After your updates do you run etc-update in the automatic mode?  If so don't do that.  
Run it and check the files it wants to update. Let it do the ones that you haven't 
modified and then look at what it's doing with each of the remaining files.

> 
> From: Jimmy Rosen <[EMAIL PROTECTED]>
> Date: 2004/01/13 Tue AM 09:53:45 EST
> To: [EMAIL PROTECTED]
> Subject: [gentoo-user] Problem? : emerge -pu system: baselayout overwrites make.conf
> 
> I've been using gentoo for a while now. Every time I have updated 
> baselayout it has overwritten the make.conf file automatically with a 
> default file. I've tried protecting it but to no avail.
> 
> Is this as it should be?
> 
> I'm asking because it's about time for another system update
> emerge -pu system
> and that will bring in another update to baselayout, as well as a whole 
> bunch of other stuff.
> As baselayout is somewhere in the middle of this, and before portage itself 
> is updated and emerge-ing the system is restarted, the make.conf file will 
> be overwritten in the middle of my system update. Now, since that will 
> overwrite my use flags, does it mean the rest of the update will be 
> compiled with the default use and make flags?
> 
> I'd be glad if someone could enlighten me on this particular pickle.
> 
> Harebrafolk
> Jimmy
> 
> 
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