[dune] Add shim for coqtop.byte

We add a shim for running the byte version of coqtop. This fixes the
Coq part of #9727 , the Dune part is still open at
https://github.com/ocaml/dune/issues/108 but this PR includes a
workaround.

Unfortunately we have to introduce a small inefficiency in the build
process as we build both byte and native versions of plugins for this
work reliable.

As this is a choice done during bootstrap it won't be easy to fix
until we have our own `dune coqtop` command and we can control the
rules depending on the final target.

This should affect the `check` target so still fast builds should be
possible, but if this is a problem we could add a `byteboot` target to
help.

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