* Leave some system data for inspection

There is not much benefit in being active when removing this data. It's
actively harmful when one tries to read the block number in runtime
APIs in the context of a block.

* Update the expected root hash

This is excepted since now we persist new members.

* Revert extrinsics_root to `take`

It's going away in one of the following PRs anyway

* Update the state root once again

* Update the comment on the storage items that are left in the storage

Excluding ExtrinsicsRoot since it's going away