Added some old files

CalculateAbundancesStrict is a lightly modified version of
CalculateAbundances that uses the correct "strict" files.

KillAmbiguous is like AssignReads, but different. How? Magic.
Makefile and configure script now honor genome

In the past, I just mapped everything to yeast, but this is really much
better.  I think I caught everywhere it matters.

I had to stop using samtools reheader to fix the header, since I
couldn't know that the chromosomes would be in the same order (and, for
the flies, they aren't)
Allow a ? direction in RunConfig
Allow for calculating FPKMs with ambiguous reads

Previously I've been ignoring the ambiguous reads, but it's not clear
that this doesn't change the expression estimates.  These changes should
allow that tracking to happen.
Makefile uses the $(@D) special variable
Fix changes in glob pattern for finding reads
Changes to properly handle finding ambiguous reads

I'd written it wrong the first time.  It seems to actually work now. Go
me!