exclude deleted files in the fixup script
# What does this PR do?

Running `make fixup` after a file is deleted on a branch causes `black` to exit with an error. 

`Error: Invalid value for 'SRC ...': Path /path/to/deleted/file' does not exist.`

This PR resolves the error by setting the `git diff` flag `--diff-filter=d` to exclude deleted files from the list of modified files.
_The documentation is not available anymore as the PR was closed or merged._