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.
Either I'm confused (very possible) or this is incorrect. I think the taxonomy goes:
- every {read} has one _primary_ and zero or more _secondary_ {alignments}
- every {alignment} has one _representative_ and zero or more _supplementary_ {linear alignments}