I run Debian Stretch (testing) as my daily driver, and at some point I stopped being able to start programs like start Synaptic, Gparted, Synaptic etc. without manually typing
gksu(do). The solution is as simple as it is seemingly unnecessary and stupid:
sudo apt install policykit-1-gnome
The problem is apparent upon reading the description:
This implementation was originally designed for GNOME 2, but most
GNOME-based desktop environments, including GNOME 3, GNOME Flashback,
MATE and Cinnamon, have their own built-in PolicyKit agents and no
longer use this one. The remaining users of this implementation
are XFCE and Unity.
Reported as Debian bug #843224. My first?
D’oh, I wrote this on November 5, 2016. I’ll still publish it anyway in case it’ll still help someone searching for a solution.