert code and helpers when staging review
+            self.revert_code_and_helpers(original_helper_code)
+            return
+
+    def revert_code_and_helpers(self, original_helper_code: dict[Path, str]) -> None:
+        self.write_code_and_helpers(
+            self.function_to_optimize_source_code, original_helper_code, self.function_to_optimize.file_path
+        )
 
     def establish_original_code_baseline(
         self,
diff --git a/codeflash/optimization/optimizer.py b/codeflash/optimization/optimizer.py
index 83073d6d9..b7a81611f 100644
--- a/codeflash/optimization/optimizer.py
+++ b/codeflash/optimization/optimizer.py
@@ -14,6 +14,13 @@
 from codeflash.code_utils import env_utils
 from codeflash.code_utils.code_utils import cleanup_paths, get_run_tmp_file
 from codeflash.code_utils.env_utils import get_pr_number, is_pr_draft
+from codeflash.code_utils.git_utils import (
+    check_running_in_git_repo,
+    create_detached_worktree,
+    create_diff_from_worktree,
+    create_worktree_snapshot_commit,
+    remove_worktree,
+)
 from codeflash.either import is_successful
 from codeflash.models.models import ValidCode
 from codeflash.telemetry.posthog_cf import ph
@@ -48,6 +55,8 @@ def __init__(self, args: Namespace) -> None:
         self.functions_checkpoint: CodeflashRunCheckpoint | None = None
         self.current_function_being_optimized: FunctionToOptimize | None = None  # current only for the LSP
         self.current_function_optimizer: FunctionOptimizer | None = None
+        self.current_worktree: Path | None = None
+        self.patch_files: list[Path] = []
 
     def run_benchmarks(
         self, file_to_funcs_to_optimize: dict[Path, list[FunctionToOptimize]], num_optimizable_functions: int
@@ -252,6 +261,10 @@ def run(self) -> None:
         if self.args.no_draft and is_pr_draft():
             logger.warning("PR is in draft mode, skipping optimization")
             return
+
+        if self.args.worktree:
+            self.worktree_mode()
+
         cleanup_paths(Optimizer.find_leftover_instrumented_test_files(self.test_cfg.tests_root))
 
         function_optimizer = None
@@ -260,7 +273,6 @@ def run(self) -> None:
             file_to_funcs_to_optimize, num_optimizable_functions
         )
         optimizations_found: int = 0
-        function_iterator_count: int = 0
         if self.args.test_framework == "pytest":
             self.test_cfg.concolic_test_root_dir = Path(
                 tempfile.mkdtemp(dir=self.args.tests_root, prefix="codeflash_concolic_")
@@ -296,8 +308,8 @@ def run(self) -> None:
                     except Exception as e:
                         logger.debug(f"Could not rank functions in {original_module_path}: {e}")
 
-                for function_to_optimize in functions_to_optimize:
-                    function_iterator_count += 1
+                for i, function_to_optimize in enumerate(functions_to_optimize):
+                    function_iterator_count = i + 1
                     logger.info(
                         f"Optimizing function {function_iterator_count} of {num_optimizable_functions}: "
                         f"{function_to_optimize.qualified_name}"
@@ -327,6 +339,22 @@ def run(self) -> None:
                             )
                         if is_successful(best_optimization):
                             optimizations_found += 1
+                            if self.current_worktree:
+                                read_writable_code = best_optimization.unwrap().code_context.read_writable_code
+                                relative_file_paths = [
+                                    code_string.file_path for code_string in read_writable_code.code_strings
+                                ]
+                                patch_path = create_diff_from_worktree(
+                                    self.current_worktree,
+                                    relative_file_paths,
+                                    self.current_function_optimizer.function_to_optimize.qualified_name,
+                                )
+                                self.patch_files.append(patch_path)
+                                if i < len(functions_to_optimize) - 1:
+                                    create_worktree_snapshot_commit(
+                                        self.current_worktree,
+                                        f"Optimizing {functions_to_optimize[i + 1].qualified_name}",
+                                    )
                         else:
                             logger.warning(best_optimization.failure())
                             console.rule()
@@ -337,6 +365,10 @@ def run(self) -> None:
                             function_optimizer.cleanup_generated_files()
 
             ph("cli-optimize-run-finished", {"optimizations_found": optimizations_found})
+            if len(self.patch_files) > 0:
+                logger.info(
+                    f"Created {len(self.patch_files)} patch(es) ({[str(patch_path) for patch_path in self.patch_files]})"
+                )
             if self.functions_checkpoint:
                 self.functions_checkpoint.cleanup()
             if hasattr(self.args, "command") and self.args.command == "optimize":
@@ -388,7 +420,46 @@ def cleanup_temporary_paths(self) -> None:
         if hasattr(get_run_tmp_file, "tmpdir"):
             get_run_tmp_file.tmpdir.cleanup()
             del get_run_tmp_file.tmpdir
-        cleanup_paths([self.test_cfg.concolic_test_root_dir, self.replay_tests_dir])
+        paths_to_clean = [self.test_cfg.concolic_test_root_dir, self.replay_tests_dir]
+        if self.current_worktree:
+            remove_worktree(self.current_worktree)
+        cleanup_paths(paths_to_clean)
+
+    def worktree_mode(self) -> None:
+        if self.current_worktree:
+            return
+        project_root = self.args.project_root
+        module_root = self.args.module_root
+
+        if check_running_in_git_repo(module_root):
+            relative_module_root = module_root.relative_to(project_root)
+            relative_optimized_file = self.args.file.relative_to(project_root) if self.args.file else None
+            relative_tests_root = self.test_cfg.tests_root.relative_to(project_root)
+            relative_benchmarks_root = (
+                self.args.benchmarks_root.relative_to(project_root) if self.args.benchmarks_root else None
+            )
+
+            worktree_dir = create_detached_worktree(module_root)
+            if worktree_dir is None:
+                logger.warning("Failed to create worktree. Skipping optimization.")
+                return
+            self.current_worktree = worktree_dir
+            # TODO: use a helper function to mutate self.args and self.test_cfg
+            self.args.module_root = worktree_dir / relative_module_root
+            self.args.project_root = worktree_dir
+            self.args.test_project_root = worktree_dir
+            self.args.tests_root = worktree_dir / relative_tests_root
+            if relative_benchmarks_root:
+                self.args.benchmarks_root = worktree_dir / relative_benchmarks_root
+
+            self.test_cfg.project_root_path = worktree_dir
+            self.test_cfg.tests_project_rootdir = worktree_dir
+            self.test_cfg.tests_root = worktree_dir / relative_tests_root
+            if relative_benchmarks_root:
+                self.test_cfg.benchmark_tests_root = worktree_dir / relative_benchmarks_root
+
+            if relative_optimized_file is not None:
+                self.args.file = worktree_dir / relative_optimized_file
 
 
 def run_with_args(args: Namespace) -> None:
diff --git a/codeflash/telemetry/sentry.py b/codeflash/telemetry/sentry.py
index b7ff00094..97bfb2db1 100644
--- a/codeflash/telemetry/sentry.py
+++ b/codeflash/telemetry/sentry.py
@@ -14,7 +14,7 @@ def init_sentry(enabled: bool = False, exclude_errors: bool = False) -> None:  #
         )
 
         sentry_sdk.init(
-            dsn="https://4b9a1902f9361b48c04376df6483bc96@o4506833230561280.ingest.sentry.io/4506833262477312",
+            dsn="",
             integrations=[sentry_logging],
             # Set traces_sample_rate to 1.0 to capture 100%
             # of transactions for performance monitoring.
diff --git a/tests/test_code_utils.py b/tests/test_code_utils.py
index a10f50a56..0ab78d2ef 100644
--- a/tests/test_code_utils.py
+++ b/tests/test_code_utils.py
@@ -357,7 +357,7 @@ def test_cleanup_paths(multiple_existing_and_non_existing_files: list[Path]) ->
 
 def test_generate_candidates() -> None:
     source_code_path = Path("/Users/krrt7/Desktop/work/codeflash/cli/codeflash/code_utils/coverage_utils.py")
-    expected_candidates = [
+    expected_candidates = {
         "coverage_utils.py",
         "code_utils/coverage_utils.py",
         "codeflash/code_utils/coverage_utils.py",
@@ -367,7 +367,8 @@ def test_generate_candidates() -> None:
         "Desktop/work/codeflash/cli/codeflash/code_utils/coverage_utils.py",
         "krrt7/Desktop/work/codeflash/cli/codeflash/code_utils/coverage_utils.py",
         "Users/krrt7/Desktop/work/codeflash/cli/codeflash/code_utils/coverage_utils.py",
-    ]
+        "/Users/krrt7/Desktop/work/codeflash/cli/codeflash/code_utils/coverage_utils.py"
+    }
     assert generate_candidates(source_code_path) == expected_candidates
 
 

From b955ad8787b78f43ec622398d672110240a6eb02 Mon Sep 17 00:00:00 2001
From: mohammed <mohammed18200118@gmail.com>
Date: Mon, 11 Aug 2025 15:25:49 +0300
Subject: [PATCH 02/18] worktrees changes

---
 codeflash/code_utils/git_utils.py            | 12 ++++++++----
 codeflash/lsp/beta.py                        | 15 +++++++++++----
 codeflash/lsp/server.py                      |  1 +
 codeflash/optimization/function_optimizer.py |  4 ++++
 codeflash/optimization/optimizer.py          | 11 ++++++-----
 5 files changed, 30 insertions(+), 13 deletions(-)

diff --git a/codeflash/code_utils/git_utils.py b/codeflash/code_utils/git_utils.py
index 3374ef32c..4f043edf4 100644
--- a/codeflash/code_utils/git_utils.py
+++ b/codeflash/code_utils/git_utils.py
@@ -15,7 +15,7 @@
 from rich.prompt import Confirm
 from unidiff import PatchSet
 
-from codeflash.cli_cmds.console import logger
+from codeflash.cli_cmds.console import console, logger
 from codeflash.code_utils.compat import codeflash_cache_dir
 from codeflash.code_utils.config_consts import N_CANDIDATES
 
@@ -212,13 +212,17 @@ def create_detached_worktree(module_root: Path) -> Optional[Path]:
     current_time_str = time.strftime("%Y%m%d-%H%M%S")
     worktree_dir = worktree_dirs / f"{git_root.name}-{current_time_str}"
 
-    result = subprocess.run(["git", "worktree", "add", "-d", str(worktree_dir)], cwd=git_root, check=True)
+    result = subprocess.run(
+        ["git", "worktree", "add", "-d", str(worktree_dir)],
+        cwd=git_root,
+        check=True,
+        stdout=subprocess.DEVNULL if console.quiet else None,
+        stderr=subprocess.DEVNULL if console.quiet else None,
+    )
     if result.returncode != 0:
         logger.error(f"Failed to create worktree: {result.stderr}")
         return None
 
