You could do worse then really digging deep into emacs org-mode and learning it well.
It takes what you are doing to a much higher level but doesn't exist on the web yet.
Also (as mentioned elsewhere) get yourself up here https://demo.sandstorm.io/demo
This whole area is very underserved in how people
interact with their computers, glad to see people
pushing at it.
Are there any tools other than org-mode that you have your eye on?
outliner
org-tangle/org-babel, literate programming and/or http://www.howardism.org/Technical/Emacs/literate-devops.htm...
broadly exportable format
calendar/todo/personal information management
etc etc
I'm not aware of anything else that covers that territory.
However Xiki and IPython (Jupyter now) do have some of the aspects of the "computational document" that I think of in this broader context.
I believe that when people have tools that allow them to visualize their thoughts they can become more rational as well as more productive.
I like emacs org-mode too. I would like to add functionality to CrushPaper that is similar to some aspects of emacs org-mode. But, first I need more feedback on the current iteration.
Try to avoid the popup modal dialog boxes ie for creating a new note. Focus on fluid note editing within the document.
Alt+enter to end a note? What is the absolute most fluid way you can give the user to create a sibling?