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"How about YaST and SaX for starters"
I've been trying to get 3D to work on SuSE 9.1 with SuSE's ATI driver in the sense that I been trying to get /usr/X11/bin/fgl_glxgears to show some gears rather than just immediately bombing out with the error: couldn't get fbconfig. But so far no luck. Maybe I'll try ATI's driver or buy a Nvidia card instead.
My point is that SaX - actually SaX2 - puts a comment in /etc/X11/XF86Config to please not hand edit the file. On the other hand, SaX2 does not support tweaking the file for support of 3D.
I don't know much about xml but maybe some of such problem would disappear if XF86Config instead was in xml format such that it could be edited both with an xml aware editor (=future SaX2) and a flat file editor without stepping on each others toes while still being human readable at a glance which it would not be if stored in a traditional database.