If you have a mix of modified and deleted files and only want to stage deleted files to the index, you can use git ls-files as a filter.
git ls-files --deleted | xargs git add
If you only want this to apply to part of the file tree, give one or more subdirectories as arguments to ls-files:
git ls-files --deleted -- lib/foo | xargs git add
To do the same for only modified files, use the --modified (-m) option instead of --deleted (-d).