Alanine Dipeptide Example Traj

Mainly, this is a first draft for one of the examples. It gets a first TIS-valid trajectory out of a single frame from alanine dipeptide. It also suggests some possibly useful refactoring to minimize what the user has to do. There's plenty of cleanup still to do in this, but I wanted to merge it so that it keeps up to date with further changes.

Also, replaced EnsembleFactory's TISEnsemble with a SequentialEnsemble and added a few tests to testensemble.