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