Refactor how we process Secrets

[pleshakov]

Currently, Secret are processed differently than other Gateway API resources.

Refactor Secret processing so that it is done similarly to other Gateway API resources: we can move Secrets into the graph, so they are processed as the rest of the resources. After we build the graph, we can build the configuration that will include the secrets to be written on the file disk.

Aha! Link: https://nginx.aha.io/features/NKG-52