Reverted the sorting to use to the CheckpointNumber

Reverted to the CheckpointNumber for sorting in the GetFrom query, added the CheckpointNumber to the compound index that mongo should use. This avoids the scanAndSort problem in query.
All the queries that use the compound index should benefit of this.
Also added a check to drop the previous index and replace it with with new one, this is done to use the new assembly as a drop in update (without manually touching the indexes in the database).