When the "Apply system-wide..." button is pressed, changes are written
to /etc/environment. However, this file is written incorrectly because
the username/password is omitted.  Also there is no no_proxy setting for
the ignored hosts.

This is easy to observe.  Change the gnome-network-preferences.  Press
"Apply system-wide".  Open a terminal and

set | grep proxy; cat /etc/environment

to observe the differences.

-- 
Setting the network proxy doesn't change the synaptic proxy settings 
(gnome-network-preferences) for authenticated proxies
https://bugs.launchpad.net/bugs/300271
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