fix bug in tophat.sh

Fix a small but deadly bug in tophat.sh which meant the bam found by
findBamFiles was the wrong one, and everything had count = 0.
Was caused by a bad ln -s command.
add fix to findXFiles.sh which stops recursion

We don't want the findXFiles functions in common.sh to be recursive, or
they may be confused by other matching file in subdirectories, e.g. bams
in tophat_out.