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I'd like to make a clean diff of a directory that allows me to later use a gui patch program for windows to apply the diffile.

If possible I don't want to have to deal with hardcoded paths in the diffile.

Also what program can I use for gui patching?

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Our compare and merge tool ECMerge does that. It can produce patches (open a folder diff and export a patch) then apply them, the GUI patch application let you review the effect of the patch in a temporary folder (and you just have to press the Write results button to actually finalize the application).

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