git add(1) -u .
Add file contents to the index
-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.
source manpages: git-add