-    print(result.stdout)
-
     # Get uncommitted diff from the original repo
     repository = git.Repo(module_root, search_parent_directories=True)
     uni_diff_text = repository.git.diff(None, "HEAD", ignore_blank_lines=True, ignore_space_at_eol=True)
diff --git a/codeflash/lsp/beta.py b/codeflash/lsp/beta.py
index b99185be7..c374e9ecb 100644
--- a/codeflash/lsp/beta.py
+++ b/codeflash/lsp/beta.py
@@ -9,6 +9,7 @@
 from pygls import uris
 
 from codeflash.api.cfapi import get_codeflash_api_key, get_user_id
+from codeflash.code_utils.git_utils import create_diff_from_worktree
 from codeflash.code_utils.shell_utils import save_api_key_to_rc
 from codeflash.either import is_successful
 from codeflash.lsp.server import CodeflashLanguageServer, CodeflashLanguageServerProtocol
@@ -331,17 +332,23 @@ def perform_function_optimization(  # noqa: PLR0911
             "message": f"No best optimizations found for function {function_to_optimize_qualified_name}",
         }
 
+    # generate a patch for the optimization
+    relative_file_paths = [code_string.file_path for code_string in code_context.read_writable_code.code_strings]
+    patch_path = create_diff_from_worktree(
+        server.optimizer.current_worktree,
+        relative_file_paths,
+        server.optimizer.current_function_optimizer.function_to_optimize.qualified_name,
+    )
+
     optimized_source = best_optimization.candidate.source_code.markdown
     speedup = original_code_baseline.runtime / best_optimization.runtime
 
     server.show_message_log(f"Optimization completed for {params.functionName} with {speedup:.2f}x speedup", "Info")
-    diff_patch_files = server.optimizer.patch_files
 
     # CRITICAL: Clear the function filter after optimization to prevent state corruption
+    server.optimizer.cleanup_temporary_paths()
     server.optimizer.args.function = None
-    server.optimizer.patch_files = []
     server.optimizer.current_worktree = None
-    server.optimizer.cleanup_temporary_paths()
     server.show_message_log("Cleared function filter to prevent state corruption", "Info")
 
     return {
@@ -350,5 +357,5 @@ def perform_function_optimization(  # noqa: PLR0911
         "message": "Optimization completed successfully",
         "extra": f"Speedup: {speedup:.2f}x faster",
         "optimization": optimized_source,
-        "diff_patch_files": diff_patch_files,
+        "patch_path": patch_path,
     }
diff --git a/codeflash/lsp/server.py b/codeflash/lsp/server.py
index 753487f9e..5d2f84992 100644
--- a/codeflash/lsp/server.py
+++ b/codeflash/lsp/server.py
@@ -55,6 +55,7 @@ def prepare_optimizer_arguments(self, config_file: Path) -> None:
         args = parse_args()
         args.config_file = config_file
         args.no_pr = True  # LSP server should not create PRs
+        args.worktree = True
         args = process_pyproject_config(args)
         self.args = args
         # avoid initializing the optimizer during initialization, because it can cause an error if the api key is invalid
diff --git a/codeflash/optimization/function_optimizer.py b/codeflash/optimization/function_optimizer.py
index 18f356d08..c9d479782 100644
--- a/codeflash/optimization/function_optimizer.py
+++ b/codeflash/optimization/function_optimizer.py
@@ -1252,6 +1252,10 @@ def process_review(
                 trace_id=self.function_trace_id, is_optimization_found=best_optimization is not None
             )
 
+        # If worktree mode, do not revert code and helpers, we create snapshot commit after each function optimization
+        if self.args.worktree:
+            return
+
         if raise_pr and (
             self.args.all
             or env_utils.get_pr_number()
diff --git a/codeflash/optimization/optimizer.py b/codeflash/optimization/optimizer.py
index b7a81611f..33db70e2e 100644
--- a/codeflash/optimization/optimizer.py
+++ b/codeflash/optimization/optimizer.py
@@ -414,16 +414,17 @@ def cleanup_replay_tests(self) -> None:
             cleanup_paths([self.replay_tests_dir])
 
     def cleanup_temporary_paths(self) -> None:
-        if self.current_function_optimizer:
-            self.current_function_optimizer.cleanup_generated_files()
-
         if hasattr(get_run_tmp_file, "tmpdir"):
             get_run_tmp_file.tmpdir.cleanup()
             del get_run_tmp_file.tmpdir
-        paths_to_clean = [self.test_cfg.concolic_test_root_dir, self.replay_tests_dir]
+
         if self.current_worktree:
             remove_worktree(self.current_worktree)
-        cleanup_paths(paths_to_clean)
+            return
+
+        if self.current_function_optimizer:
+            self.current_function_optimizer.cleanup_generated_files()
+        cleanup_paths([self.test_cfg.concolic_test_root_dir, self.replay_tests_dir])
 
     def worktree_mode(self) -> None:
         if self.current_worktree:

From 4e3f9ecacd74c2bcefcbd196359144da5a6a1d37 Mon Sep 17 00:00:00 2001
From: mohammed <mohammed18200118@gmail.com>
Date: Mon, 11 Aug 2025 15:27:53 +0300
Subject: [PATCH 03/18] revert sentry

---
 codeflash/telemetry/sentry.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/codeflash/telemetry/sentry.py b/codeflash/telemetry/sentry.py
index 97bfb2db1..b7ff00094 100644
--- a/codeflash/telemetry/sentry.py
+++ b/codeflash/telemetry/sentry.py
@@ -14,7 +14,7 @@ def init_sentry(enabled: bool = False, exclude_errors: bool = False) -> None:  #
         )
 
         sentry_sdk.init(
-            dsn="",
+            dsn="https://4b9a1902f9361b48c04376df6483bc96@o4506833230561280.ingest.sentry.io/4506833262477312",
             integrations=[sentry_logging],
             # Set traces_sample_rate to 1.0 to capture 100%
             # of transactions for performance monitoring.

From 50df6d7d032134e581affe65604ee9c391f1a6e6 Mon Sep 17 00:00:00 2001
From: mohammed <mohammed18200118@gmail.com>
Date: Mon, 11 Aug 2025 17:25:21 +0300
Subject: [PATCH 04/18] patch new line

---
 codeflash/code_utils/git_utils.py | 8 ++++++--
 codeflash/lsp/server.py           | 3 ++-
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/codeflash/code_utils/git_utils.py b/codeflash/code_utils/git_utils.py
index 4f043edf4..e3f4bb474 100644
--- a/codeflash/code_utils/git_utils.py
+++ b/codeflash/code_utils/git_utils.py
@@ -259,13 +259,17 @@ def remove_worktree(worktree_dir: Path) -> None:
 def create_diff_from_worktree(worktree_dir: Path, files: list[str], fto_name: str) -> Path:
     repository = git.Repo(worktree_dir, search_parent_directories=True)
     uni_diff_text = repository.git.diff(None, "HEAD", *files, ignore_blank_lines=True, ignore_space_at_eol=True)
-    uni_diff_text = uni_diff_text.strip()
+
     if not uni_diff_text:
         logger.warning("No changes found in worktree.")
         return None
+
+    if not uni_diff_text.endswith("\n"):
+        uni_diff_text += "\n"
+
     # write to patches_dir
     patches_dir.mkdir(parents=True, exist_ok=True)
     patch_path = patches_dir / f"{worktree_dir.name}.{fto_name}.patch"
     with patch_path.open("w", encoding="utf8") as f:
-        f.write(uni_diff_text + "\n")
+        f.write(uni_diff_text)
     return patch_path
diff --git a/codeflash/lsp/server.py b/codeflash/lsp/server.py
index 5d2f84992..8b7bbd320 100644
--- a/codeflash/lsp/server.py
+++ b/codeflash/lsp/server.py
@@ -56,6 +56,7 @@ def prepare_optimizer_arguments(self, config_file: Path) -> None:
         args.config_file = config_file
         args.no_pr = True  # LSP server should not create PRs
         args.worktree = True
+        args.verbose = True
         args = process_pyproject_config(args)
         self.args = args
         # avoid initializing the optimizer during initialization, because it can cause an error if the api key is invalid
@@ -77,7 +78,7 @@ def show_message_log(self, message: str, message_type: str) -> None:
             "Debug": MessageType.Debug,
         }
 
-        lsp_message_type = type_mapping.get(message_type, MessageType.Info)
+        lsp_message_type = type_mapping.get(message_type, MessageType.Debug)
 
         # Send log message to client (appears in output channel)
         log_params = LogMessageParams(type=lsp_message_type, message=message)

From e32e93f1812e7349d0c58c75a6b73679a589c806 Mon Sep 17 00:00:00 2001
From: mohammed <mohammed18200118@gmail.com>
Date: Tue, 12 Aug 2025 12:26:19 +0300
Subject: [PATCH 05/18] fixes

---
 codeflash/lsp/beta.py               | 274 +++++++++++++---------------
 codeflash/optimization/optimizer.py |  63 ++++---
 2 files changed, 166 insertions(+), 171 deletions(-)

diff --git a/codeflash/lsp/beta.py b/codeflash/lsp/beta.py
index c374e9ecb..885ffdb9a 100644
--- a/codeflash/lsp/beta.py
+++ b/codeflash/lsp/beta.py
@@ -46,44 +46,27 @@ def get_optimizable_functions(
     file_path = Path(uris.to_fs_path(params.textDocument.uri))
     server.show_message_log(f"Getting optimizable functions for: {file_path}", "Info")
 
-    # Save original args to restore later
-    original_file = getattr(server.optimizer.args, "file", None)
-    original_function = getattr(server.optimizer.args, "function", None)
-    original_checkpoint = getattr(server.optimizer.args, "previous_checkpoint_functions", None)
+    server.optimizer.worktree_mode()
 
-    server.show_message_log(f"Original args - file: {original_file}, function: {original_function}", "Info")
+    args = server.optimizer.args
 
-    try:
-        # Set temporary args for this request only
-        server.optimizer.args.file = file_path
-        server.optimizer.args.function = None  # Always get ALL functions, not just one
-        server.optimizer.args.previous_checkpoint_functions = False
+    original_relative_file_path = file_path.relative_to(args.base_project_root)
 
-        server.show_message_log("Calling get_optimizable_functions...", "Info")
-        optimizable_funcs, _, _ = server.optimizer.get_optimizable_functions()
+    server.optimizer.args.file = server.optimizer.current_worktree / original_relative_file_path
+    server.optimizer.args.function = None  # Always get ALL functions, not just one
+    server.optimizer.args.previous_checkpoint_functions = False
 
-        path_to_qualified_names = {}
-        for path, functions in optimizable_funcs.items():
-            path_to_qualified_names[path.as_posix()] = [func.qualified_name for func in functions]
+    server.show_message_log(f"Calling get_optimizable_functions for {server.optimizer.args.file}...", "Info")
+    optimizable_funcs, _, _ = server.optimizer.get_optimizable_functions()
 
-        server.show_message_log(
-            f"Found {len(path_to_qualified_names)} files with functions: {path_to_qualified_names}", "Info"
-        )
-        return path_to_qualified_names
-    finally:
-        # Restore original args to prevent state corruption
-        if original_file is not None:
-            server.optimizer.args.file = original_file
-        if original_function is not None:
-            server.optimizer.args.function = original_function
-        else:
-            server.optimizer.args.function = None
-        if original_checkpoint is not None:
-            server.optimizer.args.previous_checkpoint_functions = original_checkpoint
-
-        server.show_message_log(
-            f"Restored args - file: {server.optimizer.args.file}, function: {server.optimizer.args.function}", "Info"
-        )
+    path_to_qualified_names = {}
+    for functions in optimizable_funcs.values():
+        path_to_qualified_names[file_path] = [func.qualified_name for func in functions]
+
+    server.show_message_log(
+        f"Found {len(path_to_qualified_names)} files with functions: {path_to_qualified_names}", "Info"
+    )
+    return path_to_qualified_names
 
