I have PORTDIR="/usr/gentoo/portage" in my make.conf instead of default "/usr/portage", and after each baselayout upgrade I need to manually remove /usr/portage directory, which is empty (only the .keep file). Looks like this is caused by "kdir /usr/portage" line in baselayout ebuilds. Would it be possible to make baselayout honor user's PORTDIR setting?
done