Python3

This PR is pretty big:

1. Full python2/3 compatible code, using a lot of `__future__` imports, some functions from `six`, the python2/3 compabilitiy library (its a single file and a copy is included in mdtraj, so it's just using that one). Also, a really helpful library to find some of the issues was `futurize` http://python-future.org/automatic_conversion.html, which points out a lot of stuff in the code that needs to change.

2. Remove remaining c code in `src/ext`. It wasn't actually being compiled (the directives to compile it in setup.py had already been removed.

2a. Then it seemed silly to have all of the code in `src/python`, with nothing of value besides `python` inside `src/`, so I just moved the `src/python` directory to `MSMBuilder`.

3. Tests on travis now run automatically on both python2.7 and python3.3.

4. I noticed there there were two copies of the hubscore reference data, in `reference/hub_ref` and `reference/transition_path_theory/hub_ref`. I deleted one.