I have spent some time and have modules compiling.  I chose to use a
command line flag for pyjs.py and allow the previous functionality to
remain unchanged.  You have to specify that you want pyjs to compile
as modules.  I made sure that all tests still pass (on Windows) after
my modifications.

I did not see anywhere that pyjaco.append_module was being used for so
I started my changes here.

I have two tests that run under "tests/as_module/simple/".  Once you
run the test you will see a file that ends with .run.  That is the
javascript file that causes the js code to run.  It uses the
$PY.run_module function I added to builtins.

I decided that it would be best to pass modules a reference to the
__builtins__ module.  This will allow us to modify the pyjaco
namespace without needing to update any compiled code and it just
feels cleaner than reaching for a global __builtins__ object.  The
code could still fallback to the global __builtins__ object if
wanted.  I think it would be best if there was only one global
javascript object used for pyjaco in the future.

The run_module function also sets __name__ so that "if __name__ ==
'__main__'" initialization can be used.

Anyways, I was hoping for some feedback/thoughts.