Restructuring of store and transaction packages

o.n.k.i.
  nioneo.store --> store.{record,id}
  transaction.xaframework --> transaction.{log,state,command}

And various other classes moved to a more logical place.
Merge pull request #3106 from tinwelint/2.2-remove-xa-packages

[2.2] Restructuring of store and transaction packages
Makes clear three transactions application modes

Internal, external and recovery. This means that we no longer "piggy back"
on recovery mode for external transactions being applied in HA.

This distinction exposed a problem where we evicted nodes unnecessarily
when deleting relationships, even in internal application mode. Another
problem with patching relationship chain caches was exposed and fixed.

This commit also removes the global "recovered status" from stores since
that is no longer applicable to 2.2 where many transactions can apply
commits at the same time. This state has now moved to each transaction
instead.