fix(presets): create skill overrides when skills_source is marketplace

When a project had `"skills_source": "marketplace"` in integration.json
alongside `"ai_skills": false` in init-options.json, `_register_skills()`
silently skipped writing the local SKILL.md override.  Two guards both
needed relaxing:

1. `_get_skills_dir()` returned None early for non-kimi agents when
   ai_skills was false, so _register_skills never reached the
   create_missing_skills check at all.
2. `create_missing_skills` was gated on `ai_skills_enabled`, so even
   if the skills dir existed the new skill file would not be created.

For marketplace-sourced projects a local SKILL.md is required to shadow
the marketplace plugin version.  Both checks now treat ai_skills as
effectively enabled when skills_source == "marketplace".

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: echarrod

src/specify_cli/presets.py

@@ -1109,7 +1109,7 @@ def _get_skills_dir(self) -> Optional[Path]:
             The skills directory ``Path``, or ``None`` if skills were not
             enabled and no native-skills fallback applies.
         """
-        from . import load_init_options, _get_skills_dir
+        from . import load_init_options, _get_skills_dir, _read_integration_json
 
         opts = load_init_options(self.project_root)
         if not isinstance(opts, dict):
@@ -1119,7 +1119,9 @@ def _get_skills_dir(self) -> Optional[Path]:
             return None
 
         ai_skills_enabled = bool(opts.get("ai_skills"))
-        if not ai_skills_enabled and agent != "kimi":
+        integration_data = _read_integration_json(self.project_root)
+        skills_source = integration_data.get("skills_source")
+        if not ai_skills_enabled and agent != "kimi" and skills_source != "marketplace":
             return None
 
         skills_dir = _get_skills_dir(self.project_root, agent)
@@ -1244,7 +1246,7 @@ def _register_skills(
         if not skills_dir:
             return []
 
-        from . import SKILL_DESCRIPTIONS, load_init_options
+        from . import SKILL_DESCRIPTIONS, load_init_options, _read_integration_json
         from .agents import CommandRegistrar
         from .integrations import get_integration
 
@@ -1255,14 +1257,20 @@ def _register_skills(
         if not isinstance(selected_ai, str):
             return []
         ai_skills_enabled = bool(init_opts.get("ai_skills"))
+        integration_data = _read_integration_json(self.project_root)
+        skills_source = integration_data.get("skills_source")
+        # When skills_source is "marketplace" the user needs a local SKILL.md to
+        # shadow the marketplace plugin version, so treat ai_skills as effectively
+        # enabled regardless of the init-options flag.
+        ai_skills_effective = ai_skills_enabled or skills_source == "marketplace"
         registrar = CommandRegistrar()
         integration = get_integration(selected_ai)
         agent_config = registrar.AGENT_CONFIGS.get(selected_ai, {})
         # Native skill agents (e.g. codex/kimi/agy/trae) 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"
+        create_missing_skills = ai_skills_effective and agent_config.get("extension") != "/SKILL.md"
 
         written: List[str] = []
 

tests/test_presets.py

@@ -2289,6 +2289,39 @@ def test_skill_not_updated_when_ai_skills_disabled(self, project_dir, temp_dir):
         content = skill_file.read_text()
         assert "untouched" in content, "Skill should not be modified when ai_skills=False"
 
+    def test_skill_created_when_ai_skills_false_but_marketplace_source(self, project_dir, temp_dir):
+        """When ai_skills is False but skills_source is 'marketplace', skill override IS created.
+
+        A marketplace-integrated project sets skills_source=marketplace in integration.json
+        and ai_skills=false in init-options.json.  The preset install must still write a
+        local SKILL.md so the local file can shadow the marketplace plugin skill.
+        """
+        import json as _json
+
+        # ai_skills disabled, but integration.json declares marketplace as the source
+        self._write_init_options(project_dir, ai="claude", ai_skills=False)
+        specify_dir = project_dir / ".specify"
+        specify_dir.mkdir(parents=True, exist_ok=True)
+        integration_json = specify_dir / "integration.json"
+        integration_json.write_text(
+            _json.dumps({"skills_source": "marketplace", "integration_state_schema": 1})
+        )
+
+        # The parent skills dir must exist for _get_skills_dir() to return it,
+        # but the specific skill subdir must NOT exist yet (create_missing_skills path).
+        skills_dir = project_dir / ".claude" / "skills"
+        skills_dir.mkdir(parents=True, exist_ok=True)
+
+        manager = PresetManager(project_dir)
+        install_self_test_preset(manager)
+
+        skill_file = skills_dir / "speckit-specify" / "SKILL.md"
+        assert skill_file.exists(), (
+            "SKILL.md should be created for marketplace projects even when ai_skills=False"
+        )
+        content = skill_file.read_text()
+        assert "preset:self-test" in content, "Skill should reference preset source"
+
     def test_get_skills_dir_returns_none_for_non_string_ai(self, project_dir):
         """Corrupted init-options ai values should not crash preset skill resolution."""
         init_options = project_dir / ".specify" / "init-options.json"