Hmmm. This is definitely frustrating. My only advice is to get used to using different separate environments for different projects. There is no need to have JLD, JLD2, and HDF5 in the same environment, since they all do the same thing and presumably you wouldn’t use them all in the same project.
It makes sense that GLM would break things in this way, since it has it’s own specialized set of packages it is meant to work with.
I think that whatever you need GLM for, you should make a new project environment and only add the packages you absolutely need. It’s a frustrating change in workflow for sure. When more and more packages hit 1.0 this will definitely be easier