Function prune_once 

pub(crate) fn prune_once(id_store: &Store) -> usize

One pass: prune every (agent_id, filename) pair that has any recorded version history. Returns the number of version rows deleted (for logging; tests assert on it directly). A failure listing targets or pruning one file is logged and does not stop the sweep from covering everything else — matches native_memory_drift’s own per-item error handling.