Minor Optimizations

[RoyalBoggs]

Fixed matrix multiplications improved speed slightly, cleaned up some comments, still working on adaptations

[bowring]

getting faster!:

%%%%%%%%%%%%%%%%%%%%%%% Tripoli in Java test %%%%%%%%%%%%%%%%%%%%%%%
Elapsed time = 0.393 seconds for 1000 realizations of total = 100000
Error function = 3093.557
Change Log Ratio: 143.0 of 144.0 accepted (98.468% total)
Change Intensity: 356.0 of 530.0 accepted (66.932% total)
Change DF Gain: 60.0 of 79.0 accepted (78.813% total)
Change Baseline: 28.0 of 86.0 accepted (35.208% total)
Noise: 24.0 of 161.0 accepted (19.319% total)
Intervals: in microseconds, each from prev or zero time till new interval Interval1 75 Interval2 179 Interval3 8 Interval4 105 Interval5 16

also fix these:
https://app.codacy.com/gh/CIRDLES/Tripoli/pullRequest?prid=10043057