I found three deprecated references to /etc/make.conf in the Gentoo overlays users' guide. Of course the new filename of choice is /etc/portage/make.conf.
not our problem; we don't maintain anything in /project/. reassigning to the overlays team.
Updated deprecated paths to /etc/portage/make.conf. Thanks for reporting it. However there is also a new full updated guide in our wiki. http://wiki.gentoo.org/wiki/Overlay
*** Bug 456934 has been marked as a duplicate of this bug. ***