graph: Refactor graph item management into new graph_manager object

The graph widgets management (watching a glib receiver, adding and removing Nodes, Ports and Links) currently done in the Application and GraphView objects has been extracted into a new GraphManager object, which watches the receiver instead, pushes changes directly to the widgets, and reacts to their signals.

This seperates widget logic and management logic cleanly instead of both being mixed into the GraphView, and also reduces the code size for the Application object.