I have been working with Heavily large projects in twine for a lil while now and i am coming to the conclusion towards just how messy twine 2 still is, even with the lovely moveable passages.
Now what im proposing is that the IDE gets a VIrtual Folder system of some kind, nothing that includes itself into the actual games hmtl code file when you compile it, but something just native to the Editor, basicly something that would fit with the drag and drop style you have so lovingly given us, where you can drag a passage to a labeled virtual container, where if you open it, it acts just as the outer section of the editor, being able to add more folder structure assets for more organizing, as well as move stuff around.
I guess this could be too much to ask, depending on how you coded the editor itself, but i think it would be a god send to most of us writers/developers working on massive projects, or just who have issues with how disorganized the code can end up being (Namely beginners, and others who may be forgetful of a older project that they wanted to add too or work on more after a long period of time)
Personally i dont think its too much to ask, but knowing that if the editor is coded in a way that makes it harder to impliment i can accept it never getting into the editor, however i think it would compliment the drag and drop style more then it would harm it, as well as again a god send to most developers/writers using your editor to write or create whatever it is there making.
Anyways just a shameless request, hope its reviewed and thought through.