Fix re-layout after generating Random Tree and Random DAG

 - The Topology:: methods on an entire graph document apply a re-layout
   to **all** nodes in the document, which can move existing graph
   nodes and components around. Since none of the other generators
   do so, this is confusing.

Expand (inline) the body of Topology::directedGraphDefaultTopology
and similar, so that they apply only to the newly-generated nodes.