I'd love for Google to figure out something comparable for the Drive API (currently it's not possible to grant read/write access to a single folder; you need to grant access to the entire drive!): https://issuetracker.google.com/issues/36760598?pli=1
I think the fact that the above issue has been open for a very long time is one indication of how difficult and sensitive this type of access control API is. The Google Drive API could be a proving ground for getting the UX right for this (including tricky details like how to manage persistent access to a folder with clear disclosure and user controls).
Is it really that complicated?
Why not just create per-domain browser-controlled folders (cert-linked?) that are abstracted into a simple read/write API via the browser (with subfolders allowed under that domain's root), disallow cross-domain access... and then build browser-mediated linking for use cases where you want to flow files from (non-domain) to (domain) to (non-domain)?
So essentially local storage with better integration with the actual filesystem, that's browser-controlled.
Allowing websites to have arbitrary (even user-approved) access directly to the real filesystem seems like a bad idea, when most use cases could be handled by a browser-mediated filesystem-like abstract view.