git add -u
man from git-add
-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.
If no <filepattern> is given, default to "."; in other words, update all tracked files in the current directory and its subdirectories.