Since the old make.conf path /etc/make.conf is now officially deprecated (see also bug#452176), all ebuilds, eclasses, documentation etc. still referring to the old path should be updated now to the new default path /etc/portage/make.conf. This meta-bug is used as a tracker for all related bugs.
Assigned to user, feel free to take it away if you feel you need to track this.
Dead tracker.