Fix bugs introduduced by the improved HiSeq runfolder scanning.

Fix bugs introduduced by the improved HiSeq runfolder scanning.
This makes more progress toward analyzing a HiSeq runfolder, but
is currently lacking the ability to process the Aligned reads.

This does seem to now process the base call processing information
out of the Unaligned tree of hiseq runs.

Also all the previous runfolder versions tests pass again. (Some of my
intoduced logic was a bit off for guessing what type of runfolder it
is.)