dev-472: get rid of bwa_fix_xref()

This function causes all kinds of problems when the reference genome consists
of many short reads/contigs/chromsomes. Some of the problems are nearly
unfixable at the point where bwa_fix_xref() gets called. This commit attempts
to fix the problem at the root. It disallows chains spanning multiple contigs
and never retrieves sequences bridging two adjacent contigs. Thus all the
chaining, extension, SW and global alignments are confined to on contig only.

This commit brings many changes. I have tested it on a couple examples
including Peter Field's PacBio example. It works well so far.
dev-473: added a few assertions

to make sure the new change works as is expected
dev-474: fixed a typo
dev-475: -F outputs unit score, not raw score
r705: pairing performed on one chr only

Change of versioning: the revision number is acquired with:

  git rev-list --all --count

This counts the total number of commits across all branches.
output extra debugging information
r713: a bug in retrieving ref seq on rev
Merge branch 'master' into mem