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fix(vaults) do not leak resolved vault references to .kong_env file
### Summary When Kong prepares a `prefix` directory, it also stores current environment related to Kong in file called `.kong_env`. As Kong resolves the Vault references when it starts, the resolved values got leaked to `.kong_env` file. This was partly because for `vaults-beta` we didn't yet implement secret rotation, and we decided to also not keep the references around when they were resolved. Not that we have added the `"$refs"` property to `kong.configuration`, we can replace the values of configuration with the references before we write the `.kong_env` file. This commit fixes that.
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