Organising your notes is the thinking itself, not a chore you get out of the way first. When you decide that one note belongs next to another, or that an idea fits one topic rather than another, you have to ask yourself what it means, what it clashes with and what it is good for. Only you can make those connections, because they grow out of your context: what you already know and what you care about.
That is why handing the job to AI costs more than it seems to save. The machine gives you back a tidy system, but the order reflects how it understands the material, not how you do. You end up with an archive the AI can find its way through and that you no longer recognise as yours, and you miss exactly the moment when a loose idea becomes your own.
The line runs between administrative and intellectual work. Filing receipts, moving files by a rule or summarising a meeting is maintenance, and there AI helps a lot. Deciding how two ideas relate is something else.
None of this means keeping AI away from your ideas. It can suggest connections, synthesise your own notes or ask you questions, as long as the last step is yours: you judge what it proposes and let into your system only what truly fits. There is a practical side too. As Nick Milo puts it, AI is a brilliant amnesiac: it forgets everything between one conversation and the next. The context you give it, in files you own, is what makes it help you think instead of thinking for you. For the same reason, AI can take over the upkeep of your system once you give it the map. Maintaining is not the same as connecting.