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We can use doxygen to do the documentation, but how can I do the API Diff? Any open source or free solution for that? Or I need manually prepare? Thanks.

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I think it may benefit you to put the language you're using in your question description. Unless you're explicitly asking how to do this with doxygen, there may be language libraries that would do this. – tieTYT Dec 21 '12 at 21:02

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You probably want to take a look at the web developer's online toolbox

In particular, there is a wonderful API documentation generation service called Apiary which will probably do exactly what you need.

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