I'm eager for that feature too! The node graph engine recently got the ability to represent that concept, so now I just need to find the time to design and build the UI for it. I utilize that feature a lot in other software so it'll be really helpful to have in Graphite as well.
If you don't have a way to bundle up a collection of nodes and apply it to another object or bring it to another document with just a few clicks, that's super powerful too. I rely on that constantly in Illustrator. And constantly grumble at the fact that there's no way to have folders in the Graphic Styles palette where these collections of nodes live, since I can easily have a dozen styles for one character when I'm doing comics.
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although I just played with it and judging by the state of your layers palette there's clearly a lot of stuff to do in terms of organizing the elements of the document in general - to me, documents contain one of more layers, that contain paths, compound paths, groups of paths, and/or layers, and I can choose to place new paths at the top or bottom of any layer (or inside a clipping path); Graphite just calls every path a "layer" and this becomes very unwieldy within a few seconds of drawing shapes.
