RescueAmbiguous now works on any species

Thanks to Steven Kuntz!
Merge branch 'master' into Fall2012
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
Remove Fall2012 Specific files

These were added in the fast-forward merge, but really shouldn't be part
of master as they are specific to the Fall2012 Branch.