I used tmsu ("tag my shit up") for a while, but it required too much discipline and then I dropped it.

In addition, tools like fzf for fuzzy file-search (comes with shell integration to e.g. replace the default history search in bash) and ripgrep-all made this kind of organization unnecessary for me. It now suffices to have a vague idea where a thing is located and I can do a brute-force search in a few seconds.

The next-level filesystem argument is brought forward every few months, but I'm not buying it.