I suggest to add a deprecation note to the system preference and maybe a coding guideline as well to start phasing out the IndependentBranches system preference in favor of pushing the development for library groups and related features instead. The IndependentBranches have a lot of known holes and problems, see bug 12599. I think if we can agree to start removing it, we could tackle the features it brings separately and improve them to be better, more flexible and more granular in configuration - not being an all or nothing.