When working with Git it can be cumbersome to have to remove files from the index (marking them deleted rahter missing) if you did not delete them using git-rm. Here’s bash one-liner for that:
git rm $(git ls-files -d)
What that does is use ls-files -d to list all files in the project that are deleted from the file system, and apply the rm command to those paths to delete them from the git index.
I’ve got that aliased to grd (Git Remove Deleted).
