> - A note-taking tool that allows me to organize notes in a graph with links between them (like a wiki), not as files and folders in a tree, which enforces the invariant that every note is transitively reachable from some "root" (by following links) so I never lose a note.

There is a class of note taking apps that's becoming increasingly popular (at least I perceive it that way) that does this. They store notes in local Markdown files, and when you link between pages, they can build and render a graph based on them. For example:

- Obsidian: https://obsidian.md/

- Logseq: https://logseq.com/

- Joplin: https://joplinapp.org/ (not sure if it's built-in, but there's a plugin: https://github.com/treymo/joplin-link-graph)