 
 @server.feature("initializeFunctionOptimization")
@@ -92,16 +75,16 @@ def initialize_function_optimization(
 ) -> dict[str, str]:
     file_path = Path(uris.to_fs_path(params.textDocument.uri))
     server.show_message_log(f"Initializing optimization for function: {params.functionName} in {file_path}", "Info")
+    server.optimizer.worktree_mode()
 
-    # IMPORTANT: Store the specific function for optimization, but don't corrupt global state
     server.optimizer.args.function = params.functionName
-    server.optimizer.args.file = file_path
+    original_relative_file_path = file_path.relative_to(server.optimizer.args.base_project_root)
+    server.optimizer.args.file = server.optimizer.current_worktree / original_relative_file_path
 
     server.show_message_log(
         f"Args set - function: {server.optimizer.args.function}, file: {server.optimizer.args.file}", "Info"
     )
 
-    server.optimizer.worktree_mode()
     optimizable_funcs, _, _ = server.optimizer.get_optimizable_functions()
     if not optimizable_funcs:
         server.show_message_log(f"No optimizable functions found for {params.functionName}", "Warning")
@@ -239,123 +222,126 @@ def generate_tests(server: CodeflashLanguageServer, params: FunctionOptimization
 def perform_function_optimization(  # noqa: PLR0911
     server: CodeflashLanguageServer, params: FunctionOptimizationParams
 ) -> dict[str, str]:
-    server.show_message_log(f"Starting optimization for function: {params.functionName}", "Info")
-    current_function = server.optimizer.current_function_being_optimized
-
-    if not current_function:
-        server.show_message_log(f"No current function being optimized for {params.functionName}", "Error")
-        return {
-            "functionName": params.functionName,
-            "status": "error",
-            "message": "No function currently being optimized",
-        }
+    try:
+        server.show_message_log(f"Starting optimization for function: {params.functionName}", "Info")
+        current_function = server.optimizer.current_function_being_optimized
+
+        if not current_function:
+            server.show_message_log(f"No current function being optimized for {params.functionName}", "Error")
+            return {
+                "functionName": params.functionName,
+                "status": "error",
+                "message": "No function currently being optimized",
+            }
+
+        module_prep_result = server.optimizer.prepare_module_for_optimization(current_function.file_path)
+
+        validated_original_code, original_module_ast = module_prep_result
+
+        function_optimizer = server.optimizer.create_function_optimizer(
+            current_function,
+            function_to_optimize_source_code=validated_original_code[current_function.file_path].source_code,
+            original_module_ast=original_module_ast,
+            original_module_path=current_function.file_path,
+            function_to_tests=server.optimizer.discovered_tests or {},
+        )
 
-    module_prep_result = server.optimizer.prepare_module_for_optimization(current_function.file_path)
+        server.optimizer.current_function_optimizer = function_optimizer
+        if not function_optimizer:
+            return {"functionName": params.functionName, "status": "error", "message": "No function optimizer found"}
 
-    validated_original_code, original_module_ast = module_prep_result
+        initialization_result = function_optimizer.can_be_optimized()
+        if not is_successful(initialization_result):
+            return {"functionName": params.functionName, "status": "error", "message": initialization_result.failure()}
 
-    function_optimizer = server.optimizer.create_function_optimizer(
-        current_function,
-        function_to_optimize_source_code=validated_original_code[current_function.file_path].source_code,
-        original_module_ast=original_module_ast,
-        original_module_path=current_function.file_path,
-        function_to_tests=server.optimizer.discovered_tests or {},
-    )
+        should_run_experiment, code_context, original_helper_code = initialization_result.unwrap()
 
-    server.optimizer.current_function_optimizer = function_optimizer
-    if not function_optimizer:
-        return {"functionName": params.functionName, "status": "error", "message": "No function optimizer found"}
+        test_setup_result = function_optimizer.generate_and_instrument_tests(
+            code_context, should_run_experiment=should_run_experiment
+        )
+        if not is_successful(test_setup_result):
+            return {"functionName": params.functionName, "status": "error", "message": test_setup_result.failure()}
+        (
+            generated_tests,
+            function_to_concolic_tests,
+            concolic_test_str,
+            optimizations_set,
+            generated_test_paths,
+            generated_perf_test_paths,
+            instrumented_unittests_created_for_function,
+            original_conftest_content,
+        ) = test_setup_result.unwrap()
+
+        baseline_setup_result = function_optimizer.setup_and_establish_baseline(
+            code_context=code_context,
+            original_helper_code=original_helper_code,
+            function_to_concolic_tests=function_to_concolic_tests,
+            generated_test_paths=generated_test_paths,
+            generated_perf_test_paths=generated_perf_test_paths,
+            instrumented_unittests_created_for_function=instrumented_unittests_created_for_function,
+            original_conftest_content=original_conftest_content,
+        )
 
-    initialization_result = function_optimizer.can_be_optimized()
-    if not is_successful(initialization_result):
-        return {"functionName": params.functionName, "status": "error", "message": initialization_result.failure()}
+        if not is_successful(baseline_setup_result):
+            return {"functionName": params.functionName, "status": "error", "message": baseline_setup_result.failure()}
+
+        (
+            function_to_optimize_qualified_name,
+            function_to_all_tests,
+            original_code_baseline,
+            test_functions_to_remove,
+            file_path_to_helper_classes,
+        ) = baseline_setup_result.unwrap()
+
+        best_optimization = function_optimizer.find_and_process_best_optimization(
+            optimizations_set=optimizations_set,
+            code_context=code_context,
+            original_code_baseline=original_code_baseline,
+            original_helper_code=original_helper_code,
+            file_path_to_helper_classes=file_path_to_helper_classes,
+            function_to_optimize_qualified_name=function_to_optimize_qualified_name,
+            function_to_all_tests=function_to_all_tests,
+            generated_tests=generated_tests,
+            test_functions_to_remove=test_functions_to_remove,
+            concolic_test_str=concolic_test_str,
+        )
 
-    should_run_experiment, code_context, original_helper_code = initialization_result.unwrap()
+        if not best_optimization:
+            server.show_message_log(
+                f"No best optimizations found for function {function_to_optimize_qualified_name}", "Warning"
+            )
+            return {
+                "functionName": params.functionName,
+                "status": "error",
+                "message": f"No best optimizations found for function {function_to_optimize_qualified_name}",
+            }
+
+        # generate a patch for the optimization
+        relative_file_paths = [code_string.file_path for code_string in code_context.read_writable_code.code_strings]
+        patch_path = create_diff_from_worktree(
+            server.optimizer.current_worktree,
+            relative_file_paths,
+            server.optimizer.current_function_optimizer.function_to_optimize.qualified_name,
+        )
 
-    test_setup_result = function_optimizer.generate_and_instrument_tests(
-        code_context, should_run_experiment=should_run_experiment
-    )
-    if not is_successful(test_setup_result):
-        return {"functionName": params.functionName, "status": "error", "message": test_setup_result.failure()}
-    (
-        generated_tests,
-        function_to_concolic_tests,
-        concolic_test_str,
-        optimizations_set,
-        generated_test_paths,
-        generated_perf_test_paths,
-        instrumented_unittests_created_for_function,
-        original_conftest_content,
-    ) = test_setup_result.unwrap()
-
-    baseline_setup_result = function_optimizer.setup_and_establish_baseline(
-        code_context=code_context,
-        original_helper_code=original_helper_code,
-        function_to_concolic_tests=function_to_concolic_tests,
-        generated_test_paths=generated_test_paths,
-        generated_perf_test_paths=generated_perf_test_paths,
-        instrumented_unittests_created_for_function=instrumented_unittests_created_for_function,
-        original_conftest_content=original_conftest_content,
-    )
+        optimized_source = best_optimization.candidate.source_code.markdown
+        speedup = original_code_baseline.runtime / best_optimization.runtime
 
-    if not is_successful(baseline_setup_result):
-        return {"functionName": params.functionName, "status": "error", "message": baseline_setup_result.failure()}
-
-    (
-        function_to_optimize_qualified_name,
-        function_to_all_tests,
-        original_code_baseline,
-        test_functions_to_remove,
-        file_path_to_helper_classes,
-    ) = baseline_setup_result.unwrap()
-
-    best_optimization = function_optimizer.find_and_process_best_optimization(
-        optimizations_set=optimizations_set,
-        code_context=code_context,
-        original_code_baseline=original_code_baseline,
-        original_helper_code=original_helper_code,
-        file_path_to_helper_classes=file_path_to_helper_classes,
-        function_to_optimize_qualified_name=function_to_optimize_qualified_name,
-        function_to_all_tests=function_to_all_tests,
-        generated_tests=generated_tests,
-        test_functions_to_remove=test_functions_to_remove,
-        concolic_test_str=concolic_test_str,
-    )
+        server.show_message_log(f"Optimization completed for {params.functionName} with {speedup:.2f}x speedup", "Info")
 
-    if not best_optimization:
-        server.show_message_log(
-            f"No best optimizations found for function {function_to_optimize_qualified_name}", "Warning"
-        )
         return {
             "functionName": params.functionName,
-            "status": "error",
-            "message": f"No best optimizations found for function {function_to_optimize_qualified_name}",
+            "status": "success",
+            "message": "Optimization completed successfully",
+            "extra": f"Speedup: {speedup:.2f}x faster",
+            "optimization": optimized_source,
+            "patch_path": patch_path,
         }
-
-    # generate a patch for the optimization
-    relative_file_paths = [code_string.file_path for code_string in code_context.read_writable_code.code_strings]
-    patch_path = create_diff_from_worktree(
-        server.optimizer.current_worktree,
-        relative_file_paths,
-        server.optimizer.current_function_optimizer.function_to_optimize.qualified_name,
-    )
-
-    optimized_source = best_optimization.candidate.source_code.markdown
-    speedup = original_code_baseline.runtime / best_optimization.runtime
-
-    server.show_message_log(f"Optimization completed for {params.functionName} with {speedup:.2f}x speedup", "Info")
-
-    # CRITICAL: Clear the function filter after optimization to prevent state corruption
-    server.optimizer.cleanup_temporary_paths()
-    server.optimizer.args.function = None
-    server.optimizer.current_worktree = None
-    server.show_message_log("Cleared function filter to prevent state corruption", "Info")
-
-    return {
-        "functionName": params.functionName,
-        "status": "success",
-        "message": "Optimization completed successfully",
-        "extra": f"Speedup: {speedup:.2f}x faster",
-        "optimization": optimized_source,
-        "patch_path": patch_path,
-    }
+    finally:
+        server.optimizer.cleanup_temporary_paths()
+        # restore args and test cfg
+        if server.optimizer.original_args_and_test_cfg:
+            server.optimizer.args, server.optimizer.test_cfg = server.optimizer.original_args_and_test_cfg
+        server.optimizer.args.function = None
+        server.optimizer.current_worktree = None
+        server.optimizer.current_function_optimizer = None
diff --git a/codeflash/optimization/optimizer.py b/codeflash/optimization/optimizer.py
index 33db70e2e..86776c7fd 100644
--- a/codeflash/optimization/optimizer.py
+++ b/codeflash/optimization/optimizer.py
@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import ast
+import copy
 import os
 import tempfile
 import time
@@ -56,6 +57,7 @@ def __init__(self, args: Namespace) -> None:
         self.current_function_being_optimized: FunctionToOptimize | None = None  # current only for the LSP
         self.current_function_optimizer: FunctionOptimizer | None = None
         self.current_worktree: Path | None = None
+        self.original_args_and_test_cfg: tuple[Namespace, TestConfig] | None = None
         self.patch_files: list[Path] = []
 
     def run_benchmarks(
@@ -429,38 +431,45 @@ def cleanup_temporary_paths(self) -> None:
     def worktree_mode(self) -> None:
         if self.current_worktree:
             return
-        project_root = self.args.project_root
-        module_root = self.args.module_root
 
