I'm trying to implement diff3 algorithm and currently stuck at chunks creation stage. I already know how to get LCS between original file and "other" file and LCS between original file and "my" file. Which steps need to do to get chunks?
how to get chunks in diff3 algorithm implementation
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I don't think this really answers your question, but Subversion implements this layering exactly as you describe here. It follows the theory quite closely, so you might be able to re-use some pieces.
See http://svn.apache.org/viewvc/subversion/trunk/subversion/libsvn_diff/