Addressing some pre-existing issues, checking off a few items on the "TODO"
list, cleaning up a few details, partial work on cleaning up comments.  Still
need full documentation to be done.  Also removed Monitor component, as it
wasn't currently adding anything and needed enough overhaul that starting from
scratch is about as much effort as updating the existing version.
Since I hadn't yet done any work on version 002 (adiabatic Euler equations), I
deleted that folder and replaced it with an updated copy of version 001 as a
starting point.