Adding back in reference names
Making Segments and Paths part of common.avdl
Alleles now use Paths, and we have only one definition of Segment
Changing back to Variants in the variants API, instead of Alleles
Fixing variant methods to talk about variant scaffolds.
Adding a GraphAlignment, and making it clear when to use it versus when to use a chimeric alignment as SAM would describe it versus when to use both