Fixed calculation of total dupes removed; plus a couple of minor tidy-ups 

The new total dupes calculation was ok but I was still reporting the old one - fixed that and removed code for the old calculation.
Tidied up documentation for `-o --output` option.  I've left this as having a non-optional argument but put in a line which maps  `-o ""` to NULL.
Deleted a couple of redundant lines (which were already commented out anyways).