It would seem that vpnkit's master branch is now using packages that have been archived by opam-repository (e.g. mirage-entropy). To get things building for development it would seem users will need to add the archive repo to their opam switch (this will likely be needed in the Dockerfiles too).
#646 would help with this somewhat.
opam repo add git+https://github.com/ocaml/opam-repository-archive