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The cleanup step deletes any file the shipped manifest does not list outside the protected prefixes. A SQLite database kept under database/ (a path the installer accepts) is user state that can never appear in a manifest, so an update destroyed it. The keep-list now always includes the resolved database file of every in-installation SQLite connection, plus its -wal/-shm/-journal side files. Found by the 3.0.0-alpha.2 -> alpha.3 upgrade rehearsal.