Time to bootstrap the system (See moving from stage 1 to stage 2). If you have multiple machines on the network, all with the same version of gcc, now is the when you'll want to configure your distcc configuration.
# cd /usr/portage
# scripts/bootstrap.sh
This will take a while to run (update: took 8 hours to run). If the bootstrap script fails, and you're re-using a portage tree (or possibly other files under /opt, /usr, /var, /home, /tmp or /var/tmp), then you may need to clean out the old files. (Generally not an issue if you're doing a fresh install.)
Once that finishes, run the following command.
# emerge system
Which will also take a while to run (last time it took around 5.5 hours). Update: Took around 4.5 hours this time.
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If you add nptl to the USE setting in /etc/make.conf, and use the bootstrap-26 script, you can boot-strap an nptl capable system.
If you're going through all the work of bootstrapping, it seems worth it to make these changes. You have to unmask a linux26-header ebuild as well. You do have to use a 2.6 kernel for the system though, 2.4 will fail to boot with a 'Kernel too old' error.
You can even create or use, a different profile, by changing the /etc/make.profile sym-link. You can try the bleeding-edge stuff with a gcc 3.4.1 compiled system and lastest system libraries, or try out the hardened profile.
If all you do is run the bootstrap script you're may-as-well just use one of the stage2 or stage3 tar balls.
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