YeastPathways - Intermediate molecules share same instances

[dustine32]

For #258. Only handles YeastPathways models for now.

Basically, each reaction checks its previous step's reaction for outputs and, if any of those output classes match an input, will reuse that output instance as input.

This refactors some of the stepDirection code from https://github.com/geneontology/pathways2GO/issues/142 for reusability.

[kltm]

@dustine32 I'm going to have to trust you on this one. It's a side repo, so merge away--the blast of a mistake is unlikely to get anybody else.

[dustine32]

@kltm Thank you!