Using the Marquee tool on all shapes doesn't result in the same kind of selection that happens with the 'Select All' command: ConnectionDecorator are not selected with the Marquee tool, but they are with the 'Select All' command.
This is rather inconsistent: either one or the other should be true in both cases.
Is that expected behavior? Should I file a bug for this?
What I can see in the ECore diagram editor (I suppose it's plain GEF), is that the 'Select All' command selects all Shapes and Connections (not ConnectionDecorators which is nice), and the Marquee does exactly the same.
Are your connections really being selected? I've never been able to get Graphiti to select my connections with the marquee unless I override my way down to a point where I can call setMarqueeBehavior(GFMarqueeSelectionTool.BEHAVIOR_NODES_AND_CONNECTIONS) on Graphiti's drag tracker.
Along this same line, the getClickArea() method of ToolBehaviorProvider allows clicks across several GraphicsAlgorithms to be collapsed into the selection of one PictogramElement. But, dragging a marquee selection across the same object results in the selection of every active container shape in the hierarchy.