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I do a lot of folder comparisons for large projects and the comments, line spaces, line breaks, etc can all be ignored. I set all the options I can find for ignoring comments and such but the folder comparison still shows there's a difference between the files. When I open the files it says they are identical. Any way to set it so the FOLDER comparison view shows no changes?

Unfortunately, Code Compare does not have such feature. Please vote for this suggestion at UserVoice in order for us to create a list of features that are most necessary for our users.