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OK when I type 'startx' from the command line it fails because it's using the wrong XF86Config file. Somehow I made it use /root/XF86Config, (maybe that autoconfigurator is to blame)the one I wanted it to use is in /etc/X11/XF86Config. My question is: where do I go, what do I change to make it use the right one? Is it a hard or soft link that I need to change or am I way out in left field on that one?
XF86Config has been put in so many places throughout the years that, by default, XFree86 4.x has a prioritized list of various places where it looks for the file. So the answer is, if you delete the file it is currently using, it will go on to the next location in the list, and so on until the list is exhausted.
So deleting it would probably work. But why not just move or rename the file in / ? That way, if X doesn't find the other file, you haven't lost the one it likes.
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