This refactors `src/node/shell/state.ml` in order to trace the source of
blocks and operations. This prepares the node for the three-pass
validator.
In the procces, it adds an in-memory overlay for blocks and operations.
* Read TEZOS_PROTOCOL in json format
* Define Protocol module here
* Fix dependent modules to use Protocol defined here
* Compute hash of protocol if absent in TEZOS_PROTOCOL
