I do something like Scott describes but I try to be very aggressive with deletions ion the first pass. I know that it usually makes little sense to keep slight variants but it is often hard to choose.
As for the ones that are kept, I like the option of keeping them stacked. I have done that but am not very consistent about it (or keywording ). That is much easier to manage than the other options you described.
). That is much easier to manage than the other options you described.