Stage only deleted files with git add

Same as the @steve answer, but adding a little change:

Add --all to the end of the command to add all the files returned by the ls-files command to the index

git ls-files --deleted | xargs git add --all

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).

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Git