Removes update_deps from manage.py update command

First reason: changes to deps will often break manage.py until
you've run update_deps.sh, and I want this command to be honest
about what it can and can't do. Second reason: we're likely to
have a lot of people using the new vagrant-based dev setup
in the near future, and update_deps has weird behavior on vagrant
but everything else in this command works.
Merge pull request #1425 from learning-unlimited/manage-update

Removes update_deps from manage.py update command