-        if check_running_in_git_repo(module_root):
-            relative_module_root = module_root.relative_to(project_root)
-            relative_optimized_file = self.args.file.relative_to(project_root) if self.args.file else None
-            relative_tests_root = self.test_cfg.tests_root.relative_to(project_root)
-            relative_benchmarks_root = (
-                self.args.benchmarks_root.relative_to(project_root) if self.args.benchmarks_root else None
-            )
-
-            worktree_dir = create_detached_worktree(module_root)
+        if check_running_in_git_repo(self.args.module_root):
+            worktree_dir = create_detached_worktree(self.args.module_root)
             if worktree_dir is None:
                 logger.warning("Failed to create worktree. Skipping optimization.")
                 return
             self.current_worktree = worktree_dir
-            # TODO: use a helper function to mutate self.args and self.test_cfg
-            self.args.module_root = worktree_dir / relative_module_root
-            self.args.project_root = worktree_dir
-            self.args.test_project_root = worktree_dir
-            self.args.tests_root = worktree_dir / relative_tests_root
-            if relative_benchmarks_root:
-                self.args.benchmarks_root = worktree_dir / relative_benchmarks_root
-
-            self.test_cfg.project_root_path = worktree_dir
-            self.test_cfg.tests_project_rootdir = worktree_dir
-            self.test_cfg.tests_root = worktree_dir / relative_tests_root
-            if relative_benchmarks_root:
-                self.test_cfg.benchmark_tests_root = worktree_dir / relative_benchmarks_root
-
-            if relative_optimized_file is not None:
-                self.args.file = worktree_dir / relative_optimized_file
+            self.mutate_args_for_worktree_mode(worktree_dir)
+
+    def mutate_args_for_worktree_mode(self, worktree_dir: Path) -> None:
+        saved_args = copy.deepcopy(self.args)
+        saved_test_cfg = copy.deepcopy(self.test_cfg)
+        self.original_args_and_test_cfg = (saved_args, saved_test_cfg)
+
+        project_root = self.args.project_root
+        self.args.base_project_root = project_root  # keep a reference to the original project root
+        module_root = self.args.module_root
+        relative_module_root = module_root.relative_to(project_root)
+        relative_optimized_file = self.args.file.relative_to(project_root) if self.args.file else None
+        relative_tests_root = self.test_cfg.tests_root.relative_to(project_root)
+        relative_benchmarks_root = (
+            self.args.benchmarks_root.relative_to(project_root) if self.args.benchmarks_root else None
+        )
+
+        self.args.module_root = worktree_dir / relative_module_root
+        self.args.project_root = worktree_dir
+        self.args.test_project_root = worktree_dir
+        self.args.tests_root = worktree_dir / relative_tests_root
+        if relative_benchmarks_root:
+            self.args.benchmarks_root = worktree_dir / relative_benchmarks_root
+
+        self.test_cfg.project_root_path = worktree_dir
+        self.test_cfg.tests_project_rootdir = worktree_dir
+        self.test_cfg.tests_root = worktree_dir / relative_tests_root
+        if relative_benchmarks_root:
+            self.test_cfg.benchmark_tests_root = worktree_dir / relative_benchmarks_root
+
+        if relative_optimized_file is not None:
+            self.args.file = worktree_dir / relative_optimized_file
 
 
 def run_with_args(args: Namespace) -> None:

From ff78ce3ed1763fd0616e346a3057ba4739addeb7 Mon Sep 17 00:00:00 2001
From: mohammed <mohammed18200118@gmail.com>
Date: Tue, 12 Aug 2025 17:37:09 +0300
Subject: [PATCH 06/18] fixes

---
 codeflash/api/cfapi.py                     |  9 ++++--
 codeflash/code_utils/env_utils.py          | 19 ++++++-------
 codeflash/code_utils/formatter.py          |  4 +--
 codeflash/code_utils/git_utils.py          |  8 ++++--
 codeflash/lsp/beta.py                      | 32 ++++++++++++----------
 codeflash/lsp/helpers.py                   |  8 ++++++
 codeflash/optimization/optimizer.py        |  1 -
 codeflash/verification/concolic_testing.py |  2 +-
 8 files changed, 48 insertions(+), 35 deletions(-)
 create mode 100644 codeflash/lsp/helpers.py

diff --git a/codeflash/api/cfapi.py b/codeflash/api/cfapi.py
index 7008d13f5..22871298e 100644
--- a/codeflash/api/cfapi.py
+++ b/codeflash/api/cfapi.py
@@ -13,7 +13,12 @@
 from pydantic.json import pydantic_encoder
 
 from codeflash.cli_cmds.console import console, logger
-from codeflash.code_utils.env_utils import ensure_codeflash_api_key, get_codeflash_api_key, get_pr_number
+from codeflash.code_utils.env_utils import (
+    ensure_codeflash_api_key,
+    get_codeflash_api_key,
+    get_pr_number,
+    is_LSP_enabled,
+)
 from codeflash.code_utils.git_utils import get_current_branch, get_repo_owner_and_name, git_root_dir
 from codeflash.github.PrComment import FileDiffContent, PrComment
 from codeflash.version import __version__
@@ -101,7 +106,7 @@ def get_user_id() -> Optional[str]:
             if min_version and version.parse(min_version) > version.parse(__version__):
                 msg = "Your Codeflash CLI version is outdated. Please update to the latest version using `pip install --upgrade codeflash`."
                 console.print(f"[bold red]{msg}[/bold red]")
-                if console.quiet:  # lsp
+                if is_LSP_enabled():
                     logger.debug(msg)
                     return f"Error: {msg}"
                 sys.exit(1)
diff --git a/codeflash/code_utils/env_utils.py b/codeflash/code_utils/env_utils.py
index ab0cb16e6..eca59bfa8 100644
--- a/codeflash/code_utils/env_utils.py
+++ b/codeflash/code_utils/env_utils.py
@@ -7,10 +7,11 @@
 from pathlib import Path
 from typing import Any, Optional
 
-from codeflash.cli_cmds.console import console, logger
+from codeflash.cli_cmds.console import logger
 from codeflash.code_utils.code_utils import exit_with_message
 from codeflash.code_utils.formatter import format_code
 from codeflash.code_utils.shell_utils import read_api_key_from_shell_config
+from codeflash.lsp.helpers import is_LSP_enabled
 
 
 def check_formatter_installed(formatter_cmds: list[str], exit_on_failure: bool = True) -> bool:  # noqa
@@ -34,11 +35,12 @@ def check_formatter_installed(formatter_cmds: list[str], exit_on_failure: bool =
 
 @lru_cache(maxsize=1)
 def get_codeflash_api_key() -> str:
-    if console.quiet:  # lsp
-        # prefer shell config over env var in lsp mode
-        api_key = read_api_key_from_shell_config()
-    else:
-        api_key = os.environ.get("CODEFLASH_API_KEY") or read_api_key_from_shell_config()
+    # prefer shell config over env var in lsp mode
+    api_key = (
+        read_api_key_from_shell_config()
+        if is_LSP_enabled()
+        else os.environ.get("CODEFLASH_API_KEY") or read_api_key_from_shell_config()
+    )
 
     api_secret_docs_message = "For more information, refer to the documentation at [https://docs.codeflash.ai/getting-started/codeflash-github-actions#add-your-api-key-to-your-repository-secrets]."  # noqa
     if not api_key:
@@ -125,11 +127,6 @@ def is_ci() -> bool:
     return bool(os.environ.get("CI") or os.environ.get("GITHUB_ACTIONS"))
 
 
-@lru_cache(maxsize=1)
-def is_LSP_enabled() -> bool:
-    return console.quiet
-
-
 def is_pr_draft() -> bool:
     """Check if the PR is draft. in the github action context."""
     event = get_cached_gh_event_data()
diff --git a/codeflash/code_utils/formatter.py b/codeflash/code_utils/formatter.py
index db7fa4257..0cbbce85c 100644
--- a/codeflash/code_utils/formatter.py
+++ b/codeflash/code_utils/formatter.py
@@ -13,6 +13,7 @@
 import isort
 
 from codeflash.cli_cmds.console import console, logger
+from codeflash.lsp.helpers import is_LSP_enabled
 
 
 def generate_unified_diff(original: str, modified: str, from_file: str, to_file: str) -> str:
@@ -109,8 +110,7 @@ def format_code(
     print_status: bool = True,  # noqa
     exit_on_failure: bool = True,  # noqa
 ) -> str:
-    if console.quiet:
-        # lsp mode
+    if is_LSP_enabled():
         exit_on_failure = False
     with tempfile.TemporaryDirectory() as test_dir_str:
         if isinstance(path, str):
diff --git a/codeflash/code_utils/git_utils.py b/codeflash/code_utils/git_utils.py
index e3f4bb474..e8b6541c3 100644
--- a/codeflash/code_utils/git_utils.py
+++ b/codeflash/code_utils/git_utils.py
@@ -15,9 +15,10 @@
 from rich.prompt import Confirm
 from unidiff import PatchSet
 
-from codeflash.cli_cmds.console import console, logger
+from codeflash.cli_cmds.console import logger
 from codeflash.code_utils.compat import codeflash_cache_dir
 from codeflash.code_utils.config_consts import N_CANDIDATES
+from codeflash.lsp.helpers import is_LSP_enabled
 
 if TYPE_CHECKING:
     from git import Repo
@@ -216,8 +217,8 @@ def create_detached_worktree(module_root: Path) -> Optional[Path]:
         ["git", "worktree", "add", "-d", str(worktree_dir)],
         cwd=git_root,
         check=True,
-        stdout=subprocess.DEVNULL if console.quiet else None,
-        stderr=subprocess.DEVNULL if console.quiet else None,
+        stdout=subprocess.DEVNULL if is_LSP_enabled() else None,
+        stderr=subprocess.DEVNULL if is_LSP_enabled() else None,
     )
     if result.returncode != 0:
         logger.error(f"Failed to create worktree: {result.stderr}")
@@ -225,6 +226,7 @@ def create_detached_worktree(module_root: Path) -> Optional[Path]:
 
     # Get uncommitted diff from the original repo
     repository = git.Repo(module_root, search_parent_directories=True)
+    repository.git.add("-N", ".")  # add the index for untracked files to be included in the diff
     uni_diff_text = repository.git.diff(None, "HEAD", ignore_blank_lines=True, ignore_space_at_eol=True)
 
     if not uni_diff_text.strip():
diff --git a/codeflash/lsp/beta.py b/codeflash/lsp/beta.py
index 885ffdb9a..6cacbaff4 100644
--- a/codeflash/lsp/beta.py
+++ b/codeflash/lsp/beta.py
@@ -46,13 +46,7 @@ def get_optimizable_functions(
     file_path = Path(uris.to_fs_path(params.textDocument.uri))
     server.show_message_log(f"Getting optimizable functions for: {file_path}", "Info")
 
