Simplify command line and options processing.

Remove some special case flag processing and rely on commander.js more.
Move referrer option from System to options.js.
All of the tests pass, including our Makefile. I think we have pretty good coverage for the things that we think we mean. Of course I don't know what uses I will break because i don't really know what the command line does.  With this change I will have a better shot at fixing cases we did not know about.

FWIW my motivation is to allow scripts to be compiled after modules. Currently we cannot compile script - module - script so we cannot emulate browser or node execution sequences with our compiled code.