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Description
Today I have been reading these files and principles of work. I am not running Semantic Synchrony as it requires too many dependencies that I do not need. Major comment is that your files are not well readable with long lines. I had to use M-x set-justification-full in Emacs. They may be better legible here on web when formatted in HTML.
I am working on similar project that uses PostgreSQL and could later use any type of relational database. In your writings I find many similarities.
My work is based on what I learned from proposals by Doug Engelbart. And I have created it for reason to be able to access 15000+ references from specific index for books. That way I can personally quicker pin point and find piece of information that I need.
By using database I created various types of destinations or types of nodes. One type is the node itself itself, so I can hyperlink from any node to other. I could hyperlink from tree to any other tree which then in turn makes it similar to your system.
If project is free I recommend stepping out of Github trap and using hosting providers that respect freedom, such as Sourcehut.org https://sourcehut.org or Codeberg.org (Germany) https://codeberg.org or Trisquel GNU/Linux-libre Git Repositories
https://devel.trisquel.info/groups/trisquel or Gitlab or Gitea, Framagit, etc.