-    server.optimizer.worktree_mode()
-
-    args = server.optimizer.args
-
-    original_relative_file_path = file_path.relative_to(args.base_project_root)
-
-    server.optimizer.args.file = server.optimizer.current_worktree / original_relative_file_path
+    server.optimizer.args.file = file_path
     server.optimizer.args.function = None  # Always get ALL functions, not just one
     server.optimizer.args.previous_checkpoint_functions = False
 
@@ -75,11 +69,15 @@ def initialize_function_optimization(
 ) -> dict[str, str]:
     file_path = Path(uris.to_fs_path(params.textDocument.uri))
     server.show_message_log(f"Initializing optimization for function: {params.functionName} in {file_path}", "Info")
+    if server.optimizer is None:
+        _initialize_optimizer_if_valid(server)
     server.optimizer.worktree_mode()
+    original_args, _ = server.optimizer.original_args_and_test_cfg
 
     server.optimizer.args.function = params.functionName
-    original_relative_file_path = file_path.relative_to(server.optimizer.args.base_project_root)
+    original_relative_file_path = file_path.relative_to(original_args.project_root)
     server.optimizer.args.file = server.optimizer.current_worktree / original_relative_file_path
+    server.optimizer.args.previous_checkpoint_functions = False
 
     server.show_message_log(
         f"Args set - function: {server.optimizer.args.function}, file: {server.optimizer.args.file}", "Info"
@@ -338,10 +336,14 @@ def perform_function_optimization(  # noqa: PLR0911
             "patch_path": patch_path,
         }
     finally:
-        server.optimizer.cleanup_temporary_paths()
-        # restore args and test cfg
-        if server.optimizer.original_args_and_test_cfg:
-            server.optimizer.args, server.optimizer.test_cfg = server.optimizer.original_args_and_test_cfg
-        server.optimizer.args.function = None
-        server.optimizer.current_worktree = None
-        server.optimizer.current_function_optimizer = None
+        cleanup_the_optimizer(server)
+
+
+def cleanup_the_optimizer(server: CodeflashLanguageServer) -> None:
+    server.optimizer.cleanup_temporary_paths()
+    # restore args and test cfg
+    if server.optimizer.original_args_and_test_cfg:
+        server.optimizer.args, server.optimizer.test_cfg = server.optimizer.original_args_and_test_cfg
+    server.optimizer.args.function = None
+    server.optimizer.current_worktree = None
+    server.optimizer.current_function_optimizer = None
diff --git a/codeflash/lsp/helpers.py b/codeflash/lsp/helpers.py
new file mode 100644
index 000000000..b115e6ba7
--- /dev/null
+++ b/codeflash/lsp/helpers.py
@@ -0,0 +1,8 @@
+from functools import lru_cache
+
+from codeflash.cli_cmds.console import console
+
+
+@lru_cache(maxsize=1)
+def is_LSP_enabled() -> bool:
+    return console.quiet
diff --git a/codeflash/optimization/optimizer.py b/codeflash/optimization/optimizer.py
index 86776c7fd..1c6e8853f 100644
--- a/codeflash/optimization/optimizer.py
+++ b/codeflash/optimization/optimizer.py
@@ -446,7 +446,6 @@ def mutate_args_for_worktree_mode(self, worktree_dir: Path) -> None:
         self.original_args_and_test_cfg = (saved_args, saved_test_cfg)
 
         project_root = self.args.project_root
-        self.args.base_project_root = project_root  # keep a reference to the original project root
         module_root = self.args.module_root
         relative_module_root = module_root.relative_to(project_root)
         relative_optimized_file = self.args.file.relative_to(project_root) if self.args.file else None
diff --git a/codeflash/verification/concolic_testing.py b/codeflash/verification/concolic_testing.py
index 3fe72a764..8f30a1562 100644
--- a/codeflash/verification/concolic_testing.py
+++ b/codeflash/verification/concolic_testing.py
@@ -10,9 +10,9 @@
 from codeflash.cli_cmds.console import console, logger
 from codeflash.code_utils.compat import SAFE_SYS_EXECUTABLE
 from codeflash.code_utils.concolic_utils import clean_concolic_tests
-from codeflash.code_utils.env_utils import is_LSP_enabled
 from codeflash.code_utils.static_analysis import has_typed_parameters
 from codeflash.discovery.discover_unit_tests import discover_unit_tests
+from codeflash.lsp.helpers import is_LSP_enabled
 from codeflash.telemetry.posthog_cf import ph
 from codeflash.verification.verification_utils import TestConfig
 

From 203002dc6a7540a0797ef0a66e20ed7c52c6b775 Mon Sep 17 00:00:00 2001
From: mohammed <mohammed18200118@gmail.com>
Date: Tue, 12 Aug 2025 19:41:40 +0300
Subject: [PATCH 07/18] fix console.quiet issue

---
 codeflash/api/aiservice.py | 3 ++-
 codeflash/api/cfapi.py     | 8 ++------
 codeflash/main.py          | 3 ++-
 3 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/codeflash/api/aiservice.py b/codeflash/api/aiservice.py
index db78a64df..3ac863f80 100644
--- a/codeflash/api/aiservice.py
+++ b/codeflash/api/aiservice.py
@@ -10,8 +10,9 @@
 from pydantic.json import pydantic_encoder
 
 from codeflash.cli_cmds.console import console, logger
-from codeflash.code_utils.env_utils import get_codeflash_api_key, is_LSP_enabled
+from codeflash.code_utils.env_utils import get_codeflash_api_key
 from codeflash.code_utils.git_utils import get_last_commit_author_if_pr_exists, get_repo_owner_and_name
+from codeflash.lsp.helpers import is_LSP_enabled
 from codeflash.models.ExperimentMetadata import ExperimentMetadata
 from codeflash.models.models import AIServiceRefinerRequest, CodeStringsMarkdown, OptimizedCandidate
 from codeflash.telemetry.posthog_cf import ph
diff --git a/codeflash/api/cfapi.py b/codeflash/api/cfapi.py
index 22871298e..1cca27ac3 100644
--- a/codeflash/api/cfapi.py
+++ b/codeflash/api/cfapi.py
@@ -13,14 +13,10 @@
 from pydantic.json import pydantic_encoder
 
 from codeflash.cli_cmds.console import console, logger
-from codeflash.code_utils.env_utils import (
-    ensure_codeflash_api_key,
-    get_codeflash_api_key,
-    get_pr_number,
-    is_LSP_enabled,
-)
+from codeflash.code_utils.env_utils import ensure_codeflash_api_key, get_codeflash_api_key, get_pr_number
 from codeflash.code_utils.git_utils import get_current_branch, get_repo_owner_and_name, git_root_dir
 from codeflash.github.PrComment import FileDiffContent, PrComment
+from codeflash.lsp.helpers import is_LSP_enabled
 from codeflash.version import __version__
 
 if TYPE_CHECKING:
diff --git a/codeflash/main.py b/codeflash/main.py
index 650bdbd63..516a1327f 100644
--- a/codeflash/main.py
+++ b/codeflash/main.py
@@ -8,7 +8,7 @@
 
 from codeflash.cli_cmds.cli import parse_args, process_pyproject_config
 from codeflash.cli_cmds.cmd_init import CODEFLASH_LOGO, ask_run_end_to_end_test
-from codeflash.cli_cmds.console import paneled_text
+from codeflash.cli_cmds.console import console, paneled_text
 from codeflash.code_utils.checkpoint import ask_should_use_checkpoint_get_functions
 from codeflash.code_utils.config_parser import parse_config_file
 from codeflash.telemetry import posthog_cf
@@ -17,6 +17,7 @@
 
 def main() -> None:
     """Entry point for the codeflash command-line interface."""
+    console.quiet = False
     paneled_text(
         CODEFLASH_LOGO, panel_args={"title": "https://codeflash.ai", "expand": False}, text_args={"style": "bold gold3"}
     )

From d041dfb2cc9278fc1887be43b092bcb43d941801 Mon Sep 17 00:00:00 2001
From: mohammed <mohammed18200118@gmail.com>
Date: Tue, 12 Aug 2025 20:04:44 +0300
Subject: [PATCH 08/18] fix: quite console in lsp mode

---
 codeflash/cli_cmds/console.py | 5 +++++
 codeflash/lsp/__init__.py     | 4 ----
 codeflash/lsp/helpers.py      | 5 ++---
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/codeflash/cli_cmds/console.py b/codeflash/cli_cmds/console.py
index 34d50f268..ca8e29e26 100644
--- a/codeflash/cli_cmds/console.py
+++ b/codeflash/cli_cmds/console.py
@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import logging
+import os
 from contextlib import contextmanager
 from itertools import cycle
 from typing import TYPE_CHECKING
@@ -28,6 +29,10 @@
 DEBUG_MODE = logging.getLogger().getEffectiveLevel() == logging.DEBUG
 
 console = Console()
+
+if os.getenv("CODEFLASH_LSP"):
+    console.quiet = True
+
 logging.basicConfig(
     level=logging.INFO,
     handlers=[RichHandler(rich_tracebacks=True, markup=False, console=console, show_path=False, show_time=False)],
diff --git a/codeflash/lsp/__init__.py b/codeflash/lsp/__init__.py
index 9d75096ef..e69de29bb 100644
--- a/codeflash/lsp/__init__.py
+++ b/codeflash/lsp/__init__.py
@@ -1,4 +0,0 @@
-# Silence the console module to prevent stdout pollution
-from codeflash.cli_cmds.console import console
-
-console.quiet = True
diff --git a/codeflash/lsp/helpers.py b/codeflash/lsp/helpers.py
index b115e6ba7..dc8f8c5d6 100644
--- a/codeflash/lsp/helpers.py
+++ b/codeflash/lsp/helpers.py
@@ -1,8 +1,7 @@
+import os
 from functools import lru_cache
 
-from codeflash.cli_cmds.console import console
-
 
 @lru_cache(maxsize=1)
 def is_LSP_enabled() -> bool:
-    return console.quiet
+    return os.getenv("CODEFLASH_LSP", default="false").lower() == "true"

From d8eb12159b4567ef7beff21390d129a332a28749 Mon Sep 17 00:00:00 2001
From: mohammed <mohammed18200118@gmail.com>
Date: Wed, 13 Aug 2025 19:31:58 +0300
Subject: [PATCH 09/18] return the best explanation from the lsp optimization
 feature

---
 codeflash/lsp/beta.py                        | 15 ++++++++++++---
 codeflash/models/models.py                   |  3 +++
 codeflash/optimization/function_optimizer.py |  1 +
 3 files changed, 16 insertions(+), 3 deletions(-)

diff --git a/codeflash/lsp/beta.py b/codeflash/lsp/beta.py
index 6cacbaff4..e9fcb4339 100644
--- a/codeflash/lsp/beta.py
+++ b/codeflash/lsp/beta.py
@@ -13,6 +13,7 @@
 from codeflash.code_utils.shell_utils import save_api_key_to_rc
 from codeflash.either import is_successful
 from codeflash.lsp.server import CodeflashLanguageServer, CodeflashLanguageServerProtocol
+from codeflash.result.explanation import Explanation
 
 if TYPE_CHECKING:
     from lsprotocol import types
@@ -86,7 +87,12 @@ def initialize_function_optimization(
     optimizable_funcs, _, _ = server.optimizer.get_optimizable_functions()
     if not optimizable_funcs:
         server.show_message_log(f"No optimizable functions found for {params.functionName}", "Warning")
-        return {"functionName": params.functionName, "status": "not found", "args": None}
+        return {
+            "functionName": params.functionName,
+            "status": "error",
+            "message": "function is no found or not optimizable",
+            "args": None,
+        }
 
     fto = optimizable_funcs.popitem()[1][0]
     server.optimizer.current_function_being_optimized = fto
@@ -316,7 +322,7 @@ def perform_function_optimization(  # noqa: PLR0911
 
