The manual source is a single Texinfo file, manual/monod.texi. It is processed using various documentation tools into either online HTML documentation or a printable Postscript book. Both versions of the documentation are created by running make manual from the top-level source code directory. The head HTML page created is manual/Monod/index.html. All the other pages can be navigated to from this page. The printable Postscript version of the manual can be found as manual/monod.ps, and the printable PDF version as manual/monod.pdf. Note that PDF support in Texinfo is fairly rudimentary and you may have to tinker significantly with the TeX setup in order to generate PDF output. I've had the best luck with teTeX version 2.0.2.
The manual contains some images. These images are not saved along with the documentation source, to conserve space. The effect is that it is impossible to build the documentation, either the online or printed form, without a little additional work. The graphics must be downloaded separately: on the SourceForge web site, go to the file release area and download the latest graphics.tar.gz file in the graphics package. In the manual/ directory, create a symbolic link named graphics/ to that directory. You may have to erase an old graphics/ directory, if needed. Then you'll be able to build the documentation.
The manual contains a certain amount of mathematical formulas. It is fairly difficult to get texinfo to deal adequately with these formulas. The solution we have adopted is to prefer printed ouput to online output as far as the formulas are concerned. In the printed output, the full might of TeX will be used, while in online output, the raw commands are printed. For instance, consider T_i, which will appear neatly in the printed output but as T_i in the online output.