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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.
The nsisPatchGen utility recursively compares two directory structures looking for changes to the files and subdirectories. It produces an NSIS include file containing functions that will perform a patch upgrade from the original structure to the new.
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).
DOSConf is an installer to install, update, repair, remove and create installation and patch package. It will be developed for DOS / Win32 platforms and in the future for another operating systems, like Linux.