In my opinion this problem should be addressed at an application level
rather than in the file manager, perhaps creating a standard gnome
privilege escalation framework that apps can use to change permissions
WHEN A FILE IS SAVED. I think implementing this in the file manager and
having the escalation dialog come up whenever a user OPENS a file is the
wrong approach and would reduce the mental barrier ending up with a
system like UAC which everyone just clicks through without thinking
about.

For the moment I think determining which apps in the default install are
most often effected by this bug should be a priority. From my only
experience this problem is most often experienced in the text editors I
use: gedit and nano. Obviously people use different console editors but
gedit is the only GUI editor in the default install and as such would be
a great place to start.

The only other application that I recall this problem effecting (at the
moment anyway) is nvidia-settings which can be launched as a user but
doesn't allow the xorg.conf changes to be saved unless started with root
permissions.

@Moonsurfer_1
Just wanted to point out that you can open files as with admin privileges from 
nautilus, install the package nautilus-gksu and after you restart 
nautilus/logoff-on, you will have a right click option to open as 
administrator. I personally think this should be installed by default.

-- 
Allow user to authenticate when an operation fails because of lack of 
permissions
https://bugs.launchpad.net/bugs/389847
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