         # generate a patch for the optimization
         relative_file_paths = [code_string.file_path for code_string in code_context.read_writable_code.code_strings]
-        patch_path = create_diff_from_worktree(
+        patch_file = create_diff_from_worktree(
             server.optimizer.current_worktree,
             relative_file_paths,
             server.optimizer.current_function_optimizer.function_to_optimize.qualified_name,
@@ -327,13 +333,16 @@ def perform_function_optimization(  # noqa: PLR0911
 
         server.show_message_log(f"Optimization completed for {params.functionName} with {speedup:.2f}x speedup", "Info")
 
+        explanation = best_optimization.candidate.explanation
+        explanation_str = explanation.explanation_message() if isinstance(explanation, Explanation) else explanation
         return {
             "functionName": params.functionName,
             "status": "success",
             "message": "Optimization completed successfully",
             "extra": f"Speedup: {speedup:.2f}x faster",
             "optimization": optimized_source,
-            "patch_path": patch_path,
+            "patch_file": str(patch_file),
+            "explanation": explanation_str,
         }
     finally:
         cleanup_the_optimizer(server)
diff --git a/codeflash/models/models.py b/codeflash/models/models.py
index 1636d6889..590b88f3a 100644
--- a/codeflash/models/models.py
+++ b/codeflash/models/models.py
@@ -349,6 +349,9 @@ class OptimizedCandidate:
     explanation: str
     optimization_id: str
 
+    def set_explanation(self, new_explanation: str) -> None:
+        object.__setattr__(self, "explanation", new_explanation)
+
 
 @dataclass(frozen=True)
 class FunctionCalledInTest:
diff --git a/codeflash/optimization/function_optimizer.py b/codeflash/optimization/function_optimizer.py
index c9d479782..3a559a3b6 100644
--- a/codeflash/optimization/function_optimizer.py
+++ b/codeflash/optimization/function_optimizer.py
@@ -1227,6 +1227,7 @@ def process_review(
             file_path=explanation.file_path,
             benchmark_details=explanation.benchmark_details,
         )
+        best_optimization.candidate.set_explanation(new_explanation)
         data = {
             "original_code": original_code_combined,
             "new_code": new_code_combined,

From 48d6ccda7c88cccdd85d3ffa02ca5b4d18ca2cc4 Mon Sep 17 00:00:00 2001
From: mohammed <mohammed18200118@gmail.com>
Date: Thu, 14 Aug 2025 02:06:30 +0300
Subject: [PATCH 10/18] delimiter for lsp server logs

---
 codeflash/lsp/server_entry.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/codeflash/lsp/server_entry.py b/codeflash/lsp/server_entry.py
index dfb8dd5a3..5ea30cde8 100644
--- a/codeflash/lsp/server_entry.py
+++ b/codeflash/lsp/server_entry.py
@@ -21,7 +21,8 @@ def setup_logging() -> logging.Logger:
 
     # Set up stderr handler for VS Code output channel with [LSP-Server] prefix
     handler = logging.StreamHandler(sys.stderr)
-    handler.setFormatter(logging.Formatter("[LSP-Server] %(asctime)s [%(levelname)s]: %(message)s"))
+    # adding the :::: here for the client to easily extract the message from the log
+    handler.setFormatter(logging.Formatter("[LSP-Server] %(asctime)s [%(levelname)s]::::%(message)s"))
 
     # Configure root logger
     root_logger.addHandler(handler)

From e33ff2111a0af44876cb6679e464f278a12178db Mon Sep 17 00:00:00 2001
From: mohammed <mohammed18200118@gmail.com>
Date: Thu, 14 Aug 2025 15:19:58 +0300
Subject: [PATCH 11/18] merge main

---
 codeflash/api/aiservice.py                   |  5 ++---
 codeflash/api/cfapi.py                       |  4 ++++
 codeflash/optimization/function_optimizer.py | 16 ++++++++++------
 3 files changed, 16 insertions(+), 9 deletions(-)

diff --git a/codeflash/api/aiservice.py b/codeflash/api/aiservice.py
index 3ac863f80..a4e1c4066 100644
--- a/codeflash/api/aiservice.py
+++ b/codeflash/api/aiservice.py
@@ -249,7 +249,7 @@ def optimize_python_code_refinement(self, request: list[AIServiceRefinerRequest]
             }
             for opt in request
         ]
-        logger.info(f"Refining {len(request)} optimizations…")
+        logger.debug(f"Refining {len(request)} optimizations…")
         console.rule()
         try:
             response = self.make_ai_service_request("/refinement", payload=payload, timeout=600)
@@ -260,7 +260,7 @@ def optimize_python_code_refinement(self, request: list[AIServiceRefinerRequest]
 
         if response.status_code == 200:
             refined_optimizations = response.json()["refinements"]
-            logger.info(f"Generated {len(refined_optimizations)} candidate refinements.")
+            logger.debug(f"Generated {len(refined_optimizations)} candidate refinements.")
             console.rule()
             return [
                 OptimizedCandidate(
@@ -340,7 +340,6 @@ def get_new_explanation(  # noqa: D417
 
         if response.status_code == 200:
             explanation: str = response.json()["explanation"]
-            logger.debug(f"New Explanation: {explanation}")
             console.rule()
             return explanation
         try:
diff --git a/codeflash/api/cfapi.py b/codeflash/api/cfapi.py
index da64e622f..c6b5fe8a6 100644
--- a/codeflash/api/cfapi.py
+++ b/codeflash/api/cfapi.py
@@ -204,6 +204,8 @@ def create_staging(
     generated_original_test_source: str,
     function_trace_id: str,
     coverage_message: str,
+    replay_tests: str = "",
+    concolic_tests: str = "",
 ) -> Response:
     """Create a staging pull request, targeting the specified branch. (usually 'staging').
 
@@ -244,6 +246,8 @@ def create_staging(
         "generatedTests": generated_original_test_source,
         "traceId": function_trace_id,
         "coverage_message": coverage_message,
+        "replayTests": replay_tests,
+        "concolicTests": concolic_tests,
     }
 
     return make_cfapi_request(endpoint="/create-staging", method="POST", payload=payload)
diff --git a/codeflash/optimization/function_optimizer.py b/codeflash/optimization/function_optimizer.py
index 7f54c9815..536613c19 100644
--- a/codeflash/optimization/function_optimizer.py
+++ b/codeflash/optimization/function_optimizer.py
@@ -440,6 +440,9 @@ def determine_best_candidate(
                 # check if this code has been evaluated before by checking the ast normalized code string
                 normalized_code = ast.unparse(ast.parse(candidate.source_code.flat.strip()))
                 if normalized_code in ast_code_to_id:
+                    logger.warning(
+                        "Current candidate has been encountered before in testing, Skipping optimization candidate."
+                    )
                     past_opt_id = ast_code_to_id[normalized_code]["optimization_id"]
                     # update speedup ratio, is_correct, optimizations_post, optimized_line_profiler_results, optimized_runtimes
                     speedup_ratios[candidate.optimization_id] = speedup_ratios[past_opt_id]
@@ -588,8 +591,10 @@ def determine_best_candidate(
                         if len(possible_refinement) > 0:  # if the api returns a valid response
                             refinement_response.append(possible_refinement[0])
                     candidates.extend(refinement_response)
-                    logger.info(f"Added {len(refinement_response)} candidates from refinement")
                     original_len += len(refinement_response)
+                    logger.info(
+                        f"Added {len(refinement_response)} candidates from refinement, total candidates now: {original_len}"
+                    )
                     refinement_done = True
         except KeyboardInterrupt as e:
             self.write_code_and_helpers(
@@ -1099,11 +1104,6 @@ def find_and_process_best_optimization(
             if best_optimization:
                 logger.info("Best candidate:")
                 code_print(best_optimization.candidate.source_code.flat)
-                console.print(
-                    Panel(
-                        best_optimization.candidate.explanation, title="Best Candidate Explanation", border_style="blue"
-                    )
-                )
                 processed_benchmark_info = None
                 if self.args.benchmark:
                     processed_benchmark_info = process_benchmark_data(
@@ -1227,7 +1227,11 @@ def process_review(
             file_path=explanation.file_path,
             benchmark_details=explanation.benchmark_details,
         )
+
         best_optimization.candidate.set_explanation(new_explanation)
+
+        console.print(Panel(new_explanation_raw_str, title="Best Candidate Explanation", border_style="blue"))
+
         data = {
             "original_code": original_code_combined,
             "new_code": new_code_combined,

From 9c4195771afdec50b4b53e93b5ad126936238ea6 Mon Sep 17 00:00:00 2001
From: mohammed <mohammed18200118@gmail.com>
Date: Thu, 14 Aug 2025 16:34:38 +0300
Subject: [PATCH 12/18] small fixes

---
 codeflash/code_utils/git_utils.py            | 2 +-
 codeflash/lsp/beta.py                        | 4 ++--
 codeflash/lsp/server.py                      | 3 +--
 codeflash/main.py                            | 3 +--
 codeflash/optimization/function_optimizer.py | 2 +-
 codeflash/optimization/optimizer.py          | 4 ++--
 6 files changed, 8 insertions(+), 10 deletions(-)

diff --git a/codeflash/code_utils/git_utils.py b/codeflash/code_utils/git_utils.py
index e8b6541c3..e10c4ac60 100644
--- a/codeflash/code_utils/git_utils.py
+++ b/codeflash/code_utils/git_utils.py
@@ -258,7 +258,7 @@ def remove_worktree(worktree_dir: Path) -> None:
         logger.exception(f"Failed to remove worktree: {worktree_dir}")
 
 
-def create_diff_from_worktree(worktree_dir: Path, files: list[str], fto_name: str) -> Path:
+def create_diff_patch_from_worktree(worktree_dir: Path, files: list[str], fto_name: str) -> Path:
     repository = git.Repo(worktree_dir, search_parent_directories=True)
     uni_diff_text = repository.git.diff(None, "HEAD", *files, ignore_blank_lines=True, ignore_space_at_eol=True)
 
diff --git a/codeflash/lsp/beta.py b/codeflash/lsp/beta.py
index e9fcb4339..c90653bb8 100644
--- a/codeflash/lsp/beta.py
+++ b/codeflash/lsp/beta.py
@@ -9,7 +9,7 @@
 from pygls import uris
 
 from codeflash.api.cfapi import get_codeflash_api_key, get_user_id
-from codeflash.code_utils.git_utils import create_diff_from_worktree
+from codeflash.code_utils.git_utils import create_diff_patch_from_worktree
 from codeflash.code_utils.shell_utils import save_api_key_to_rc
 from codeflash.either import is_successful
 from codeflash.lsp.server import CodeflashLanguageServer, CodeflashLanguageServerProtocol
@@ -322,7 +322,7 @@ def perform_function_optimization(  # noqa: PLR0911
 
