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Specifically each profile is associated with a set of requirements, and a precedence value. On X startup the Xsession.d script will check for each profile whether the requirements are met, and then activate all those profiles whose requirements are met in order of precedence.
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Exactly how a profile is activated depends on the profile kind (you don't need to know this in order to use this package):
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For KDE, Freedesktop, XFCE (>= 4.2), ROX, GNUSTEP and UDE activating profiles is done by setting environment variables: KDEDIRS for KDE, XDG_CONFIG_DIRS and XDG_DATA_DIRS for both Freedesktop and XFCE, CHOICESPATH for ROX, GNUSTEP_PATHLIST for GNUSTEP (usually initialized from the various GNUSTEP_*_ROOT variables) and UDEdir for UDE. With the exception of UDEdir, which takes a single directory, each of these variables takes a precedence ordered list of root-directories (of activated profiles).
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As the default system-wide path file (/etc/gconf/<gconf-version>/path) currently doesn't include the generated path files you'll need to replace it with one that does (/usr/share/doc/desktop-profiles/examples/path is a path file which will give the same behaviour as the default gconf setup as long as no additional profiles are present).
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For GConf profiles two user-specific path files are generated. One containing the activated mandatory "configuration sources", one containing the default "configuration sources" that are activated. At the moment the default system-wide path file doesn't include these automatically, this package provides a script (/usr/sbin/path2listing) that looks at your current configuration and adapts so your configuration sources are controlled by desktop-profiles (see the man page for path2listing or the /usr/share/doc/destkop-profiles/README for more information on this).
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Environment variables will only be set if their value is different from the default value, and user-specific path files are only generated if the systemwide gconf path file will include them. This to avoid unnecessary clutter.