This library implements Josh MacDonalds xdelta binary diff algorithm in java. More information on this algorithm can be found at http://sourceforge.net/projects/xdelta.
Binary diff files are stored using the GDIFF file format for storing binary deltas.
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Library appears to work well for what I needed it for. Note, for v2.0.1 of the library, do not use trove 3 with it. I used trove 2.1.0 to avoid runtime class loading errors.