New plan:

Task                    Comparison Function  update function
Estimate Module Stats     hit/hit              component-wise maximal scores
Score Module Similarity   hit/hit              CPD-based score, updates the max.
Estimate Regulon Stats    Module Similarity    component-wise maximal scores
Score Regulon Similarity  Module Similarity    CPD-based score, updates the max.


All similarity scores have a 'same_orientation' output parameter as well as a score.

But, a slight change:  The pairwise comparison functions should NOT return summary statistics,
since now, only one level of statistics are estimated at a time.