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Add support for upgrading version 3 configurations to version 4 (#452)
### What This PR adds the ability to upgrade a configuration directory in version 3 to an equivalent one in version 4. The cli now supports the command `cli upgrade --from-dir <existing configuration dir> --to-dir <new configuration dir>`, with the intended semantics that it upgrades the configuration in `<existing configuration dir>` to the newest supported version. ### How Many places in the code (though mostly tests) is tightly coupled with internal details of version 3 and will attempt to construct and manipulate configurations directly. This PR attempts to define a version-agnostic interface that can be used instead.
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