Move Simulation#runSimulation() to CONOP#main()

Add a convenience constructor for creating a CONOP from a Simulation.
Misc code cleanups
Update to run CONOP directly
Add ability to run QNOP via CLI
Add shortcut for using RelativeOrderingPenalty
Add a quick Spock test for Run
Add support for parsing initial solution

Added some tests for Solution
Temporarily disable 'score' command from CLI