Removing multiple files from a Git repo that have already been deleted from disk
For Git 1.x
$ git add -u
This tells git to automatically stage tracked files -- including deleting the previously tracked files.
For Git 2.0
To stage your whole working tree:
$ git add -u :/
To stage just the current path:
$ git add -u .
git ls-files --deleted -z | xargs -0 git rm
might be what you are looking for.. it works for me..
You can use
git add -u
To add the deleted files to the staging area, then commit them
git commit -m "Deleted files manually"