Server implementations should have a way to modify ServerCapabilities directly

At the moment we infer the `ServerCapabilities` from the `Handlers` and `Options`. The only way for servers to alter the capabilities that we infer is if we provide a handle for doing that via `Options`. In some ways that's nice and discoverable, but it might be easier just to let the server directly modify the inferred `ServerCapbilities` before we send it back.

In many cases I think it would just be fiddly to expose things via `Options`. For example, most server capabilities for methods allow you to opt-in to client-initiated progress. At the moment we just always disable that and rely on server-initiated progress, but it would be reasonable for a server to want to opt in... but even then you probably only want to do it for certain methods. So we could have a `methodsToOptInToClientInitiatedProgress` option... or we could just let the server modify the `ServerCapabilities`.