Epic: refactoring

[aimalz]

This issue is for collecting programming issues that are driving me nuts but aren't actually holding back completion of the paper.

• Establish consistent keyword/variable names (Establish consistent keyword/variable names #15)
• Improve user interface with error checks (Improve user interface with error checks #26)
• Improve file formats (Improve file formats #51)
• Diagnostic printouts to file (Implement diagnostic printouts to file #52)
• Eliminate the abundant magic numbers and give more control to the user via an improved config file interface.
• Use qp (or pomegranate) for probability distributions to replace discrete.py, gauss.py, and gmix.py (Replace basic probability distribution construction #68)