fix(codex): defer legacy .codex cleanup until after skills fallback

Author: RbBtSn0w

src/specify_cli/__init__.py

@@ -1031,10 +1031,6 @@ def download_and_extract_template(
                             console.print("[cyan]Found nested directory structure[/cyan]")
 
                     for item in source_dir.iterdir():
-                        # Codex skills mode should not materialize legacy prompt files
-                        # from older template archives.
-                        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():
@@ -1085,11 +1081,6 @@ def download_and_extract_template(
                     elif verbose:
                         console.print("[cyan]Flattened nested directory structure[/cyan]")
 
-                if skip_legacy_codex_prompts and ai_assistant == "codex":
-                    legacy_codex_dir = project_path / ".codex"
-                    if legacy_codex_dir.is_dir():
-                        shutil.rmtree(legacy_codex_dir, ignore_errors=True)
-
     except Exception as e:
         if tracker:
             tracker.error("extract", str(e))
@@ -2121,6 +2112,14 @@ 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

@@ -770,6 +770,62 @@ 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."""
+        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.mkdir()
+        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), \
+             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=True), \
+             patch("specify_cli.shutil.which", return_value="/usr/bin/codex"):
+            result = runner.invoke(
+                app,
+                ["init", "--here", "--ai", "codex", "--ai-skills", "--script", "sh", "--no-git"],
+                input="y\n",
+            )
+
+        assert result.exit_code == 0
+        assert not (target / ".codex").exists()
 
     def test_commands_preserved_when_skills_fail(self, tmp_path):
         """If skills fail, commands should NOT be removed (safety net)."""