Dagr overhaul v1

[nh13]

@tfenne I tried splitting all the changes I have made into discrete commits so you can review one-by-one, and then after each, I can rebase and fixup. The first one up is: https://github.com/fulcrumgenomics/dagr/pull/306/commits/7c50a9e057b2f234dc8e998ebce309600b67325d

[nh13]

@tfenne I spent a bunch of time yesterday and today going over your comments. Highlights include:

• attempted to document the main traits and classes
• removed the DependencyGraph class as most of its functionality was moved elsewhere
• moved a lot of the methods in TopLikeStatusReporter to it's own dagr.api.models.Executor API.
• got rid of the need for two separate Resource classes
• reorganized the dagr.api package (made sub-packages) I generally followed your comments, and where I didn't, I made sure to respond to your comments. Therefore, I think it's in good shape for another review (ignore the server and ui projects)