So you want a diff of the output files without anything from the intermediate steps? Well, that depends on your process - if it clobbers previously seen differences, you're better off setting your process right than fudging with intermediate diff files. Now, that said, let's move on to the actual task:
Your question sounds a lot like a task for a diff tool. Did you check if your diff tool (available on *nix machines) doesn't already do the job for you? diff -u or something similar? You can also look at Text::Diff by Ovid.