The Cactus documentation
http://einsteintoolkit.org/info/documentation/UsersGuide/UsersGuidech6.html#x9-19000B2.1 (scroll down to Compiling with Extra Packages)
currently tells people to use the "extras" method for enabling access to external libraries such as HDF5, MPI etc. As I understand it, this method is deprecated in favour of the ExternalLibraries method, and both should not be used at the same time for the same library.
The documentation should be updated to describe the ExternalLibraries method, and the old method description should be moved to an appendix with a clear warning that this is deprecated.