Set root to subdirectory in file view/cleanly work with nested vaults?

Things I have tried

I have tried looking for plugins that can achieve my goal but I haven’t found any.
I have also tried working with nested vaults, but that doesn’t work to well.

What I’m trying to do

I am trying to set the “root” of the file view to a subdirectory of my vault.
I want to have one big vault for all my projects and link stuff between them, but it gets very messy with all of the subdirectories. Is there a way to set the root of the file view or to have cleanly nested vaults?