Running setup with an existing repo will fail

[chmac]

The code assumes that it can setup a repo and push to it and that this repo will be empty. We should add a check for this somehow.

Long story

When the user runs setup, they push to their own me and commands repos. Part of that process is a clone() of those repos. If the repos are not empty (which the code assumes they are), then weird stuff happens, and mostly, the setup fails. We should explicitly tell the user that they're trying to clone an existing repository instead of create a new one, something like that, but obviously more friendly and understandable.