doxygen
Automated C, C++, and Java Documentation Generator
Doxygen is the de facto standard tool for generating documentation from annotated C++ sources, but it also supports other popular programming languages such as C, Objective-C, C-sharp, PHP, Java, Python, IDL (Corba, Microsoft, and UNO/OpenOffice flavors), Fortran, and to some extent D. Doxygen also supports the hardware description language VHDL.
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