Move to VCS entities to core entity system

The version control entity api was originally a backport of the Drupal 7 entity API for ease of upgrade. It's time to go full-on D7 and start using the real entity API for all of our entities allowing us to do things like entity reference a commit from an issue. w00t.

The current plan is to abuse core's conditions array and pass in a special key for our options array. It's a little gross but we need more information than an ID and some fields in the table so it'll have to do. The controller will remap this two parameter function signature to our 3 parameter that better meets our needs requiring the minimal changes possible to ripple through the rest of our code base.