The old way of specifying the location of external libraries, from Cactus/lib/make/extras, for example setting HDF5 = yes, is not compatible with the new mechanism where you must simply include the appropriate thorn from ExternalThorns. Using both can be confusing.
I propose modifying the thorns in ExternalLibraries to check if the old mechanism has been selected, and to abort with an explanatory error message telling the user not to set, e.g. HDF5 = yes, if they are using ExternalLibraries/HDF5.
I am attaching a completely untested patch for the HDF5 thorn which implements something like this. The code to determine if the user selected HDF5 = yes was taken from the extras directory.
Comments? If this is appropriate, it can be adapted to all the thorns in ExternalLibraries.