Add some more comments
Add `--all` to `git-add` call (dirs)

The call to `git add` for directories previously used the argument `.` while
being in the target directory. In current Git versions, this produces a warning
about the upcoming changes to `git add` behavior.

To remove this warning and make `git add` behave like we want it, now and in
coming Git versions, we added the `--all` switch to the call (as suggested in
the aforementioned warning). This will include removals as well as additions in
the index.