Selecting a Node shows not only a dodgerblue rectangle around the selected node, but also a circular arrangement of Buttons. The red "X" deletes the node. The "?" and cog/gear Shape currently just call `alert`, but they could do anything that you want. The "New Link" starts the LinkingTool drawing a new Link from that Node.
GoJS defines several Panels for common uses. These include "Button", "TreeExpanderButton", "SubGraphExpanderButton", "PanelExpanderButton", "ContextMenuButton", and "CheckBoxButton". "ContextMenuButton"s are typically used inside of "ContextMenu" Panels; "CheckBoxButton"s are used in the implementation of "CheckBox" Panels.
These predefined panels can be used as if they were Panel-derived classes in calls to GraphObject.make. They are implemented as simple visual trees of GraphObjects in Panels, with pre-set properties and event handlers.
More information can be found in the GoJS Intro.
The GoJS Geometry class controls the "shape" of a Shape, whereas the Shape.fill and Shape.stroke and other shape properties control the colors and appearance of the shape. For common shape figures, there are predefined geometries that can be used by setting Shape.figure. However one can also define custom geometries.
One can construct any Geometry by allocating and initializing a Geometry of at least one PathFigure holding some PathSegments. But you may find that using the string representation of a Geometry is easier to write and save in a database. Use the static method Geometry.parse or the Shape.geometryString property to transform a geometry path string into a Geometry object.
More information can be found in the GoJS Intro.