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.
Did you intentionally delete this info (about there being exactly one non-secondary non-supplementary alignment, and about it needing to contain the sequence and quality)? If that's still true, it seems like it should still be documented.