[idubrov]

At my previous job I've built a tool that was capable of doing that (we were merging XMLs with form definitions). The main idea was an interactive mode.

Initially, tool would merge based on series of heuristics and then user would manually adjust "matching" nodes (user could say "actually, this A on the left and B on the right are the same, it's just that it was heavily modified").

[hinkley]

It seems like if the editor produced hints this would work better, but your target audience also shrinks.