         # generate a patch for the optimization
         relative_file_paths = [code_string.file_path for code_string in code_context.read_writable_code.code_strings]
-        patch_file = create_diff_from_worktree(
+        patch_file = create_diff_patch_from_worktree(
             server.optimizer.current_worktree,
             relative_file_paths,
             server.optimizer.current_function_optimizer.function_to_optimize.qualified_name,
diff --git a/codeflash/lsp/server.py b/codeflash/lsp/server.py
index 8b7bbd320..5d2f84992 100644
--- a/codeflash/lsp/server.py
+++ b/codeflash/lsp/server.py
@@ -56,7 +56,6 @@ def prepare_optimizer_arguments(self, config_file: Path) -> None:
         args.config_file = config_file
         args.no_pr = True  # LSP server should not create PRs
         args.worktree = True
-        args.verbose = True
         args = process_pyproject_config(args)
         self.args = args
         # avoid initializing the optimizer during initialization, because it can cause an error if the api key is invalid
@@ -78,7 +77,7 @@ def show_message_log(self, message: str, message_type: str) -> None:
             "Debug": MessageType.Debug,
         }
 
-        lsp_message_type = type_mapping.get(message_type, MessageType.Debug)
+        lsp_message_type = type_mapping.get(message_type, MessageType.Info)
 
         # Send log message to client (appears in output channel)
         log_params = LogMessageParams(type=lsp_message_type, message=message)
diff --git a/codeflash/main.py b/codeflash/main.py
index 516a1327f..650bdbd63 100644
--- a/codeflash/main.py
+++ b/codeflash/main.py
@@ -8,7 +8,7 @@
 
 from codeflash.cli_cmds.cli import parse_args, process_pyproject_config
 from codeflash.cli_cmds.cmd_init import CODEFLASH_LOGO, ask_run_end_to_end_test
-from codeflash.cli_cmds.console import console, paneled_text
+from codeflash.cli_cmds.console import paneled_text
 from codeflash.code_utils.checkpoint import ask_should_use_checkpoint_get_functions
 from codeflash.code_utils.config_parser import parse_config_file
 from codeflash.telemetry import posthog_cf
@@ -17,7 +17,6 @@
 
 def main() -> None:
     """Entry point for the codeflash command-line interface."""
-    console.quiet = False
     paneled_text(
         CODEFLASH_LOGO, panel_args={"title": "https://codeflash.ai", "expand": False}, text_args={"style": "bold gold3"}
     )
diff --git a/codeflash/optimization/function_optimizer.py b/codeflash/optimization/function_optimizer.py
index 536613c19..dd97f58b9 100644
--- a/codeflash/optimization/function_optimizer.py
+++ b/codeflash/optimization/function_optimizer.py
@@ -1259,7 +1259,7 @@ def process_review(
                 trace_id=self.function_trace_id, is_optimization_found=best_optimization is not None
             )
 
-        # If worktree mode, do not revert code and helpers, we create snapshot commit after each function optimization
+        # If worktree mode, do not revert code and helpers,, otherwise we would have an empty diff when writing the patch in the lsp
         if self.args.worktree:
             return
 
diff --git a/codeflash/optimization/optimizer.py b/codeflash/optimization/optimizer.py
index 1c6e8853f..929b663b0 100644
--- a/codeflash/optimization/optimizer.py
+++ b/codeflash/optimization/optimizer.py
@@ -18,7 +18,7 @@
 from codeflash.code_utils.git_utils import (
     check_running_in_git_repo,
     create_detached_worktree,
-    create_diff_from_worktree,
+    create_diff_patch_from_worktree,
     create_worktree_snapshot_commit,
     remove_worktree,
 )
@@ -346,7 +346,7 @@ def run(self) -> None:
                                 relative_file_paths = [
                                     code_string.file_path for code_string in read_writable_code.code_strings
                                 ]
-                                patch_path = create_diff_from_worktree(
+                                patch_path = create_diff_patch_from_worktree(
                                     self.current_worktree,
                                     relative_file_paths,
                                     self.current_function_optimizer.function_to_optimize.qualified_name,

From 8b74abd73ee9f9205b1a534e02ce3f4095bc5acf Mon Sep 17 00:00:00 2001
From: mohammed <mohammed18200118@gmail.com>
Date: Thu, 14 Aug 2025 16:50:15 +0300
Subject: [PATCH 13/18] unnecessarily message log

---
 codeflash/lsp/server.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/codeflash/lsp/server.py b/codeflash/lsp/server.py
index 5d2f84992..8114c94dc 100644
--- a/codeflash/lsp/server.py
+++ b/codeflash/lsp/server.py
@@ -28,7 +28,6 @@ def lsp_initialize(self, params: InitializeParams) -> InitializeResult:
             pyproject_toml_path = self._find_pyproject_toml(workspace_path)
             if pyproject_toml_path:
                 server.prepare_optimizer_arguments(pyproject_toml_path)
-                server.show_message(f"Found pyproject.toml at: {pyproject_toml_path}")
             else:
                 server.show_message("No pyproject.toml found in workspace.")
         else:

From 15008695f750ccca80bab2506938a3a337175980 Mon Sep 17 00:00:00 2001
From: ali <mohammed18200118@gmail.com>
Date: Fri, 15 Aug 2025 14:50:58 +0300
Subject: [PATCH 14/18] fix: ignore white spaces when applying temp patch to
 the detached worktree

---
 codeflash/code_utils/git_utils.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/codeflash/code_utils/git_utils.py b/codeflash/code_utils/git_utils.py
index e10c4ac60..7464bd02d 100644
--- a/codeflash/code_utils/git_utils.py
+++ b/codeflash/code_utils/git_utils.py
@@ -242,7 +242,11 @@ def create_detached_worktree(module_root: Path) -> Optional[Path]:
 
         # Apply the patch inside the worktree
         try:
-            subprocess.run(["git", "apply", patch_path], cwd=worktree_dir, check=True)
+            subprocess.run(
+                ["git", "apply", "--ignore-space-change", "--ignore-whitespace", patch_path],
+                cwd=worktree_dir,
+                check=True,
+            )
             create_worktree_snapshot_commit(worktree_dir, "Initial Snapshot")
         except subprocess.CalledProcessError as e:
             logger.error(f"Failed to apply patch to worktree: {e}")

From bdf1770363dc7625e22013521ac11dbe767503fc Mon Sep 17 00:00:00 2001
From: ali <mohammed18200118@gmail.com>
Date: Fri, 15 Aug 2025 17:49:52 +0300
Subject: [PATCH 15/18] feat: optimize current diff

---
 codeflash/discovery/functions_to_optimize.py |  6 +++---
 codeflash/lsp/beta.py                        | 18 ++++++++++++++++++
 2 files changed, 21 insertions(+), 3 deletions(-)

diff --git a/codeflash/discovery/functions_to_optimize.py b/codeflash/discovery/functions_to_optimize.py
index 3c2f4f633..db5d5e5d5 100644
--- a/codeflash/discovery/functions_to_optimize.py
+++ b/codeflash/discovery/functions_to_optimize.py
@@ -208,7 +208,7 @@ def get_functions_to_optimize(
             logger.info("Finding all functions modified in the current git diff ...")
             console.rule()
             ph("cli-optimizing-git-diff")
-            functions = get_functions_within_git_diff()
+            functions = get_functions_within_git_diff(uncommitted_changes=False)
         filtered_modified_functions, functions_count = filter_functions(
             functions, test_cfg.tests_root, ignore_paths, project_root, module_root, previous_checkpoint_functions
         )
@@ -224,8 +224,8 @@ def get_functions_to_optimize(
         return filtered_modified_functions, functions_count, trace_file_path
 
 
-def get_functions_within_git_diff() -> dict[str, list[FunctionToOptimize]]:
-    modified_lines: dict[str, list[int]] = get_git_diff(uncommitted_changes=False)
+def get_functions_within_git_diff(uncommitted_changes: bool) -> dict[str, list[FunctionToOptimize]]:  # noqa: FBT001
+    modified_lines: dict[str, list[int]] = get_git_diff(uncommitted_changes=uncommitted_changes)
     modified_functions: dict[str, list[FunctionToOptimize]] = {}
     for path_str, lines_in_file in modified_lines.items():
         path = Path(path_str)
diff --git a/codeflash/lsp/beta.py b/codeflash/lsp/beta.py
index c90653bb8..f83be319f 100644
--- a/codeflash/lsp/beta.py
+++ b/codeflash/lsp/beta.py
@@ -11,6 +11,7 @@
 from codeflash.api.cfapi import get_codeflash_api_key, get_user_id
 from codeflash.code_utils.git_utils import create_diff_patch_from_worktree
 from codeflash.code_utils.shell_utils import save_api_key_to_rc
+from codeflash.discovery.functions_to_optimize import filter_functions, get_functions_within_git_diff
 from codeflash.either import is_successful
 from codeflash.lsp.server import CodeflashLanguageServer, CodeflashLanguageServerProtocol
 from codeflash.result.explanation import Explanation
@@ -40,6 +41,23 @@ class ProvideApiKeyParams:
 server = CodeflashLanguageServer("codeflash-language-server", "v1.0", protocol_cls=CodeflashLanguageServerProtocol)
 
 
+@server.feature("getOptimizableFunctionsInCurrentDiff")
+def get_functions_in_current_git_diff(
+    server: CodeflashLanguageServer, _params: OptimizableFunctionsParams
+) -> dict[str, str | list[str]]:
+    functions = get_functions_within_git_diff(uncommitted_changes=True)
+    file_to_funcs_to_optimize, _ = filter_functions(
+        modified_functions=functions,
+        tests_root=server.optimizer.test_cfg.tests_root,
+        ignore_paths=[],
+        project_root=server.optimizer.args.project_root,
+        module_root=server.optimizer.args.module_root,
+        previous_checkpoint_functions={},
+    )
+    qualified_names: list[str] = [func.qualified_name for funcs in file_to_funcs_to_optimize.values() for func in funcs]
+    return {"functions": qualified_names, "status": "success"}
+
+
 @server.feature("getOptimizableFunctions")
 def get_optimizable_functions(
     server: CodeflashLanguageServer, params: OptimizableFunctionsParams

From 32099b423809b78c030daf16e468473a33915827 Mon Sep 17 00:00:00 2001
From: ali <mohammed18200118@gmail.com>
Date: Mon, 18 Aug 2025 02:43:36 +0300
Subject: [PATCH 16/18] fixes and getting the worktree to work with PR and
 staging

---
 codeflash/api/cfapi.py                       |  9 ++++-----
 codeflash/code_utils/git_utils.py            | 17 ++++-------------
 codeflash/models/models.py                   |  5 +----
 codeflash/optimization/function_optimizer.py |  6 +++---
 codeflash/result/create_pr.py                | 16 ++++++----------
 5 files changed, 18 insertions(+), 35 deletions(-)

diff --git a/codeflash/api/cfapi.py b/codeflash/api/cfapi.py
index c6b5fe8a6..ec0c4c708 100644
--- a/codeflash/api/cfapi.py
+++ b/codeflash/api/cfapi.py
@@ -14,7 +14,7 @@
 
 from codeflash.cli_cmds.console import console, logger
 from codeflash.code_utils.env_utils import ensure_codeflash_api_key, get_codeflash_api_key, get_pr_number
-from codeflash.code_utils.git_utils import get_current_branch, get_repo_owner_and_name, git_root_dir
+from codeflash.code_utils.git_utils import get_current_branch, get_repo_owner_and_name
 from codeflash.github.PrComment import FileDiffContent, PrComment
 from codeflash.lsp.helpers import is_LSP_enabled
 from codeflash.version import __version__
@@ -206,6 +206,7 @@ def create_staging(
     coverage_message: str,
     replay_tests: str = "",
     concolic_tests: str = "",
+    root_dir: Optional[Path] = None,
 ) -> Response:
     """Create a staging pull request, targeting the specified branch. (usually 'staging').
 
