suggestion and others
Hi, I have a small suggestion. Maybe you can do like wikipedia and have a little floating bubble with a preview of the content if you hover over the link/box. It would not be very different from opening and closing it quickly (and unlike wikipedia clicking is not like loading a new page) but still it's two clicks that many people will want to save sometimes.
Also, if you have opened a bubble and bubbles within those and you are in the middle of a huge block if would be good one could click on either side of the bubble (the sides of the column of text) to close the bubble.
Another crazy idea: if you support general embeddings, do like https://hypothes.is and wrap the website from which a particular excerpt is taken, so that when you click on the link to the source you can see where the excerpt was (like with hypothesis, it can have problems when the target website updates). I feel that using your Nutshell to summarize/collect the annotations you did on a website is much better than the way hypothes.is displays it. Or in general allowing to take an arbitrary excerpt on a website to use it as a bubble would be awesome.
It would be great to be able to have automatic bubbles being generated on keywords, like for instance if you are writing latex and you want every instance of a notation to point to its definition like in https://arxiv.org/pdf/2109.03678.pdf (see the first footnote) or if you are, say, explaining a hard thing and using big words and you want every instance of a complex word to have a link to a clarification for what it is or what you mean by that in the current context. Or you are writing a post about languages and have some sentence examples in another language and want to have an automatic bubble with the meaning of each individual word within the sentence example (or a dictionary definition, or a picture). In this use case the hints for "hey, look at this, there is a link here with a bubble" could make the text overwhelming full of hints, so allowing "invisible" links here would be useful (like in the arxiv paper). Since this use case targets people that do not know a concept they are reading, they will try to place the mouse over the thing to see if there is a bubble, no need to tell them. (Alternatively one can have less intrusive link hinting). I know you could write an external program to generate these bubbles, but you know, this smells more like a plugin to me.
Also, your Nutshell reminds me of this project http://guillefix.me/nnbias/ of a friend (that was not done to look pretty) to communicate research results. I hope it can provide you with more ideas. In particular the conversation format to show the pros and cons of something is cool and while it may not be your intention to cover this, some things come to mind that would help others change your Nutshell to emulate this or other things (different colors for bubbles, other bubble customization?)
If you prefer another using another means of communication let me know, I didn't know how to else contact you.