Doxygen is used to automatically produce cross-referenced documentation from the Mesa source code.
The Doxygen configuration files and generated files are not included in the normal Mesa distribution (they're very large). To generate Doxygen documentation, download Mesa from CVS, change to the doxygen directory and run make.
doxygen
make
For an example of Doxygen usage in Mesa, see a recent source file such as bufferobj.c.
If you're reading this page from your local copy of Mesa, and have run the doxygen scripts, you can read the documentation here