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TMSU
TMSU lets you tags your files and then access them through a nifty virtual filesystem from any other application.
This gets posted here a lot [0], and I hate everything about it.
[0] https://hn.algolia.com/?q=johnnydecimal.com
A past coworker implemented a system like this. It was awful. He was the gatekeeper because the numbers and names had to be "just so" to meet his approval, and he was the most senior person on the team. He was neurotic in general and a pain to work with.
The idea of limiting yourself to a few top-level categories in a directory hierarchy and then doing the same with subdirectories makes sense, but adding numbers is a bad idea. It just creates more work, and other people have to learn your idiosyncratic nomenclature. Just give the directories good names and get on with it. Search really isn't as bad as the article suggests, especially with something like broot [1].
[1]: https://github.com/Canop/broot
https://github.com/oniony/TMSU/wiki/FAQ#why-does-tmsu-not-au...
There are a couple very barebones wrappers around mv and rm, though they could be better (pass through arguments, etc.).
https://github.com/oniony/TMSU/wiki/Tricks-and-Tips#filesyst...