Added documentation to many of the classes, moved some around, deleted
obsolete classes

Change-Id: Ic123cd0b4e8a7bb50d130e8a8557667b91f71ff2
Updated the readme to include generic overviews of how to run and what
types of classes are in the folders.

Change-Id: If356c5d330bb354454b6b803912d328d0ab7647b
Added a basic javadoc to allow for easy traversing of my classes

Change-Id: Id06db134b3953d2d91e25536ea66b7a3afa9cf50