If we add a new lib you (the user) need to tell kicad to add it to the fp-lib-table.
The footprints within libs are downloaded automatically. (At least out of the box, or as long as you do not check "save local copy")
Nearly everyone (with a bit experience) agrees this is a bad idea though. A better solution would be a controlled update by user command.
With the current github plugin there is no good way to do this. (Hopefully this will change in future versions of kicad.)
The best option is to use a local setup where you use the footprint lib download script found in the kicad-library-utils repo.