Redo file structure to standard Java project format

[owlang]

Update ScriptManager to move to standard Java project organization outlined below. This should simplify the gradle configurations for building out the JUnit tests and allows us to bundle in XML resources that would help us to customize the look and feel of the application.

src
  |--main
  |  |--java
  |  |  |--scriptmanager
  |  |     |--charts
  |  |     |--cli
  |  |     |--objects
  |  |     |--...
  |  |     |--window_interface
  |  |--resources
  |     |--images # for GUI buttons etc
  |     |--lookandfeel # Synth xml for UX students
  |--test
     |--java
     |  |-- # junit test scripts
     |--resources
        |-- # test inputs and outputs to compare against