Hot to generate the documentation:

I. Configure doxygen.conf

1. Set a path to the doc directory, e.g.:
   OUTPUT_DIRECTORY       = /home/marcin/ape/doc
   HTML_OUTPUT            = /home/marcin/ape/doc

2. Set a path to the footer file, e.g.:
   HTML_FOOTER            = /home/marcin/ape/doxygen-footer.txt
     
3. Set paths to directories you want to use, e.g.:
   INPUT                  = ./model/ \
                            ./view/ \
                            ./analysis/ \
                            ./interface/ \
                            ./readwrite/
                            

II. Use doxygen to generate the documentation (move to ape directory):
    doxygen ./ape/doxygen.conf
   
   You can use doxygenwizard to generate the documentation.
