Yes. You can still choose stuff built specifically for your architecture (depending on which iso you downloaded), but you won't be compiling anything with a stage3 install. Thus, you will be unable to tweak optimizer flags and USE variable stuff.
Spoke too soon. You still have the option to build all of your "user-level" apps. What you'll be skipping is the "emerge -u system" step. To get a list of what this will do, you can do an 'emerge -up system' and see what it looks like (if you already have a stage1 system running). I'm pretty sure this is mostly stuff like awk, sed, perl, python, etc. All of the stuff that you need to have a "functioning" gentoo box.
With the stage3 setup, you'd install most of your user-level apps like mozilla, gnome/kde, <whatever else you want>.
HTH
-- Stephen W. Juranich [EMAIL PROTECTED] Electrical Engineering http://students.washington.edu/sjuranic University of Washington http://ssli.ee.washington.edu/ssli
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