We just published the Beta preview of the Microsoft XmlDiff and Patch functionality. This is currently published as a web app on the
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http://www.GotDotNet.com/team/xmltools
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and allows to compare and produce a diff for two arbitrary xml files.
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The final release will follow soon and will include the downloadable Microsoft XmlDiff and Patch library and tools. In addition to Diff it will allow patching the original XML file with the changes to get the final XML file.
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Please send any comments/feedback to wdxtools@xxxxxxxxxxxxx
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 XSL-List info and archive:  http://www.mulberrytech.com/xsl/xsl-list