Epic alignment changes

Highlights of the changes:
* For alignment, we align to all STR regions at once, rather than only to the regions with STRs of specific motif. To accommodate this, the index structure has changed (and decreased in size significantly). I added a message to warn anyone trying to use the old index with the new version.
* Since we no longer need to detect what the repeat motif is, I have removed the FFTW dependency. This resulted in deleting tons of code from the detection step.
* I also cleaned up/got rid of a lot of code that is no longer being used. Still need to go through and correct what compiler warnings remain and add coverage tests (besides the ones from third party software).

Results:
* Alignment is now much more sensitive, aligning something like 60% more reads.
*  Speed is similar to what it was with the new alignment speedups added a couple months ago. I need to do some more tests for this.
* Memory usage is ~half what it used to be due to the smaller index.
* At least on the one Mac I tested, it compiled very nicely and all checks except multithreading worked, thanks to the awesomeness of Gordy.