Prediction appears to be working for a simple repo - with testing for the MAE. There appears to be a problem with the matrices as some columns contain all 0 values.
Issues in commit_matrix.rb solved! -- Need to mash_lists every time as we cannot be sure everything is the same before the most recent ancestor.

-- Only works in ruby 1.9.3
-- Need to make sure topological order is being preserved in this new method.