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.
Strictly speaking, a primary alignment won't necessarily contain the full sequence/quality if the read has been trimmed prior to alignment.

I deleted the "By convention,...are false" text as I felt that "an alternative to the primary alignment" was more concise and conveyed a many-to-1 mapping.