Normally print "started/finished demux" message

unless quiet is specifified on the CLI, we should print a "Starting
Demux" and "Finished Demux" message.
Use reads vs read pairs correctly in status line

If we're doing paired end, we now print "processed N read pairs", not
"processed N reads".
Refactor copypasted code out, fix bugs

Now there's a single smaller function that processes the combo read
pair. This fixed a copypaste where with IL reads, the barcode structs
were having their counts updated correctly, but for the PE read code
there was a bug. Will do this with single end mode too.
Fix git tag versioning

Git tags were'nt being detected properly, breaking the version strings