In the User Installation Docs, if you jump down to Starting from Stage 2 it states: "export CONFIG_PROTECT="-*" # emerge -p system [lists the packages to be installed] # emerge system Note: The export CONFIG_PROTECT="-*" line ensures that any new scripts installed to /etc will overwrite the old scripts (stored in sys- apps/baselayout), bypassing Portage's new config file management support. Type emerge --help config for more details." This same statement should be at the beginning of starting from stage 3, assuming another bug about emerge overwriting compiler options you set is resolved. Otherwise you get a number of configuration files that should've been updated. At the end of the install docs should be a reminder that you may want to reset CONFIG_PROTECT. Reproducible: Always Steps to Reproduce: 1. 2. 3.
This is actually something that we don't want to do, see bug 14049.
