Java exception registering and cancelling all jobs.

Added a test for a java exception during execution which most likely means
that there had been an error in the configuration xml file.
Added a function for cancelling all jobs in a run, plus optional cleaning up --
removing all of the folders created during the run.
Script for cancelling all jobs in a run + optional cleanup
Config files now saved with the simulation output

Condiguration file and the simulation xml is now copied inside the simulation
output folder when the simulation is run the first time.
A function to look for that configuration and read it is added to complement
the original function that needs the path to config.
Not passing the config, but looking for it in the simulation folder

The configuration file is now taken from the simulation output folder
using the SimulationRunner class methods.
Removed unnecessary printing
Simple simulation output archiver script