How about "git add -u"? from the docs:
-u, --update Only match <filepattern> against already tracked files in the index rather than the working tree. That means that it will never stage new files, but that it will stage modified new contents of tracked files and that it will remove files from the index if the corresponding files in the working tree have been removed. -- You received this message because you are subscribed to the Google Groups "Git for human beings" group. To view this discussion on the web visit https://groups.google.com/d/msg/git-users/-/BENjVQWHeI8J. To post to this group, send email to git-users@googlegroups.com. To unsubscribe from this group, send email to git-users+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/git-users?hl=en.