The object store I have created offers a fast, convenient way to attach multiple tags to each object. Each tag is a single value which can be a string, number, boolean, datetime stamp, etc..
You can still organize things using folders, but you can query for things based off their tags as well.
So, you'd tag all these files with .. what? "pnpm, node_modules"?
find $HOMEBREW_PREFIX/opt/pnpm/libexec/lib/node_modules -type f | wc -l
1450
For your .pdf or .docx that are just lumped into $HOME/Documents, I'm with you, they don't exactly need "folders" but a _filesystem_ based only on tags would be horrific in any python or node shop since their primitive unit is a file within a folder
You can still organize things using folders, but you can query for things based off their tags as well.