Adding Smith-Waterman and Knowns-Only consensus modes to indel realignment

This commit modifies the following:

* Fleshes out and tests our constant gap penalty Smith-Waterman implementation
* Refactors indel realignment to separate consensus generation from the realignment process
* Adds Smith-Waterman and Knowns-only consensus generation modes

This PR is against the indel realigner topic branch. After this merges, I plan to squash that branch down, and do some sort of rebase/merge against our refactored master. There are several things outstanding:

* More end-to-end verification
* Unit tests for the Smith-Waterman consensus generation mode that are separate from the Smith-Waterman implementation