Fix native skill preset cleanup

Author: afurm

src/specify_cli/integrations/claude/__init__.py

@@ -71,7 +71,7 @@ def setup(
                 f"project_root ({project_root_resolved})"
             )
 
-        dest = self.commands_dest(project_root).resolve()
+        dest = self.skills_dest(project_root).resolve()
         try:
             dest.relative_to(project_root_resolved)
         except ValueError as exc:

src/specify_cli/presets.py

@@ -717,6 +717,10 @@ def _register_skills(
         ai_skills_enabled = bool(init_opts.get("ai_skills"))
         registrar = CommandRegistrar()
         agent_config = registrar.AGENT_CONFIGS.get(selected_ai, {})
+        # Native skill agents (e.g. codex/kimi/agy) materialize brand-new
+        # preset skills in _register_commands() because their detected agent
+        # directory is already the skills directory. This flag is only for
+        # command-backed agents that also mirror commands into skills.
         create_missing_skills = ai_skills_enabled and agent_config.get("extension") != "/SKILL.md"
 
         written: List[str] = []
@@ -1042,14 +1046,15 @@ def remove(self, pack_id: str) -> bool:
         if registered_skills:
             self._unregister_skills(registered_skills, pack_dir)
             try:
-                from . import NATIVE_SKILLS_AGENTS
+                from .agents import CommandRegistrar
             except ImportError:
-                NATIVE_SKILLS_AGENTS = set()
-            registered_commands = {
-                agent_name: cmd_names
-                for agent_name, cmd_names in registered_commands.items()
-                if agent_name not in NATIVE_SKILLS_AGENTS
-            }
+                CommandRegistrar = None
+            if CommandRegistrar is not None:
+                registered_commands = {
+                    agent_name: cmd_names
+                    for agent_name, cmd_names in registered_commands.items()
+                    if CommandRegistrar.AGENT_CONFIGS.get(agent_name, {}).get("extension") != "/SKILL.md"
+                }
 
         # Unregister non-skill command files from AI agents.
         if registered_commands:

tests/test_presets.py

@@ -2352,6 +2352,55 @@ def test_kimi_skill_updated_even_when_ai_skills_disabled(self, project_dir, temp
         metadata = manager.registry.get("self-test")
         assert "speckit-specify" in metadata.get("registered_skills", [])
 
+    def test_kimi_new_skill_created_even_when_ai_skills_disabled(self, project_dir, temp_dir):
+        """Kimi native skills should still receive brand-new preset commands."""
+        self._write_init_options(project_dir, ai="kimi", ai_skills=False)
+        skills_dir = project_dir / ".kimi" / "skills"
+        skills_dir.mkdir(parents=True, exist_ok=True)
+
+        preset_dir = temp_dir / "kimi-new-skill"
+        preset_dir.mkdir()
+        (preset_dir / "commands").mkdir()
+        (preset_dir / "commands" / "speckit.research.md").write_text(
+            "---\n"
+            "description: Kimi research workflow\n"
+            "---\n\n"
+            "preset:kimi-new-skill\n"
+        )
+        manifest_data = {
+            "schema_version": "1.0",
+            "preset": {
+                "id": "kimi-new-skill",
+                "name": "Kimi New Skill",
+                "version": "1.0.0",
+                "description": "Test",
+            },
+            "requires": {"speckit_version": ">=0.1.0"},
+            "provides": {
+                "templates": [
+                    {
+                        "type": "command",
+                        "name": "speckit.research",
+                        "file": "commands/speckit.research.md",
+                    }
+                ]
+            },
+        }
+        with open(preset_dir / "preset.yml", "w") as f:
+            yaml.dump(manifest_data, f)
+
+        manager = PresetManager(project_dir)
+        manager.install_from_directory(preset_dir, "0.1.5")
+
+        skill_file = skills_dir / "speckit-research" / "SKILL.md"
+        assert skill_file.exists()
+        content = skill_file.read_text()
+        assert "preset:kimi-new-skill" in content
+        assert "name: speckit-research" in content
+
+        metadata = manager.registry.get("kimi-new-skill")
+        assert "speckit-research" in metadata.get("registered_skills", [])
+
     def test_kimi_preset_skill_override_resolves_script_placeholders(self, project_dir, temp_dir):
         """Kimi preset skill overrides should resolve placeholders and rewrite project paths."""
         self._write_init_options(project_dir, ai="kimi", ai_skills=False, script="sh")
@@ -2404,6 +2453,63 @@ def test_kimi_preset_skill_override_resolves_script_placeholders(self, project_d
         assert ".specify/memory/constitution.md" in content
         assert "for kimi" in content
 
+    def test_agy_skill_restored_on_preset_remove(self, project_dir, temp_dir):
+        """Agy preset removal should restore native skills instead of deleting them."""
+        self._write_init_options(project_dir, ai="agy", ai_skills=True)
+        skills_dir = project_dir / ".agent" / "skills"
+        self._create_skill(skills_dir, "speckit-specify", body="before override")
+
+        core_command = project_dir / ".specify" / "templates" / "commands" / "specify.md"
+        core_command.write_text(
+            "---\n"
+            "description: Restored core specify workflow\n"
+            "---\n\n"
+            "restored core body\n"
+        )
+
+        preset_dir = temp_dir / "agy-override"
+        preset_dir.mkdir()
+        (preset_dir / "commands").mkdir()
+        (preset_dir / "commands" / "speckit.specify.md").write_text(
+            "---\n"
+            "description: Agy override\n"
+            "---\n\n"
+            "preset agy body\n"
+        )
+        manifest_data = {
+            "schema_version": "1.0",
+            "preset": {
+                "id": "agy-override",
+                "name": "Agy Override",
+                "version": "1.0.0",
+                "description": "Test",
+            },
+            "requires": {"speckit_version": ">=0.1.0"},
+            "provides": {
+                "templates": [
+                    {
+                        "type": "command",
+                        "name": "speckit.specify",
+                        "file": "commands/speckit.specify.md",
+                    }
+                ]
+            },
+        }
+        with open(preset_dir / "preset.yml", "w") as f:
+            yaml.dump(manifest_data, f)
+
+        manager = PresetManager(project_dir)
+        manager.install_from_directory(preset_dir, "0.1.5")
+
+        skill_file = skills_dir / "speckit-specify" / "SKILL.md"
+        assert "preset agy body" in skill_file.read_text()
+
+        assert manager.remove("agy-override") is True
+        assert skill_file.exists()
+        restored = skill_file.read_text()
+        assert "restored core body" in restored
+        assert "name: speckit-specify" in restored
+
     def test_preset_skill_registration_handles_non_dict_init_options(self, project_dir, temp_dir):
         """Non-dict init-options payloads should not crash preset install/remove flows."""
         init_options = project_dir / ".specify" / "init-options.json"