makedox is a script to generate QUDA's doxygen pages. Assuming you have wget and doxygen (preferably 1.7.3) installed, running "makedox" will download the current QUDA master and have doxygen generate the browseable HTML. To take a snapshot of another branch, run "makedox <branch>" instead. Finally, to generate the pages for a new release, run "makedox -v <ver>" (where <ver> might be "0.3.2", for example). The real purpose of this repository is to hold the pages themselves, found in the gh-pages branch and published automatically to http://lattice.github.com/quda-ref/ when pushed to GitHub.