flattened alignments, GSSW integration

The reference-relative realignment results now appear to be quite solid.
However, the testing has been over only 10k (simulated) reads, and more will be
required to ensure the migration is really complete.

This version should perform substantially better than older versions of glia
did.  Expect a 8-16 fold speedup due to the introduction of a generalized
implementation of a striped Smith-Waterman algorithm capable of operating on
directed graphs.