Better names and repo cleanup

[mikemhenry]

We should move old stuff into the attic and also have better names for things, like MoleculePipeline that is used for LargeMoleculePipeline and SmallMoleculePipeline

[mikemhenry]

Lets remove the "small" and "large" description and just call it MoleculePipeline for now

Later if we need to have a separate pipeline, we can come up with a new name