Looks very interesting! Two questions:
From a quick look around in the repo, I couldn't find which CRDT lib you're using. Which one are you using? I've used yjs in the past but getting the document out of yjs into a db was a pain.
Second: we're also building a tool that connects a lot of information because research tools are very fragmented as well. What is your philosophy on how to connect the information while still keeping things structured and understandable? We've found that e.g. node networks are incredibly hard to understand when the data and logic behind them gets complex. We also found that when users are not restricted in their information entering (e.g. a markdown file), most will not enforce their own structure and it gets disorganised quickly. Did you try to solve that or is it more the users problem?
nice that yjs worked for you :)
We're blocking where custom options don't make sense - which are a few since context is often constrained in our domain - but will probably enable users to do their own stuff with plugins. That way, the platform hopefully stays usable but extendable..