Switch to tophat for mapping

STAR was having lots of false negatives, where it wasn't reporting
mappings for reads that were potentially ambiguous between two
Drosophila species. Switched (back) to tophat, which includes making a
number of the bowtie indices automatically (but not yet all the
reference files. Soon.)
Newlines to make the config.make a little cleaner
Tweaks to get the Tophat based mapping to work.

Turns out the "transcriptome" flag doesn't actually create the
directories, and instead uses that as a base name for .bt2 or whatever.

Also, I forgot to remove the "conversion" to accepted_hits.bam, which
tophat makes automatically.
Simple script to convert BAM files to FASTQ for SL

Sure, I *could* use bam2fastx, but this has some nice features like
keeping the different files from each sample named (almost)
appropriately, and all that jazz.