Try to make Aligned result directories optional in hiseq runs.

Try to make Aligned result directories optional in hiseq runs.

The previous implementation tried to match Aligned & Unaligned
directories by parsing the Aligned directories config file for
its the unaligned raw sequence directory.

Needless to say that didn't work if there wasn't an Aligned
directory.

This version tries to match them by comparing the suffix in
Aligned<Suffix> and Unaligned<Suffix>. Then the runfolder generation
code will still generate a runfolder if there's no aligned directory.