Logging cleanup modify py

* Logging cleanup
 * Removed many System.out and System.err calls
 * Replaced log4j logger instantiations with slf4j loggers
 * Added a log4j-jetty.properties and system arguments to have jetty use log4j

* Editing Python Transformations
 * Refactored the PyTransform commands to remove redundancy
 * Added SubmitEditPythonTransformationCommand to enable users to edit python transformations
 * Added Edit PyTransform button to column drop down menu
 * Brought WorksheetR2RMLJenaModelParser up to date with the rest of the code to apply commands like the ApplyHistoryFromR2RMLModelCommand does, so it now supports chaining transforms.