The 'make clean' command attempts to clean various intermediate LaTeX files, including all files with extension idx. It happens that idx files are also an internal file extension for Git, and the current command deletes those as well. On my machine any use of the 'make clean' command resulted in a corrupted local Git repository.
(more specifically the file ./.git/objects/pack/pack-c49c1de4ceec35c76b288915398aea0f2d87bfa1.idx)
This corrected 'make clean' ensures no file from the .git repository is ever deleted.