Bugs, Convenience, b_update_consensus

Refactored a bit to make structs less private, and therefore more
amenable to interrogation for troubleshooting purposes.

Added b_update_consensus. Currently does same as matlab version, picks
seq of most abundant raw.

Fixed index issue in nwalign.

Fixed a few small bugs/name inconsistencies.
fam_update implemented, cluster.c architecture

Added fam_update functionality. Changed architecture of container
objects, these now have arrays of pointers to their children, which are
added by an xxx_add_yyy(xxx* foo, yyy* bar) function.

bi still TBD on this. Will need to make xxx_remove_yyyy(…) functions as
well.

Fixed other bugs. All should compile and pass test.c checks.
Merge branch 'nwalign'