By working on Pd's manual, I can see the current priority is to look first in the directory containing the patch, then in the search paths. I still want to maintain that structure. I just think that the order of the paths should be different, first with "standard paths" (which includes 'extra') then the user added paths.
I think you are right that the core "extra" externals should have priority. We've clearly de-emphasized users during everything into "extra" so, at this point, there shouldn't be much to break for people's setups.
That's my macOS perspective. I suppose the situation might be a little different for some Linux packages?
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