On Mar 10, 2011, at 6:30 AM, Jesús J. Guerrero Botella wrote:
> 
> 
> Another random cause I can think of would be some of the cruft
> cleaning scripts that there are around and that are not part of
> Gentoo.
> 
> On a more paranoid though, it could also be a rootkit, or maybe your
> box was hacked.
> 
> But, otherwise, you removed it, maybe without noticing.
> 
> --depclean would never remove this, even if it was buggy enough to
> remove all your kernels (which it isn't) it wouldn't remove all the
> files that do not belong to the package, and there are thousands of
> these in any kernel tree that's been configured and/or compiled.
> Hence, the non-empty directories would never be removed either.
> 
> -- 
> Jesús Guerrero Botella
> 
> 

If you have anything you wish me to check, I will.
But I know that I did not remove it.

I su'd in the terminal, started the updates, and as mentioned eventually saw 
the nvidia-drivers complaining about not finding a .config.
That is what led me to discover the missing directory.
I update the system regularly.

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