What's the best way to organize files on a disk?

Question

Work organization

What's the best way to organize files on a disk?
Let's take a banal example: let's say I'm preparing for the Olympiads and the Unified State Examination in physics and mathematics. Let's say I have books to prepare, I write all sorts of documents in LaTeX (I decide on a draft, transfer to LaTeX to make it beautiful, although search suffers here, the same Markdown or org mode would be better), I want all these files as to structure. I have two ways:

.
├── olymp
│   ├── math
│   └── physics
└── USE
    ├── math
    └── physics

or

.
├── math
│   ├── olymp
│   └── USE
└── physics
    ├── olymp
    └── USE

In other words, there are two (even more, but two will be enough for an example) ways to organize information. The question is how to resolve this uncertainty?

It would be very nice to put everything in one folder and tag files (KDE has this feature).

Answer 1

Who prevents to combine? You can write a script that will run through the folders and automatically create links.

.
├── olymp
│   ├── math
│   └── physics
├── USE
│   ├── math
│   └── physics
├── math
│   ├── olymp (символьная ссылка на /olymp/math)
│   └── USE   (символьная ссылка на /USE/math)
└── physics
    ├── olymp (символьная ссылка на /olymp/physics)
    └── USE   (символьная ссылка на /USE/physics)

Answer 2

Depends on how easy it is to search.
Whichever "tag" feels more important becomes the main category.
PS In my case, frequently used folders are bound to the keys 1, 2, 3, 4 - and it doesn't really matter how they are organized.

Answer 3

Still, things are better. That's clearer. The Olympiad is somehow secondary, but the scans of books, ready-made solutions and other things related to a specific subject will be in one place.
And another piece of advice not related to your question. Be sure to make regular backups. I realized this on my own skin when, many years ago, when reinstalling the system, I erased the folder with my thesis.