Clean up of packages, resolves many circular dependencies.

No functionality changes, only moving classes to correct packages.

o Move UpdateMode to the index component, resolves all but one remaining circular dependency in the new kernel code.
o Moved ThreadToStatementContextBridge into core along with the NodeManager and friends, removes 44 circular package dependencies.
o Moves kernel implementation classes into the impl package and away from the kernel API.
o Deletes a few unused classes.