Yep, but it is not easy problem, I don't know any existing app that does it well.
The thing is that really useful tool would implement several types of referencing, because there are several equally important ways for doing it, i.e. sometimes I need to have just an arrow pointing from reference to destination, sometimes I want a tag, which after clicking on will embed destination in reference place, sometimes I want just some kind of preview.
Well, it is "spatially linear". Maybe if you could reference one part of text in some other parts it would be better.
What I mean is that context you are saying about is linear, which doesn't happen often in thoughts. If you have several deep bullet hierarchies and your context happens to contain some items in their leaves, there is nothing that will help you see this context at once without destroying current structure...
I don't like it.
First, you had titled this Show HN "structure for your thoughts", and I was expecting exactly that. Instead of what I had expected, I have just seen another linear TODO list which I can use maybe for shopping list, at most.
Second, honestly, how is it better than Google Docs or any other collaborative text-editing tool?