Refactoring CLI to simplify and integrate with Spark model better

NOT READY FOR MERGE
Anywho, a meaningful answer: I'm not sure about `adam-scripts`, but we use `scripts` for more project admin/cleanup related scripts. Most of the scripts in `scripts` are related to release administration, Jenkins, and the like. I think `bin` is a good place to put scripts that users may want to execute. Ideally, the "testing" scripts would be moved out into a separate "adam-regression" repository.