First of all - thanks for excellent job!!! Very well done!
However I would like to propose a feature to consider.
It will be very cool to have ability to mark clone class for exclusion, to be ignored. Let say I have complex property setter, same in different layers. I know it is duplication, but have no other choice...
I would like to eliminate it from report if used exactly as stored in library and get warning if implementation is similar but different. Do you see the point?
Even if half done, just skipping warnings on some code marked to ignore this way, will be useful.