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Resolve inherit_from correctly without namespace (rubocop#3421)
The current implementation of `load_file` will load the hash from a config, then apply the base_configs to that hash, before converting it to a proper `Config` object. This can clobber inherited configuration since merging will happen in resolve_inheritance, but will just keep the keys from both and then when `add_missing_namespaces` is called, one will be dropped. Since `Config` inherits from `Hash`, there shouldn't be a problem with doing the `resolve_*` methods after the `config = Config.new` line since all the normal Hash methods are available (.delete specifically).
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