I think the issue is that the config.h files hide the namespace macros
from doxygen.
No[*], I broke the permissions on the preprocess script. Should be fixed
now.
[*] I suppose it's possible you broke the config.h files as well, but I
don't see any relevant changes there between Nov 17th (the last date the
docs built successfully) and today, so I don't think so.
Ben
--
http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
- Sir Arthur Conan Doyle