One question is if we want to document Inkscape source and Python extension API in the same document
Not sure what you mean by this, but I suppose it's better if they're separate. Doesn't Doxygen generate one page per class/module/interface/whatever? So they would both be automatically linked from an 'index' page...
We could reuse the same configuration or create a new one, imo depends on the relative size of additional changes needed. Perhaps just adding *.py to FILE_PATTERNS and the extension directory to INPUT would do the job and doxygen will index everything nicely? I'm going to experiment with some dummy documentation comments in extensions and see how it'll work.
Btw http://wiki.inkscape.org/wiki/index.php/Doxygen_documentation "Inkscape Doxygen Documentation is not currently available online"
any specific reason for this? Or it's just the ease of generating it locally that renders it unnecessary?
Cheers, Mois