Delete plugin links on root upgrade

[dra27]

This is the last part of #4619, which it turns out is a bit simpler and less dirty than I feared.

This Dockerfile demonstrates the problem:

FROM ocaml/opam:debian-ocaml-4.12
WORKDIR /src/test
RUN sudo chown opam /src/test
RUN opam pin add -n dose3 5.0.1-1 ; opam install dune dose3 opam-file-format mccs cmdliner ; opam install opam-dune-lint --deps-only
RUN opam exec -- dune init project foo
RUN echo > dune-project '(lang dune 2.8)\n(generate_opam_files true)(source (github foo/bar))(package (name foo))'
RUN opam exec -- dune build
WORKDIR /src
RUN sudo chown opam /src
#RUN git clone https://github.com/dra27/opam.git -b clear-plugins
#Comment out the line below and uncomment the line above to get the fix
RUN git clone https://github.com/ocaml/opam.git
WORKDIR /src/opam
RUN opam exec -- ./configure && opam exec -- make
WORKDIR /src/test
RUN opam install opam-state.2.0.8
RUN opam pin -yn opam-dune-lint 'https://github.com/ocurrent/opam-dune-lint.git#bf451c8cf2d4f2be3c7d979b613c79588b55a172'
RUN opam dune-lint
RUN sudo rm /usr/bin/opam && sudo cp /src/opam/opam /usr/bin/opam
RUN opam update
RUN opam dune-lint

and swapping the cloned repo over fixes the problem.