Support native cloning of Graph object, remove all methods related to cloning and accessing cloned objects

[clue]

// old
$new = $graph->createGraphClone();

// new replacement
$new = clone $graph;

// old (removed due to ambiguity and limited support)
$graph->createGraphCloneEdgeless();
$graph->createGraphCloneVertices($vertices);
$graph->createGraphCloneEdges($edges);
$graph->createVertexClone($vertex);
$graph->createEdgeClone($edge);
$graph->createEdgeCloneInverted($edge);
$graph->getEdgeClone($edge);
$graph->getEdgeCloneInverted($edge);

Among others, this done in preparation for #131 (also refs #58).
Builds on top of #177, #175 and others.