The aforementioned workaround needs to have an appropriate XAUTHORITY
environment variable defined.

To sudo without doing this (e.g., from a command line process), try
something like the following:

# assumes the $USER and $HOME directories are defined somehow
DBUS_SESSION=$(grep -v "^#" $HOME/.dbus/session-bus/`cat 
/var/lib/dbus/machine-id`-0) 
sudo -u $USER $DBUS_SESSION gconftool-2 --type string --set /system/proxy/mode 
manual

-- 
gconfd does not refresh cache when sudo-ing current user to modify setting
https://bugs.launchpad.net/bugs/290647
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