feat: Use Benedict for better dictionary management

[thomaspinder]

Feature Request

When handling complex dictionary structures, Benedict makes tasks such as indexing easier. We should transition all dictionaries to use Benedict.

A clear place where this will be helpful is in selecting and updating individual parameters. In Benedict, the syntax could be as simple as

def update_param_value(self, key: str, value: jax.Array) -> None:
    self.params[key] = value

In Benedict, the key could be kernel.lengthscale whereas with regular nested dictionaries, one would have to write something more complex to index with ['kernel']['lengthscale'].