Improve Naming / Organization

[evanberkowitz]

Some things are weirdly named by historical accident. For example, generator/metropolis.py should probably be named generator/villain.py or generator/neighborhood.py or something like that. But it's not metropolis? Every generator is metropolized.

• [x] generator/metropolis.py --> `generator/
• [x] generator/constraint.py --> generator/worldline.py
• [x] HolonomyUpdate --> ... something else, since it's not actually a holonomy.
• [x] action.py should probably be a submodule which contains villain.py and worldline.py.
• [x] observable/topology.py --> observable/winding.py
• [x] Ensemble.configurations is plural while Ensemble.{index,weight} is singular. I think the singular is preferred.

I think that's it for now.