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.
Yes, I feel that:

> The first linear alignment in the read will be designated as the primary alignment; the remaining linear alignments will be designated as supplementary alignments.

Is more specific than "By convention, ... should be present." and is therefore preferable.