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Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D. Doxygen is developed under Linux and Mac OS X, but is set-up to be highly portable. As a result, it runs on most other Unix flavors as well. Furthermore, executables for Windows are available.
Docutils is an open-source text processing system for processing plaintext documentation into useful formats, such as HTML or LaTeX. It includes reStructuredText, the easy to read, easy to use, what-you-see-is-what-you-get plaintext markup language.