Migrate numerous factories to `ServerEnvironment.Builder`

[armiol]

Right now we already have StorageFactory, TransportFactory and Sharding, that are configured at runtime depending on the server environment. It's becoming a configuration mess, with several obligatory parts that the Spine developers have to remember.

In scope of this issue we need to try migrate from the distinct factories into a single ServerEnvironment.Builder. It is going to be a single configuration point, which is much easier for comprehension.