Actually yeah that sounds pretty good.
For Desktop/Finder/Explorer you'd just need a nice UI.
Searching Documents/projects/etc would be the same just maybe faster?
All the arbitrary stuff like ~/.npm/**/* would stop cluttering up my ls -la in ~ and could be stored in their own tables whose names I genuinely don't care about. (This was the dream of ~/Library, no?)
[edit] Ooooh, I get it now. This doesn't solve namespacing or traversal.