Files are named hierarchically with periods. I have top-level categories that have changed little over the years. `con.` for concepts, `lit.` for documents, `proj.` for projects... you get the point, I'm not listing all of them unless someone really just wants me to.
My go-to example is always Star Wars. `lore.sw` is my top-level Star Wars note. I also have `lore.sw.chron` which is the chronological watching order. There's also `game.sw` which contains a list of Star Wars games I've found.
This extends to non-note files as well. For images of something I use `.img.[date].#.[ext]`, so for example I have some pictures of my cat named `ppl.neck.img.2024.03.15.1.raw`. I have a video of him murdering a bird too, `ppl.neck.vid.2024.05.22.murdering-a-bird.mp4`... As you can see, sometimes I replace the number with a nice title.
The modularity of it all is great. I can add anything anywhere at any point in the hierarchy without having to re-name things. I name things exactly what they are. The hierarchy can be sparse, parent notes don't have to exist. I can name something `stuff.something.i-dont-know.gif` without having any notes for `stuff.` or `stuff.something.`
I have notes on paper as well, and they use the same system, with the hierarchical name printed in bold at the top of the paper. `self.passwords` is a paper note for obvious reasons. I also keep most of my `sys.internal.` documentation on paper because my computer might not work when I need it most, though a lot of them do have computer versions which I just print out when I change because it's too much to write by hand.