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VERY IMPORTANT SAFETY TIP
Do NOT do what I just did. I tried to use this on the entire "interactions" folder. Windows choked, puked, and died a horrible BSOD as it tried to launch over 3000 processes of WinMerge! Very painful! Multiple files that were open at the time were corrupted by the crash.
Thankfully I have Windows 7 Ultimate and was able to recover the files on the "previous versions" tab in Windows folders properties.
Just use this on a single mod, maybe 50 or so XML files, at a time and you should be fine!
If you want to check a whole folder of the extracts, just use WinMerge by hand and it will run in a single process.
Clarification: You can, of course, use the entire XML extracts in the "OLD" and "NEW" folder fields, just don't put hundreds or thousands of files into the "Your XML File" - each of which launches a new instance of WinMerge.