fix(codex): preserve existing .codex while skipping legacy prompt extraction

Author: RbBtSn0w

src/specify_cli/__init__.py

@@ -1031,6 +1031,10 @@ def download_and_extract_template(
                             console.print("[cyan]Found nested directory structure[/cyan]")
 
                     for item in source_dir.iterdir():
+                        # In Codex skills mode, do not materialize legacy prompt
+                        # templates under .codex/prompts.
+                        if skip_legacy_codex_prompts and ai_assistant == "codex" and item.name == ".codex":
+                            continue
                         dest_path = project_path / item.name
                         if item.is_dir():
                             if dest_path.exists():
@@ -2112,14 +2116,6 @@ def init(
                                     # so leaving stale commands is non-fatal.
                                     console.print("[yellow]Warning: could not remove extracted commands directory[/yellow]")
 
-            # In Codex skills mode, remove legacy prompt layout after skills
-            # installation/fallback completes so prompt artifacts are not left
-            # behind in the project tree.
-            if selected_ai == "codex" and ai_skills:
-                legacy_codex_dir = project_path / ".codex"
-                if legacy_codex_dir.is_dir():
-                    shutil.rmtree(legacy_codex_dir, ignore_errors=True)
-
             if not no_git:
                 tracker.start("git")
                 if is_git_repo(project_path):

tests/test_ai_skills.py

@@ -770,49 +770,20 @@ def fake_download(project_path, *args, **kwargs):
         assert result.exit_code == 0
         mock_skills.assert_called_once()
         assert mock_skills.call_args.kwargs.get("overwrite_existing") is True
-        assert not (target / ".codex").exists()
 
-    def test_codex_ai_skills_removes_legacy_codex_dir_after_fallback(self, tmp_path):
-        """Codex skills init should not leave legacy .codex prompt directory behind."""
+    def test_codex_ai_skills_here_mode_preserves_existing_codex_dir(self, tmp_path, monkeypatch):
+        """Codex --here skills init should not delete a pre-existing .codex directory."""
         from typer.testing import CliRunner
 
         runner = CliRunner()
-        target = tmp_path / "codex-cleanup-new"
-
-        def fake_download(project_path, *args, **kwargs):
-            prompts_dir = project_path / ".codex" / "prompts"
-            prompts_dir.mkdir(parents=True, exist_ok=True)
-            (prompts_dir / "speckit.specify.md").write_text("---\ndescription: Legacy prompt\n---\n\nBody.\n")
-
-        with patch("specify_cli.download_and_extract_template", side_effect=fake_download), \
-             patch("specify_cli.ensure_executable_scripts"), \
-             patch("specify_cli.ensure_constitution_from_template"), \
-             patch("specify_cli.install_ai_skills", return_value=True), \
-             patch("specify_cli.is_git_repo", return_value=False), \
-             patch("specify_cli.shutil.which", return_value="/usr/bin/codex"):
-            result = runner.invoke(
-                app,
-                ["init", str(target), "--ai", "codex", "--ai-skills", "--script", "sh", "--no-git"],
-            )
-
-        assert result.exit_code == 0
-        assert not (target / ".codex").exists()
-
-    def test_codex_ai_skills_here_mode_removes_legacy_codex_dir(self, tmp_path, monkeypatch):
-        """Codex --here skills init should not leave legacy .codex prompt directory behind."""
-        from typer.testing import CliRunner
-
-        runner = CliRunner()
-        target = tmp_path / "codex-cleanup-here"
+        target = tmp_path / "codex-preserve-here"
         target.mkdir()
+        existing_prompts = target / ".codex" / "prompts"
+        existing_prompts.mkdir(parents=True)
+        (existing_prompts / "custom.md").write_text("custom")
         monkeypatch.chdir(target)
 
-        def fake_download(project_path, *args, **kwargs):
-            prompts_dir = project_path / ".codex" / "prompts"
-            prompts_dir.mkdir(parents=True, exist_ok=True)
-            (prompts_dir / "speckit.specify.md").write_text("---\ndescription: Legacy prompt\n---\n\nBody.\n")
-
-        with patch("specify_cli.download_and_extract_template", side_effect=fake_download), \
+        with patch("specify_cli.download_and_extract_template", return_value=target), \
              patch("specify_cli.ensure_executable_scripts"), \
              patch("specify_cli.ensure_constitution_from_template"), \
              patch("specify_cli.install_ai_skills", return_value=True), \
@@ -825,7 +796,8 @@ def fake_download(project_path, *args, **kwargs):
             )
 
         assert result.exit_code == 0
-        assert not (target / ".codex").exists()
+        assert (target / ".codex").exists()
+        assert (existing_prompts / "custom.md").exists()
 
     def test_commands_preserved_when_skills_fail(self, tmp_path):
         """If skills fail, commands should NOT be removed (safety net)."""