Fixed thread issue.  What was happening was that I didn't know what really happened with Thread.join().  The thread that calls it waits until that thread stops, but it doesn't do anything to make it stop.  So to fix this, I replaced the Runnable implementation with a new Thread implementation that stayed in run() because of a boolean that you could change to make it stop.  Then when you want it to close, change the boolean and then join.
Fixed minor things found by FindBugs plugin
Kind of fixed graphics display, but still funky so I'm going to go with triangles instead; however, wanted to keep this in case I wanted to go back.
merge attempt
neighbors are now displayable, similar to how Dr. Torbert did his
thought that I had done this earlier - removal of image related stuff
Displaying neighbors now works
applied new formatting to files not yet formatted