Staging Deleted files

Use git rm foo to stage the file for deletion. (This will also delete the file from the file system, if it hadn't been previously deleted. It can, of course, be restored from git, since it was previously checked in.)

To stage the file for deletion without deleting it from the file system, use git rm --cached foo

Even though it's correct to use git rm [FILE], alternatively, you could do git add -u.

According to the git-add documentation:

-u --update

Update the index just where it already has an entry matching [FILE]. This removes as well as modifies index entries to match the working tree, but adds no new files.

If no [FILE] is given when -u option is used, all tracked files in the entire working tree are updated (old versions of Git used to limit the update to the current directory and its subdirectories).

Upon which the index will be refreshed and files will be properly staged.

To stage all manually deleted files you can use:

git rm $(git ls-files --deleted)

To add an alias to this command as git rm-deleted, run:

git config --global alias.rm-deleted '!git rm $(git ls-files --deleted)'