Store config.yaml and state.yaml In A Separate Directory By Default

Storing the `config.yaml` and `state.yaml` in separate directories would be extremely beneficial especially when using the Docker container route as this would allow for a persistable Docker volume to be used instead of a Bind mount. This can already be achieved in a Docker environment for the certs file. See [Docker Compose Volumes section here](https://github.com/chrivers/bifrost/pull/79#issuecomment-2645351108) for how volumes can be used over bind mounts

It would also allow for future improvements to be made further up the chain such as in the Docker build file, the example `config.yaml` file could be automatically cloned to the directory with all of its correct permissions.