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Patchamama is a binary patch maker/applier that works on directory tree. It can be used in application deployment, large scale project patching (including source and binary data). It use bsdiff for the binary diff job and 7zip for compression.
tardiff is a perl utility that enables easy patch creation for two different versions of a build/install tree in tarball format. tardiff uses advanced mechanisms to determine differences (visit homepage for a thorough description).