Remove deprecated doctrine

In order to fix #89.

It's an early PR open to suggestions. As of now it should work on its own, here's what i did :

1. Removed references to all deprecated doctrine classes
2. Renamed the used doctrine classes to remove `Entity` (as it's also usable for documents)
3. Added an option to specify what doctrine object manager to use (again for orm / odm distinction)
4. Updated the doctrine specific documentation

I didn't change tests though.