By dbus part I really meant PolicyKit “mechanism". The mechanism is a
separate program. Basically the mechanism is started with root
privileges and acts as a dbus server to which you can connect from your
client application (nvidia-settings) which is also called “agent”. When
you request the authorisation from the agent (which runs unprivileged)
you can call a function which is part of the mechanism. This function is
the one which should write the settings to the xorg.conf.

Maybe you could make your xconfigWriteConfigFile() function create an
array of strings which then you could pass to the mechanism's function
“kit_file_set_contents ()” (see the link below)  so that the contents of
the xorg.conf are set to whatever nvidia-settings generated. In this way
you can keep the parser in the agent and have just one function in the
mechanism.

http://hal.freedesktop.org/docs/PolicyKit/polkit-kit-file.html

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nvidia-settings doesn't have permissions to write xorg.conf
https://bugs.launchpad.net/bugs/200868
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