You can create the tree structure from a relation. Not a primitive data store operation at all. Just add the attribute: parent directory and voila.

So often we want to look up 'the last file I printed' or 'that message I got from Bob'. Instead of just creating that lookup, we have to go spelunking.

Hell, every major app creates it's own abstractions because the OS/Filesystem doesn't have anything useful. Email systems organize messages and tags; document editors have collections of document aspects they store in a structured blob. Instead of asking the OS to do that.