Comment and rename code

Started providing docstrings to classes and functions based on the comments
present in the source code. Renamed several functions and variables, being
careful to ensure they are called in other files with the (new) correct name.

Removed the -n (number) option from mirscanTrainer.py.
Renaming of scripts

Renamed score_cut.py to fit in with the other script filenames and
mirscanExecute.py to mirscanScorer.py to better reflect its role.
Bugfixes (typo)
Finished documenting the source code for the main scripts

The main scripts (Trainer, Scorer and Cutter) have all functions documents with
doctrings, the name variables are sane and the layout of the code is more
rational.

mirscanModule.py is not ready, pending evaluation of the hairpin  criteria
feature objects. Functions below the file parsing methods are perhaps best
placed in a separate file since they are only used for the criteria rule files.
Refactored mirscanCriteria out of mirscanModule

All classes and functions pertaining to the hairpin criteria features have been
refactored from mirscanModule.py to mirscanCriteria.py. These functions are only
relevant to criteria features and criteria features do not call any of the
remaining functions of mirscanModule.py.

All executable scripts and mirscanModule.py have proper docstring documentation
and sane variable names. Only the functions related to criteria features must
still be cleaned up.
Removed criteria prototype files

Given the presence of example prototype files under the examples folder, these
files are redundant.
Renamed mirscanModule to mirscanIO

New name is more descriptive of the functions therein.
Imports adjusted for new name mirscanModule (mirscanIO)
Updated call to ViennaRNA to prevent ps output of fold
Updated description of scripts
Merge branch 'develop'