Refactor usages of Graph

Created by: gkirgizov

Currently evo operators and other users of the Graph (& OptGraph) access specifics of its implementations.

What requires refactoring (this list may be incomplete):

accesses to internal graph.operator
direct usages of graph.nodes -- instead they must modify Graph through some general public method like add_node
connect_nodes and disconnect_nodes sound like add_edge and remove_edge -- and that should be part of the general graph interface
node_children also sounds like a general abstract method

All changes must be accompanied with tests checking that nothing has been broken.

All this points to one simple aim: all usages of the Graph must happen through public interface This is a necessary step for abstracting GraphOptimiser for new domains.