test(codex): cover fresh-dir suppression of legacy .codex layout

Author: RbBtSn0w

src/specify_cli/__init__.py

@@ -1085,6 +1085,13 @@ def download_and_extract_template(
                     elif verbose:
                         console.print("[cyan]Flattened nested directory structure[/cyan]")
 
+                # For fresh-directory Codex skills init, suppress legacy
+                # prompt-based layout extracted from older archives.
+                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))

tests/test_ai_skills.py

@@ -11,6 +11,7 @@
 """
 
 import re
+import zipfile
 import pytest
 import tempfile
 import shutil
@@ -799,6 +800,36 @@ def test_codex_ai_skills_here_mode_preserves_existing_codex_dir(self, tmp_path,
         assert (target / ".codex").exists()
         assert (existing_prompts / "custom.md").exists()
 
+    def test_codex_ai_skills_fresh_dir_does_not_create_codex_dir(self, tmp_path):
+        """Fresh-directory Codex skills init should not leave legacy .codex from archive."""
+        target = tmp_path / "fresh-codex-proj"
+        archive = tmp_path / "codex-template.zip"
+
+        with zipfile.ZipFile(archive, "w") as zf:
+            zf.writestr("template-root/.codex/prompts/speckit.specify.md", "legacy")
+            zf.writestr("template-root/.specify/templates/constitution-template.md", "constitution")
+
+        fake_meta = {
+            "filename": archive.name,
+            "size": archive.stat().st_size,
+            "release": "vtest",
+            "asset_url": "https://example.invalid/template.zip",
+        }
+
+        with patch("specify_cli.download_template_from_github", return_value=(archive, fake_meta)):
+            specify_cli.download_and_extract_template(
+                target,
+                "codex",
+                "sh",
+                is_current_dir=False,
+                skip_legacy_codex_prompts=True,
+                verbose=False,
+            )
+
+        assert target.exists()
+        assert (target / ".specify").exists()
+        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)."""
         from typer.testing import CliRunner