Refactor and Clean Up the Existing Codebase

[andrewbwm]

This is an umbrella issue to group together all of the existing issues that deal with code/design refactoring and cleanup

• [x] #24
• [x] #19
• [ ] #14
• [x] #7
• [ ] #16

[andrewbwm]

We should also cleanup gym_wrapper.pyas part of this refactoring. For example removing leftovers such as add_reverse_edges.