Finish polishing the simulator (adjust comments and setup a regular simulation loop)

Modifies the simulator loop to run a normal simulation from the
provided active node.  Ran some tests to confirm that the simulator
runs and stops as commanded by the UI.
Merge branch 'dev' of https://github.com/csalmon/ConnectionTester into dev

Conflicts:
	Connection Test/src/userInterface/HomeBlock.java
Update Simulator