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

src/specify_cli/integrations/_migrate_commands.py

@@ -2,6 +2,7 @@
 from __future__ import annotations
 
 import os
+from pathlib import PurePath
 
 import typer
 
@@ -461,6 +462,9 @@ 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:
@@ -478,7 +482,13 @@ 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
-    stale_keys = set(old_files) - set(new_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.  Manifest keys are stored
+    # in POSIX form, so normalize the exclusions the same way before subtracting
+    # (an integration may build paths with os.path.join / backslashes).
+    exclusions = {PurePath(p).as_posix() for p in integration.stale_cleanup_exclusions()}
+    stale_keys = (set(old_files) - set(new_files)) - exclusions
     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

@@ -393,6 +393,18 @@ 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

@@ -282,6 +282,17 @@ 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

@@ -2272,6 +2272,58 @@ 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"
+
+        # Simulate a user editing their settings: add a custom key that the
+        # integration does not manage.  It must survive the upgrade.
+        before["editor.fontSize"] = 17
+        settings.write_text(json.dumps(before), encoding="utf-8")
+
+        result = _run_in_project(project, [
+            "integration", "upgrade", "copilot",
+            "--script", "sh", "--force",
+        ])
+        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.get("editor.fontSize") == 17, (
+            "user-defined settings must be preserved 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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