It's difficult for me to give feedback as I'm too opinionated at some level (ie see my "computational document" comment). I'm also a grumpy vim/emacs diehard in general so your keybindings are never going to be to my taste.

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?