Not possible to save custom controller profiles

In #102, a user was confused about not being able to update the core info files; trying to do so results in a `EROFS (Read-only file system)` error. For data that is supposed to be read only like core and content databases, this is benign though a bit confusing.

> Correct, the .info files are shipped with the Flatpak, and are updated periodically through the Flatpak package.
>
> Would like to disable Online Updater menu items for components that are handled through Flatpak:
> - Info files
> - Assets
> - Shaders
> - Joystick Autoconfig
> - Database

_Originally posted by @RobLoach in https://github.com/flathub/org.libretro.RetroArch/issues/102#issuecomment-461519964_

However, joystick autoconfig is different. It's desirable to ship with some autoconfig so that common controllers are supported, but users may need to be able to configure their own controllers that aren't in the database. In particular, the Settings -> Inputs -> User 1 Binds -> User 1 Save Autoconfig button can never work. It always fails with "Error saving controller profile." Even if the user does copy an autoconfig file from a non-Flatpak install, that file will be ignored.

Is there any way to overlay .var/app/org.libretro.RetroArch/config/retroarch/autoconfig on top of the /app/share version? Or maybe RetroArch needs to grow support for a list of directories instead of just one.