chore: split out unrelated integration-upgrade fix

Move the stale_cleanup_exclusions / executable-bit upgrade fix
(base.py, copilot, _migrate_commands.py, test_integration_subcommand.py)
out of this PR into its own change. This PR is now scoped purely to the
/speckit.converge command.

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

Author: BenBtg

src/specify_cli/integrations/_migrate_commands.py

@@ -461,9 +461,6 @@ def integration_upgrade(
                 raise _SharedTemplateRefreshError(
                     f"Failed to refresh shared infrastructure for '{key}': {exc}"
                 ) from exc
-            if os.name != "nt":
-                from .. import ensure_executable_scripts
-                ensure_executable_scripts(project_root)
         new_manifest.save()
         _write_integration_json(project_root, installed_key, installed_keys, settings)
         if installed_key == key:
@@ -481,10 +478,7 @@ def integration_upgrade(
     # Phase 2: Remove stale files from old manifest that are not in the new one
     old_files = old_manifest.files
     new_files = new_manifest.files
-    # Exclude integration-declared paths that use conditional manifest tracking
-    # (e.g. merge targets like .vscode/settings.json) so they are never deleted
-    # as "stale" while still being actively managed.
-    stale_keys = (set(old_files) - set(new_files)) - integration.stale_cleanup_exclusions()
+    stale_keys = set(old_files) - set(new_files)
     if stale_keys:
         stale_manifest = IntegrationManifest(key, project_root, version="stale-cleanup")
         stale_manifest._files = {k: old_files[k] for k in stale_keys}

src/specify_cli/integrations/base.py

@@ -393,18 +393,6 @@ def command_filename(self, template_name: str) -> str:
         """
         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.
 

src/specify_cli/integrations/copilot/__init__.py

@@ -282,17 +282,6 @@ def command_filename(self, template_name: str) -> str:
         """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.
 

tests/integrations/test_integration_subcommand.py

@@ -2272,51 +2272,6 @@ def test_upgrade_migrates_opencode_legacy_dir(self, tmp_path):
             f"found: {[f.name for f in core_remaining]}"
         )
 
-    def test_upgrade_preserves_existing_vscode_settings(self, tmp_path):
-        """Regression: copilot upgrade must not stale-delete .vscode/settings.json.
-
-        On init the file is created and recorded in the manifest. On upgrade,
-        setup() merges into the now-existing file and intentionally stops
-        tracking it, so without ``stale_cleanup_exclusions()`` the Phase 2
-        stale cleanup would delete it (destroying the user's settings).
-        """
-        project = _init_project(tmp_path, "copilot")
-        settings = project / ".vscode" / "settings.json"
-        assert settings.is_file(), "init should create .vscode/settings.json"
-        before = json.loads(settings.read_text(encoding="utf-8"))
-        assert before, "settings.json should contain managed defaults"
-
-        result = _run_in_project(project, [
-            "integration", "upgrade", "copilot",
-            "--script", "sh",
-        ])
-        assert result.exit_code == 0, result.output
-
-        assert settings.is_file(), ".vscode/settings.json must survive upgrade"
-        after = json.loads(settings.read_text(encoding="utf-8"))
-        assert after == before, "managed settings must be intact after upgrade"
-
-    def test_upgrade_restores_executable_bit_on_shared_scripts(self, tmp_path):
-        """Regression: scripts refreshed by the managed-refresh step stay +x."""
-        if os.name == "nt":
-            pytest.skip("POSIX execute bits are not meaningful on Windows")
-        project = _init_project(tmp_path, "copilot")
-        script = project / ".specify" / "scripts" / "bash" / "check-prerequisites.sh"
-        assert script.is_file()
-        # Simulate a perms-losing install (e.g. wheel extraction dropping +x).
-        script.chmod(0o644)
-        assert not (script.stat().st_mode & 0o111)
-
-        result = _run_in_project(project, [
-            "integration", "upgrade", "copilot",
-            "--script", "sh",
-        ])
-        assert result.exit_code == 0, result.output
-
-        assert script.stat().st_mode & 0o111, (
-            "shared .sh scripts must be executable after upgrade"
-        )
-
 
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