Hi Bill,
Some aspects of "compound nodes" exist in the groups interface
in Cytoscape 3. You can group nodes and collapse the groups, but
set the collapsed groups to show as a nested network. The
cytoscape.js compound nodes features which allow you to manipulate
the nodes inside of a compound node and resize the compound node
as a result is difficult to implement in the Cytoscape 3 rendering
engine, which was designed with a focus on very large networks.
The feature request is on the list, but I'm not sure it will make
Cytoscape 3.2.
-- scooter