From Emergent

Using the AX_PROG_DOXYGEN autoconf macro, configure contains support for running Doxygen to produce a wide variety of source code documentation automatically. Over time, we plan to improve this documentation by incrementally adding human comments and automatically including this stuff into relevant pages on the wiki.

Step 0: Install/configure Doxygen

OSX

You first need to install Doxygen and follow the instructions in the graphical interface. You'll also need MacTeX and you will have to add /Applications/Doxygen.app/Contents/Resources to your path.