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/base.py

@@ -393,6 +393,18 @@ class IntegrationBase(ABC):
         """
         return f"speckit.{template_name}.md"
 
+    def stale_cleanup_exclusions(self) -> set[str]:
+        """Return project-relative paths that upgrade must never stale-delete.
+
+        During ``integration upgrade``, files recorded in a previous manifest
+        but absent from the freshly written one are treated as stale and
+        removed.  Conditionally-tracked files (e.g. a settings file that the
+        integration merges into when it already exists, and therefore stops
+        tracking) would otherwise be deleted even though they are still
+        managed.  Subclasses list such paths here to protect them.
+        """
+        return set()
+
     def commands_dest(self, project_root: Path) -> Path:
         """Return the absolute path to the commands output directory.