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.
The flags for a representative alignment are encoded as a primary alignment (at least, that is how the [SAM spec](http://samtools.github.io/hts-specs/SAMv1.pdf) reads to me). It seems like the representative/primary/supplementary split is [fairly recent](http://sourceforge.net/p/samtools/mailman/message/30849568/); might be helpful to get comment from @lh3 on this one.