ns-3 requires Doxygen version 1.5.4 or greater to fully build all items, although earlier versions of Doxygen will mostly work.
Type "./waf --doxygen" or "./waf --doxygen-no-build" to build the documentation. The doc/ directory contains configuration for Doxygen (doxygen.conf) and main.h. The Doxygen build process puts html files into the doc/html/ directory, and latex filex into the doc/latex/ directory.
sudo apt-get install doxygen graphviz imagemagick sudo apt-get install texlive texlive-extra-utils texlive-latex-extra
You shouldn't have to change anything in doxygen.conf.
What version of ns-3 are you using? What version of doxygen?
Thanks,
Peter