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* 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>