Added Clean feature (-c/--clean), Pep8 test now displays code, fixed opts.input

Clean Feature can now completely rebuild the code tree.  Clean does not keep anything within the folder.

Pep8 will now display where the errors are found within the code when running a nosetests from command line.

There was a bug in the input option that did not fail as desired.  In addition, there was no support for user expansion.  These have been fixed.