(*)For example, I've set up a new system. I want to preserve most of the system defaults, and especially if there is a new feature I don't know about, I don't want to remove it from the conf-file. But there are about 20 settings I really want to keep. So I have a script with lots of lines such as:
gconftool -t string -s /apps/metacity/general/button_layout 'menu:minimize,maximize,close'
I can run these commands inside a running GNOME session, and they immediately take effect.
[Sadly, KDE doesn't have such a system, as far as I can tell. It's impossible to script the setup of a KDE system in a non-brittle way]
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