Cleanup of class files and updates to support simulation entities and semaphores

There are a decent number of changes in the pull request.  Some you may like more than others which is why I made it against the amknapp-master branch you've got.

* Cleanup of class files in bin.
* Cleanup of .svn directories.
* Writing out of PrecisionHistograms to files compatible with gnu plot.
* Modification to the Semaphore class
  - Fixed the constructors (waitingList needs to be initialized)
  - Removed synchronized keyword that was causing deadlock
  - Changed the logic about how the number of resources work
* Change the terminate call in SimulationProcess to not remove the process from the list of all processes.  This is potentially controversial.  I think a better fix might be to have a similar thing to waitFor(Process) that waits for the process to passivate rather than terminate.
* Modified RandomStream so that not all streams share the same seed (and therefore sequence of numbers) by default.
* Removed the call to system.exit if the scheduler queue was empty.  I was running into a situation with one passive simulation entity not getting re-activated because I hit this and so my very last process did not get to finish up.  There may be a more elegant solution.