I’ve been using BeyondCompare for many years and it is one of the best folder/file comparison tool on the market. Today I installed BC V4 and I see they have added a patch feature that allows you to apply a patch file to a folder. It isn’t working yet, but from what I see, it looks like something I have been waiting for. It will enable you to resolve conflicts as you apply the patch to each file. BTW, they also release BC V4 for OSX.