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We’re using Team Foundation Server for source control, but Microsoft’s diff/merge tool is CRAP compared to Beyond Compare. We had configured Visual Studio’s TFS integration to use BC for file comparisons, but not for merges. I found a great article on how to configure that (for multiple tools, not just BC) today.
(I haven’t tried merging with this yet, so be sure to test it!)
Update - October 3, 2008