Cleanup: remove dead code and improve layout

This is a cleanup PR addressing several issues:

o Removes the variant simulator (issue #27)
o Improves CLI code layout and removes the need for irritating symlinks when developing (issue #24)

Also updates the README to more accurately reflect the current state of the project.
I'd prefer we kept the future module - I develop on python 2.7.* and this module insures it will run with python 3.*