mainly working on style in MATLAB

I added points 8 and 9 to the list ( https://gist.github.com/bbarker/6551884 ), and went over runComparisonScript as the main example. It might be nice to check out http://www.mathworks.com/help/matlab/ref/inputparserclass.html for optional inputs - I will explore a bit more on this and check with Ronan.