Function prune_missing_in 

pub fn prune_missing_in(cache_dir: &Path) -> usize

Remove the entry file for every registered root whose project_root no longer exists on disk, plus every entry file that cannot be parsed at all (so unreadable files cannot accumulate forever), returning the number of files removed. Removal is per-file remove_file; there is no rewrite of surviving entries, so pruning cannot disturb a registration written concurrently with it. Deliberately NOT called from load_roots_in — that must stay side-effect-free so a read-only command cannot mutate machine state; callers invoke this explicitly.