diff --git a/pkgs/clan-cli/clan_cli/config/__init__.py b/pkgs/clan-cli/clan_cli/config/__init__.py
index d74d2db4..cc119a91 100644
--- a/pkgs/clan-cli/clan_cli/config/__init__.py
+++ b/pkgs/clan-cli/clan_cli/config/__init__.py
@@ -231,10 +231,10 @@ def set_option(
     settings_file.parent.mkdir(parents=True, exist_ok=True)
     with open(settings_file, "w") as f:
         json.dump(new_config, f, indent=2)
-        if settings_file.resolve().is_relative_to(get_clan_flake_toplevel()):
-            commit_file(
-                settings_file, commit_message=f"Set option {option_description}"
-            )
+        print(file=f)  # add newline at the end of the file to make git happy
+
+    if settings_file.resolve().is_relative_to(get_clan_flake_toplevel()):
+        commit_file(settings_file, commit_message=f"Set option {option_description}")
 
 
 # takes a (sub)parser and configures it
diff --git a/pkgs/clan-cli/clan_cli/git.py b/pkgs/clan-cli/clan_cli/git.py
index 72db4c11..12ba4df5 100644
--- a/pkgs/clan-cli/clan_cli/git.py
+++ b/pkgs/clan-cli/clan_cli/git.py
@@ -48,7 +48,7 @@ def _commit_file_to_git(repo_dir: Path, file_path: Path, commit_message: str) ->
     )
     # add the file to the git index
     try:
-        subprocess.run(cmd, cwd=repo_dir, check=True)
+        subprocess.run(cmd, check=True)
     except subprocess.CalledProcessError as e:
         raise ClanError(
             f"Failed to add {file_path} to git repository {repo_dir}:\n{shlex.join(cmd)}\n exited with {e.returncode}"
@@ -80,7 +80,6 @@ def _commit_file_to_git(repo_dir: Path, file_path: Path, commit_message: str) ->
     try:
         subprocess.run(
             cmd,
-            cwd=repo_dir,
             check=True,
         )
     except subprocess.CalledProcessError as e: