Added Clean feature, Updated JSON Processing, Minor bug fixes

* Improved error handling for JSON processing.  User will be warned when the JSON file does not match up with expectations, for example when a keyword is not found ('deviceclasses' vs 'deviceClasses').  Included are also deprecation warnings.

* Clean Feature can now completely rebuild the code tree.  Clean does not keep anything within the folder.

* Updated Comment Feature. Comments can now be included within the JSON file.  They may be either /* */ for block, or // for single line, or # for single line.

* 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 home (i.e. '~username/') expansion.  These have been fixed.