Documentation: Make it clear when the __key argument should be used and when clone should be called

[etrepum]

Description

It's a common mistake for people to assume that they just pass __key around, but the reality is that you should never ever use __key except when implementing a constructor or clone method.

Another common mistake is to assume that clone is something that can be used to duplicate a node. It's not. It should be considered a private method that is only called internally.

There is some relevant documentation about this $cloneWithProperties and various invariants but people keep running into this so we should add more docs.