How do you organize files?

Hierarchy in file system was a great invention, popularized by Unix. Files in directory, directory in directory. Creating a tree. Files get designated place in the file system. People are using in well functioning manners, at least as I think they are doing, and I am unable to.

I have spend countless minutes to think just how I would put certain files, what would be the name of the directory, where should it be allocated, how would I access it, can it be done quickly, will I remember where I have put it?

Think for example, the source code of programs. should I put them in 'code' named folder. Then what would I name the folder where I am learning Ocaml. Where would I put this source of Raylib, the various markdown files, what happens to got repos I own and fetch. Well, writing this I am getting the feel that the answer to this maybe self exploratory for this example.

Think another one. PDF documents. There are a lot of PDFs I have here and there. Books on various subjects - from math, physics, CS to botany, mycology. Papers of various kinds. Article, RFC, manual, specification, and many more. How do I arrange them in accessible way? I don't know how to do at the way that would satisfy my thoughts.

How about the media download using Torrent, or the contents I am trying to make. Just make a folder on desktop! Help me!

I find myself wondering how many other experienced computer users do it on their machines. I lost my mind in it.