Your JDex is your PKM
It might be my fault, but there can be confusion between what's your Johnny.Decimal system and, for those of you who are into 'personal knowledge management', what's your PKM system.
What's PKM?
If you're not into PKM, here's a quick primer. People enjoy storing 'personal knowledge': facts and thoughts and notes about whatever it is that they're doing or learning or anything.
Then they like thinking about exactly how to store this personal knowledge, because if you just chuck a bunch of notes in a folder you're unlikely to have a good time. That just became personal knowledge management, or PKM.
It's massive. Some significant percentage of YouTube is taken up by PKM. Discords and forums abound. Creators-a-plenty worship the god that is PKM.
What's not PKM?
I've never framed Johnny.Decimal as PKM; ref. that post I linked at the start. This is a conscious decision: for those who aren't into all that, and just want a way to neatly organise their files, I don't want it to feel like you have to join a cult just to be organised. You don't. You can keep it simple, be organised, and play outside.
But of course there isn't a clean break between these things. The Venn diagram of JD×PKM would look like a solar eclipse. So how do the two intersect?
JD is your PKM
The misconception is that you have this Johnny.Decimal system -- say, Life Admin -- and you have a PKM system. That might look like this.

All I mean when I say that JD is your PKM is that every piece of personal knowledge that you would like to manage must be linked to an ID in your system. In our highly contrived, too-neat-to-be-real example, it looks like this.

Nothing doesn't have an ID
That's all it is. If you're a good Decimal there should be no notion of a thing in your life that you can't fit into one of your IDs. That applies to personal knowledge in exactly the same what that it applies to your electricity bill or the confirmation of the flight you just booked.
And if you don't have an ID? Create one. You might need to create a new area or category to hold it. Do that.
'How do I PKM?' is answered
So the question of how to organise one's personal knowledge is that you organise it just like anything else. In a neat system, where nothing is buried too deep, where like concepts live near each other.
Johnny.Decimal, in other words.
100% human. 0% AI. Always.