@@ -218,12 +219,10 @@ def create_staging(
     :param coverage_message: Coverage report or summary.
     :return: The response object from the backend.
     """
-    relative_path = explanation.file_path.relative_to(git_root_dir()).as_posix()
+    relative_path = explanation.file_path.relative_to(root_dir).as_posix()
 
     build_file_changes = {
-        Path(p).relative_to(git_root_dir()).as_posix(): FileDiffContent(
-            oldContent=original_code[p], newContent=new_code[p]
-        )
+        Path(p).relative_to(root_dir).as_posix(): FileDiffContent(oldContent=original_code[p], newContent=new_code[p])
         for p in original_code
     }
 
diff --git a/codeflash/code_utils/git_utils.py b/codeflash/code_utils/git_utils.py
index 7464bd02d..b4f658097 100644
--- a/codeflash/code_utils/git_utils.py
+++ b/codeflash/code_utils/git_utils.py
@@ -18,7 +18,6 @@
 from codeflash.cli_cmds.console import logger
 from codeflash.code_utils.compat import codeflash_cache_dir
 from codeflash.code_utils.config_consts import N_CANDIDATES
-from codeflash.lsp.helpers import is_LSP_enabled
 
 if TYPE_CHECKING:
     from git import Repo
@@ -213,19 +212,11 @@ def create_detached_worktree(module_root: Path) -> Optional[Path]:
     current_time_str = time.strftime("%Y%m%d-%H%M%S")
     worktree_dir = worktree_dirs / f"{git_root.name}-{current_time_str}"
 
-    result = subprocess.run(
-        ["git", "worktree", "add", "-d", str(worktree_dir)],
-        cwd=git_root,
-        check=True,
-        stdout=subprocess.DEVNULL if is_LSP_enabled() else None,
-        stderr=subprocess.DEVNULL if is_LSP_enabled() else None,
-    )
-    if result.returncode != 0:
-        logger.error(f"Failed to create worktree: {result.stderr}")
-        return None
+    repository = git.Repo(git_root, search_parent_directories=True)
+
+    repository.git.worktree("add", "-d", str(worktree_dir))
 
     # Get uncommitted diff from the original repo
-    repository = git.Repo(module_root, search_parent_directories=True)
     repository.git.add("-N", ".")  # add the index for untracked files to be included in the diff
     uni_diff_text = repository.git.diff(None, "HEAD", ignore_blank_lines=True, ignore_space_at_eol=True)
 
@@ -234,7 +225,7 @@ def create_detached_worktree(module_root: Path) -> Optional[Path]:
         return worktree_dir
 
     # Write the diff to a temporary file
-    with tempfile.NamedTemporaryFile(mode="w+", suffix=".codeflash.patch", delete=False) as tmp_patch_file:
+    with tempfile.NamedTemporaryFile(mode="w", suffix=".codeflash.patch", delete=False) as tmp_patch_file:
         tmp_patch_file.write(uni_diff_text + "\n")  # the new line here is a must otherwise the last hunk won't be valid
         tmp_patch_file.flush()
 
diff --git a/codeflash/models/models.py b/codeflash/models/models.py
index 590b88f3a..1d47fb7d4 100644
--- a/codeflash/models/models.py
+++ b/codeflash/models/models.py
@@ -343,15 +343,12 @@ class TestsInFile:
     test_type: TestType
 
 
-@dataclass(frozen=True)
+@dataclass
 class OptimizedCandidate:
     source_code: CodeStringsMarkdown
     explanation: str
     optimization_id: str
 
-    def set_explanation(self, new_explanation: str) -> None:
-        object.__setattr__(self, "explanation", new_explanation)
-
 
 @dataclass(frozen=True)
 class FunctionCalledInTest:
diff --git a/codeflash/optimization/function_optimizer.py b/codeflash/optimization/function_optimizer.py
index dd97f58b9..3a16a843a 100644
--- a/codeflash/optimization/function_optimizer.py
+++ b/codeflash/optimization/function_optimizer.py
@@ -1228,7 +1228,7 @@ def process_review(
             benchmark_details=explanation.benchmark_details,
         )
 
-        best_optimization.candidate.set_explanation(new_explanation)
+        best_optimization.candidate.explanation = new_explanation
 
         console.print(Panel(new_explanation_raw_str, title="Best Candidate Explanation", border_style="blue"))
 
@@ -1250,9 +1250,9 @@ def process_review(
 
         if raise_pr and not self.args.staging_review:
             data["git_remote"] = self.args.git_remote
-            check_create_pr(**data)
+            check_create_pr(**data, root_dir=self.project_root)
         elif self.args.staging_review:
-            create_staging(**data)
+            create_staging(**data, root_dir=self.project_root)
         else:
             # Mark optimization success since no PR will be created
             mark_optimization_success(
diff --git a/codeflash/result/create_pr.py b/codeflash/result/create_pr.py
index 51f6b48af..fcac3580e 100644
--- a/codeflash/result/create_pr.py
+++ b/codeflash/result/create_pr.py
@@ -10,12 +10,7 @@
 from codeflash.cli_cmds.console import console, logger
 from codeflash.code_utils import env_utils
 from codeflash.code_utils.code_replacer import is_zero_diff
-from codeflash.code_utils.git_utils import (
-    check_and_push_branch,
-    get_current_branch,
-    get_repo_owner_and_name,
-    git_root_dir,
-)
+from codeflash.code_utils.git_utils import check_and_push_branch, get_current_branch, get_repo_owner_and_name
 from codeflash.code_utils.github_utils import github_pr_url
 from codeflash.code_utils.tabulate import tabulate
 from codeflash.code_utils.time_utils import format_perf, format_time
@@ -189,6 +184,7 @@ def check_create_pr(
     replay_tests: str,
     concolic_tests: str,
     git_remote: Optional[str] = None,
+    root_dir: Optional[Path] = None,
 ) -> None:
     pr_number: Optional[int] = env_utils.get_pr_number()
     git_repo = git.Repo(search_parent_directories=True)
@@ -196,9 +192,9 @@ def check_create_pr(
     if pr_number is not None:
         logger.info(f"Suggesting changes to PR #{pr_number} ...")
         owner, repo = get_repo_owner_and_name(git_repo)
-        relative_path = explanation.file_path.relative_to(git_root_dir()).as_posix()
+        relative_path = explanation.file_path.relative_to(root_dir).as_posix()
         build_file_changes = {
-            Path(p).relative_to(git_root_dir()).as_posix(): FileDiffContent(
+            Path(p).relative_to(root_dir).as_posix(): FileDiffContent(
                 oldContent=original_code[p], newContent=new_code[p]
             )
             for p in original_code
@@ -247,10 +243,10 @@ def check_create_pr(
         if not check_and_push_branch(git_repo, git_remote, wait_for_push=True):
             logger.warning("⏭️ Branch is not pushed, skipping PR creation...")
             return
-        relative_path = explanation.file_path.relative_to(git_root_dir()).as_posix()
+        relative_path = explanation.file_path.relative_to(root_dir).as_posix()
         base_branch = get_current_branch()
         build_file_changes = {
-            Path(p).relative_to(git_root_dir()).as_posix(): FileDiffContent(
+            Path(p).relative_to(root_dir).as_posix(): FileDiffContent(
                 oldContent=original_code[p], newContent=new_code[p]
             )
             for p in original_code

From 6e619aa5bc4e7bb209e45e5e8d887ec46a23a056 Mon Sep 17 00:00:00 2001
From: ali <mohammed18200118@gmail.com>
Date: Mon, 18 Aug 2025 23:39:39 +0300
Subject: [PATCH 17/18] comment

---
 codeflash/optimization/optimizer.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/codeflash/optimization/optimizer.py b/codeflash/optimization/optimizer.py
index 929b663b0..ce857f201 100644
--- a/codeflash/optimization/optimizer.py
+++ b/codeflash/optimization/optimizer.py
@@ -341,6 +341,7 @@ def run(self) -> None:
                             )
                         if is_successful(best_optimization):
                             optimizations_found += 1
+                            # create a diff patch for successful optimization
                             if self.current_worktree:
                                 read_writable_code = best_optimization.unwrap().code_context.read_writable_code
                                 relative_file_paths = [

From 7fccd601873e9f833b979087c4f0e55e3f8622f8 Mon Sep 17 00:00:00 2001
From: ali <mohammed18200118@gmail.com>
Date: Tue, 19 Aug 2025 03:42:46 +0300
Subject: [PATCH 18/18] fix linting issue

---
 codeflash/api/cfapi.py                       | 6 +++---
 codeflash/optimization/function_optimizer.py | 5 +++--
 codeflash/result/create_pr.py                | 2 +-
 3 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/codeflash/api/cfapi.py b/codeflash/api/cfapi.py
index ec0c4c708..25b155ddf 100644
--- a/codeflash/api/cfapi.py
+++ b/codeflash/api/cfapi.py
@@ -204,9 +204,9 @@ def create_staging(
     generated_original_test_source: str,
     function_trace_id: str,
     coverage_message: str,
-    replay_tests: str = "",
-    concolic_tests: str = "",
-    root_dir: Optional[Path] = None,
+    replay_tests: str,
+    concolic_tests: str,
+    root_dir: Path,
 ) -> Response:
     """Create a staging pull request, targeting the specified branch. (usually 'staging').
 
diff --git a/codeflash/optimization/function_optimizer.py b/codeflash/optimization/function_optimizer.py
index 3a16a843a..e719a9ebd 100644
--- a/codeflash/optimization/function_optimizer.py
+++ b/codeflash/optimization/function_optimizer.py
@@ -1244,15 +1244,16 @@ def process_review(
             "coverage_message": coverage_message,
             "replay_tests": replay_tests,
             "concolic_tests": concolic_tests,
+            "root_dir": self.project_root,
         }
 
         raise_pr = not self.args.no_pr
 
         if raise_pr and not self.args.staging_review:
             data["git_remote"] = self.args.git_remote
-            check_create_pr(**data, root_dir=self.project_root)
+            check_create_pr(**data)
         elif self.args.staging_review:
-            create_staging(**data, root_dir=self.project_root)
+            create_staging(**data)
         else:
             # Mark optimization success since no PR will be created
             mark_optimization_success(
diff --git a/codeflash/result/create_pr.py b/codeflash/result/create_pr.py
index fcac3580e..cf842125e 100644
--- a/codeflash/result/create_pr.py
+++ b/codeflash/result/create_pr.py
@@ -183,8 +183,8 @@ def check_create_pr(
     coverage_message: str,
     replay_tests: str,
     concolic_tests: str,
+    root_dir: Path,
     git_remote: Optional[str] = None,
-    root_dir: Optional[Path] = None,
 ) -> None:
     pr_number: Optional[int] = env_utils.get_pr_number()
     git_repo = git.Repo(search_parent_directories=True)