This resonates strongly with the product we are working on, featuring a new paradigm to "go beyond" filesystems and address this very problem.

While I don't have a solution for you today, if you shoot me an email (see profile) I'd be honored to extend an early invitation once we get into beta :)

I use the PARA system across all my platforms and it works great. https://fortelabs.com/blog/para/

And it should go without saying on hn that the everything software you seek is emacs org-mode ;)