Interesting that this comes up again with Ubuntu Trusty continuing to retain Xorg. Is anyone familiar enough with Mir and Wayland to comment on how those packages approach this kind of thing?
We really need some hard boundaries set between non-interactive and interactive requests to open files.
Sensible ones too - not "ask about every file", but maybe "grant process access to this folder in my documents folder, without recursive access".
Even better would be "fire this backup utility first, then grant access".