That's what I'm saying. I don't see all my notes at the same time; I never try to see the entire picture nor do I ever worry about composing a new note, thinking it would just get lost in my mess. My knowledge graph looks like a complex web of interconnected nodes. I have over two thousand indexed notes and a few thousand plain-text, unindexed ones. The tools I've listed above do help you to find what you need easily. I treat my notes as my "personalized Wikipedia" - I don't need to know how it is organized or structured, where specific things physically exist, or in which file a specific text of a note sits. It is noise, but it is useful noise, because I have instruments to "extract music" out of it.