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.
> Re supplemental vs. secondary -- I still think the original language was clearer. In particular, when you say there "... can be one or more secondary or supplementary alignments", I think that's misleading. IIUC, there can only be secondary alignments and supplementary linear alignments -- the two modifiers apply at different levels of the hierarchy. (Life would be easier if the levels and modifiers had clearer names, but they don't.)

OK, I see what you're finding ambiguous now. I'll clarify that.