fix: handle deleted files in stage() — use git rm for missing paths

devgen/modules/diff_builder.py

@@ -128,7 +128,7 @@ class FileGrouper:
             deepest = max(candidates, key=lambda p: len(Path(p).parts))
             parent_path = str(Path(deepest).parent)
             new_key = "root" if parent_path == "." else parent_path
-            groups[new_key].extend(groups.pop(deepest))
+            groups.setdefault(new_key, []).extend(groups.pop(deepest))
         return groups
 
 

devgen/modules/git_ops.py

@@ -105,11 +105,16 @@ class GitOperator:
     # ------------------------------------------------------------------ actions
 
     def stage(self, files: list[str]) -> None:
-        """``git add`` the given paths."""
+        """Stage the given paths — ``git add`` for existing files, ``git rm`` for deleted."""
         if not files:
             return
+        existing = [f for f in files if Path(self.cwd or ".").joinpath(f).exists()]
+        deleted = [f for f in files if f not in existing]
         try:
-            self._run(["git", "add", *files])
+            if existing:
+                self._run(["git", "add", *existing])
+            if deleted:
+                self._run(["git", "rm", *deleted])
         except GitError as e:
             raise GitError(f"Could not stage files: {e}") from e
 

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "devgen-cli"
-version = "0.2.5"
+version = "0.2.7"
 description = "A collection of developer tools"
 readme = "README.md"
 requires-python = ">=3.10"

setup.py

@@ -6,7 +6,7 @@ from setuptools import find_packages, setup
 
 setup(
     name="devgen-cli",
-    version="0.2.5",
+    version="0.2.7",
     packages=find_packages(),
     include_package_data=True,
     install_requires=[

uv.lock

@@ -180,7 +180,7 @@ wheels = [
 
 [[package]]
 name = "devgen-cli"
-version = "0.2.5"
+version = "0.2.7"
 source = { editable = "." }
 dependencies = [
     { name = "anthropic" },