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Resolves the duplicate repo instantiation errors from the previous merge
commit. They all had to do with repos that twitter_scrooge and scalafmt
have in commmon with scala_proto. Given that, passing the `scala_proto`
boolean parameter of `scala_toolchains` into the `twitter_scrooge` and
`scalafmt_repositories` functions seemed the easiest workaround for now.
I picked up the `**kwargs` + `kwargs.pop()` pattern up from:
- bazel-contrib/rules_python#2289
It seems to be a pattern for passing through hidden, purely internal
parameters, not to be relied upon by any external users.
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