Not too sure what you mean on the bounding box thing, like the little border around elements?
If you want to dismiss the sidebar just click the little ">>" or press "f". Hiding the breadcrumbs in the focus mode is on my todo list. Thanks for the list, I genuinely appreciate it.
I've been chasing a onenote alternative for some time, this looks promising. I have to add, I loved the old Onenote heirachy, notebooks down the left (rotated labels), sections across the top, pages down the right.
And more screen shots always help for those too lazy to trial. And add some default notebook/section/note naming, so people can just click and start adding notes.
Great work
I really like the instant-text suggestion. I might be able to make it so when you have the "insert" menu open it'll automatically insert a markdown element if you just start typing. I'm a little busy with uni right now so I'm not sure how quickly I can get through anything, although I am open to pull requests.
I think you took the 'webapp' UX model a bit too far (where everything must be click, animation, multiple choice. Not even right click). Few modern web apps do these things well. One is checkvist.
Your target user likes the keyboard (coders, writers). Listen to them (us)