I have uploaded my submission to the titular assignment here to have a permanent reference to the project in the future. The structure is as follows.
run - Execute the jar in this directory, passing it the command text file. This will execute the program and print the results of the simulation to std out. cruft - Extra files generated in the process of diagramming the system. code - The Java code detailing the system itself. submission - The files that will be submitted. Report.pdf contains all the files in a paper-like form.