Because rebar_core handles skipping apps, we had to specialcase the
handling in the case of update-deps because it has to do its own dep
handling. The way this was done is not particularly clean, but there
currently does not exist another way for a command to signal rebar_core
that it doesn't want rebar_core to pay attention to skip_apps.
With this change, however, you can update-deps even with local
conflicting changes/commits by simply skipping the deps you don't wish
to update, or whitelisting he ones you do wish to update.