Function write_managed_skill_file_manifest 

pub fn write_managed_skill_file_manifest(
    base_path: &Path,
    new_managed_paths: &BTreeSet<String>,
)

Record new_managed_paths as the manifest for the NEXT call to cleanup_stale_managed_skill_files. Best-effort: a write failure is logged, not propagated — losing this write only means the next materialization’s stale-file cleanup is skipped once, not a correctness issue for the current one.