The build_from_json label pass only covered the clustered/update paths; the raw
`extract --no-cluster` path writes the merged node list directly, so colliding
basenames stayed un-disambiguated there. Factor the logic into a shared
_file_label_reassignments core with a list-based variant
(disambiguate_file_labels_in_nodes) and apply it on the raw merged nodes.
Caught by the clean-venv edge-case battery.