Update alignment docs

This is my follow on to #95; it'll need to be rebased after #95 merges before it can be merged in.

This provides more explicit definitions for the supplementary/secondary alignment flags, the cigar operators, and some of the alignment specific fields.
@dglazer Supplemental vs. separate are still discussed separately below.

> Also -- did you delete the "they are rare" comments intentionally? I found them useful in understanding the way these models work in practice, similar to how we give guidance above on the typical number of RGs per RGSet and the typical number of reads per RG. It's not normative, but it is helpful.

I did, because while those generalizations hold for traditional DNA processing pipelines, there are certain protocols that make heavy use of multi-mapped reads (for example, some RNA-seq methods).