> And in any real application you will need to interact with plenty of folders users cannot be expected to know, like Appdata.
I think a lot of what you'd store in Appdata in a "real" application will remain in browser storage or pulled from the server. A single file or folder with app settings, drafts, etc. should suffice. And even settings are probably better stored server side for user convenience so they can easily switch devices.
3. Native will allow for features from the kernel that
browsers do not impliment.
4. You cannot plan for how people will use such a wide feature as the Filesystem. Saying 'X and Y should fit' requires a significant amount of honest research and testing, with a very good reason as to why the change is necessary.
I think a lot of what you'd store in Appdata in a "real" application will remain in browser storage or pulled from the server. A single file or folder with app settings, drafts, etc. should suffice. And even settings are probably better stored server side for user convenience so they can easily switch devices.