Indel realigner region patching

This pull request rewrites a lot of the indel target generation code to use the ADAM ReferenceRegion model, and eliminates the Indel/SNP Sets. This fixes indel realignment when running on samples with multiple chromosomes, and also reduces the size of indel realignment targets.

The next work on this target branch will involve the introduction of other consensus generation methods (e.g., knowns only, Smith-Waterman) to indel realignment.