Fix misc formatting issues & dead code
Refactor processing read pairs in non-combo mode

Get rid of a lot of cruft from the single barcode mode. Now there's a
single function that processes a read pair in single barcode mode.
Remove the -u/-U flags; take name from out prefix

This removes the unbarcode read file CLI flag, instead the name of the
unknown output file is generated automagically from the output prefix,
for each output read mode.
Update TODO.md

Add some more todos