fix: preserve .vscode/settings.json and script +x bit on integration upgrade (#3020)

* fix: preserve .vscode/settings.json and script +x bit on integration upgrade

During 'specify integration upgrade', Phase 2 stale-cleanup removes files
present in the old manifest but absent from the new one. Copilot's setup()
merges into an existing .vscode/settings.json and stops tracking it, so the
file was being deleted on upgrade (destroying user settings). Add a
stale_cleanup_exclusions() hook that integrations use to protect such
conditionally-tracked merge targets. Also restore the executable bit on
shared .sh scripts after the managed-refresh step on POSIX.

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

* fix: address review on stale-cleanup fix

- Normalize stale_cleanup_exclusions() to POSIX before subtracting from
  manifest keys, so exclusions built with os.path.join / backslashes still
  match on Windows.
- Strengthen test_upgrade_preserves_existing_vscode_settings to add a
  user-defined key and assert it survives the upgrade (via --force, exercising
  the merge + stale-cleanup path) instead of the brittle after == before check.

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

---------

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

src/specify_cli/integrations/copilot/__init__.py

@@ -282,6 +282,17 @@ class CopilotIntegration(IntegrationBase):
         """Copilot commands use ``.agent.md`` extension."""
         return f"speckit.{template_name}.agent.md"
 
+    def stale_cleanup_exclusions(self) -> set[str]:
+        """Protect ``.vscode/settings.json`` from upgrade stale-deletion.
+
+        ``setup()`` records this file in the manifest only when it creates it;
+        when it already exists the file is merged and intentionally left
+        untracked.  On upgrade the untracked-but-existing file would otherwise
+        be flagged stale and deleted, destroying user settings (and the file
+        the integration still manages).
+        """
+        return {".vscode/settings.json"}
+
     def post_process_skill_content(self, content: str) -> str:
         """Inject shared hook guidance into Copilot skill content.