feat(copilot): warn before skills default rollout (#3256)

* feat(copilot): default to skills mode

* feat(copilot): warn before skills default rollout

* Make Copilot skills warning test less brittle

---------

Co-authored-by: root <kinsonnee@gmail.com>

src/specify_cli/integrations/copilot/__init__.py

@@ -57,6 +57,17 @@ def _allow_all() -> bool:
     return True
 
 
+def _warn_legacy_markdown_default() -> None:
+    """Warn that Copilot's default markdown scaffold is being phased out."""
+    warnings.warn(
+        "Copilot legacy markdown mode is deprecated and will stop being the "
+        'default in a future Spec Kit release; pass --integration-options "--skills" '
+        "to opt in to Copilot skills mode now.",
+        UserWarning,
+        stacklevel=3,
+    )
+
+
 class _CopilotSkillsHelper(SkillsIntegration):
     """Internal helper used when Copilot is scaffolded in skills mode.
 
@@ -316,6 +327,8 @@ class CopilotIntegration(IntegrationBase):
         self._skills_mode = bool(parsed_options.get("skills"))
         if self._skills_mode:
             return self._setup_skills(project_root, manifest, parsed_options, **opts)
+        if "skills" not in parsed_options:
+            _warn_legacy_markdown_default()
         return self._setup_default(project_root, manifest, parsed_options, **opts)
 
     def _setup_default(