git add seems not works for these deleted files, so how to commit the changes?
$ git status
# On branch master
# Changes not staged for commit:
# (use "git add/rm <file>..." to update what will be committed)
# (use "git checkout -- <file>..." to discard changes in working directory)
#
# deleted: ci/ci/__init__.py
# deleted: ci/ci/settings.py
# deleted: ci/ci/urls.py
# deleted: ci/ci/wsgi.py
# deleted: ci/manage.py
#
no changes added to commit (use "git add" and/or "git commit -a")