fix(integration): preserve ai_skills on use for skills-mode Copilot (#3550) (#3551)

`specify integration use copilot` against a Copilot install configured with
`--integration-options "--skills"` dropped `"ai_skills": true` from
init-options.json and regenerated extension commands in the legacy
`.agent.md`/`.prompt.md` layout, contradicting `integration.json`'s stored
`parsed_options.skills: true`.

`_update_init_options_for_integration` only inspected `SkillsIntegration` /
the instance `_skills_mode` flag. On the `use` path no `setup()` runs, so the
freshly-resolved Copilot instance has `_skills_mode == False` and the stored
skills intent in `parsed_options` was ignored. Thread the resolved
`parsed_options` through and treat `parsed_options["skills"]` as skills mode.

Adds a regression test that resets the registry singleton's `_skills_mode` to
simulate a fresh process (in-process singleton reuse otherwise masks the bug).

Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous)


Copilot-Session: 06fb6ae9-f444-4dfd-ab3f-d0669c5d0604

Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com>

Author: mnriem

src/specify_cli/integrations/_helpers.py

@@ -260,6 +260,7 @@ def _update_init_options_for_integration(
     project_root: Path,
     integration: Any,
     script_type: str | None = None,
+    parsed_options: dict[str, Any] | None = None,
 ) -> None:
     """Update init-options.json to reflect *integration* as the active one.
 
@@ -278,7 +279,17 @@ def _update_init_options_for_integration(
     opts["speckit_version"] = _get_speckit_version()
     if script_type:
         opts["script"] = script_type
-    if isinstance(integration, SkillsIntegration) or getattr(integration, "_skills_mode", False):
+    # Skills mode is either intrinsic (SkillsIntegration), set on the instance
+    # during setup() (_skills_mode), or requested via parsed options (e.g.
+    # Copilot's --skills, persisted as parsed_options["skills"]). The latter is
+    # the only signal available on the `use` path, where no setup() runs and a
+    # fresh integration instance has _skills_mode == False (issue #3550).
+    skills_mode = (
+        isinstance(integration, SkillsIntegration)
+        or getattr(integration, "_skills_mode", False)
+        or bool((parsed_options or {}).get("skills"))
+    )
+    if skills_mode:
         opts["ai_skills"] = True
     else:
         opts.pop("ai_skills", None)
@@ -334,7 +345,9 @@ def _set_default_integration(
             ) from exc
 
     _write_integration_json(project_root, key, installed_keys, settings)
-    _update_init_options_for_integration(project_root, integration, script_type=resolved_script)
+    _update_init_options_for_integration(
+        project_root, integration, script_type=resolved_script, parsed_options=parsed_options
+    )
 
 
 def _set_default_integration_or_exit(*args: Any, **kwargs: Any) -> None:

tests/integrations/test_integration_subcommand.py

@@ -1566,6 +1566,43 @@ def test_use_installed_integration_sets_default(self, tmp_path):
         assert opts["integration"] == "codex"
         assert opts["ai"] == "codex"
 
+    def test_use_preserves_copilot_skills_mode(self, tmp_path):
+        """`use` on a skills-mode Copilot keeps ``ai_skills`` (issue #3550).
+
+        Re-selecting the same skills-mode Copilot must not drop ``ai_skills``
+        from init-options.json nor regenerate extension commands in the legacy
+        ``.agent.md``/``.prompt.md`` layout.
+        """
+        project = _init_project(tmp_path, "copilot", integration_options="--skills")
+
+        opts = json.loads((project / ".specify" / "init-options.json").read_text(encoding="utf-8"))
+        assert opts.get("ai_skills") is True, "precondition: init recorded skills mode"
+
+        result = _run_in_project(project, ["extension", "add", "git"])
+        assert result.exit_code == 0, f"extension add failed: {result.output}"
+
+        # Simulate a fresh process: `use` in real life runs in its own process
+        # where the registry's Copilot instance has _skills_mode == False (it is
+        # only set during setup()). In-process test invocations otherwise reuse
+        # the singleton left in skills mode by init, masking the bug (#3550).
+        from specify_cli.integrations import get_integration
+
+        get_integration("copilot")._skills_mode = False
+
+        result = _run_in_project(project, ["integration", "use", "copilot"])
+        assert result.exit_code == 0, result.output
+
+        opts = json.loads((project / ".specify" / "init-options.json").read_text(encoding="utf-8"))
+        assert opts.get("ai_skills") is True, "ai_skills must survive `use copilot`"
+
+        # No legacy command-layout files should be regenerated for the
+        # skills-mode agent.
+        assert not (project / ".github" / "agents" / "speckit.git.feature.agent.md").exists()
+        assert not (project / ".github" / "prompts" / "speckit.git.feature.prompt.md").exists()
+        assert (
+            project / ".github" / "skills" / "speckit-git-feature" / "SKILL.md"
+        ).exists()
+
     def test_use_requires_installed_integration(self, tmp_path):
         project = _init_project(tmp_path, "claude")
         old_cwd = os.getcwd()