1) Fixes to the SCEE/SCNB changes
2) Adds a "applayer" command to "energy" to force ParmEd to use the OpenMM
   application layer to create an OpenMM system instead of the ParmEd API
   (primarily useful to validate the ParmEd API if you're skeptical).
3) Add an option to suppress copious amounts of output from the "change" command
4) Improve help menus and error reporting.