MASON was designed to do repeated jobs at the command line, and so  
for the time being only has fairly rudimentary tools for running  
batch simulations via the GUI.

On the command line there is a simple hook for you to customize a  
simulation according to the run-number it was: the 'jobs' parameter.   
If you use the doLoop() method to run MASON from the command-line,  
you can specify

	-repeat 10

Which means "run this simulation 10 times, with 10 different random  
number seeds, and set the job number of each simulation to 0 .. 9".   
Then, each time the simulation is run, doLoop() sets  the 'job'  
variable in the SimState to the next larger value.

	state.job++;		// ... or whatever

In your SimState.start() method, you can test for the value of this  
variable to know what job number you're running.  This would enable  
you to differentiate among different jobs. Note however that if  
you're running under the GUI, the job value is not incremented.  This  
is just some code we neglected to do, because we so rarely do "jobs"  
at the GUI level -- we always do batch stuff on the command line.   
But it wouldn't be hard to add in.