See this bug [1] and blueprint [2]. The people involved with those might be interested in our solution (a visual warning, while allowing nautilus to run as root) or might convince us that we're wasting time because nautilus should never be run as root anyway. I'd be interested to see.
Ryan [1] https://bugs.launchpad.net/ubuntu/+source/nautilus/+bug/12154 [2] https://launchpad.net/ubuntu/+spec/privileged-nautilus
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