I just installed unclutter on Ubuntu 12.04, Gnome 3, but it uses standard settings, and there is no way i can change them from terminal, not to mention i need to apply them from the very start.
I think the only way is to find Unclutter in the default script that runs it. But I dont know where it is and where to find it.
It is not in the startup applications, I checked.
rgrep -I unclutter /home/
only to find that actually the configuration is system-wide. ;-) – James Haigh Jul 2 '13 at 15:25