Update default media type to v3

We'll soon flip the default media type ahead of the API's switch to `application/vnd.github.v3+json`. See the [API blog post][post] for details. 

Since this will introduce changes to some resource responses, we'll bump the version to `3.0.0`. We'll take the opportunity to remove a few remaining deprecations as well.

[post]: http://developer.github.com/changes/2014-01-07-upcoming-change-to-default-media-type/

/cc @jasonrudolph