Data updater does not delete removed files

Recently, after removing Proton 5.21 from chimera-data, the data updater successfully updated the data, however, it did not delete the removed files.

The data updater should remove files that are no longer in the chimera-data repo.

Locate the data updater entry point and trace how it synchronizes files from the chimera-data repository. Reproduce the update after a source file is removed, then verify that the corresponding local file is also removed and that existing update behavior still works.

Written by the indexing model from the issue text.