I've built a fairly hacky solution to this before (for a different package manager) - it can be pretty simple:

    node_modules/
        versions/
            a@1.0.0
                node_modules/
                    c -> ../../c@1.0.0
            b@1.0.0
                node_modules/
                    c -> ../../c@1.0.0
            c@1.0.0/
            c@2.0.0/
        a -> versions/a@1.0.0
        b -> versions/b@1.0.0
        c -> versions/c@2.0.0