supernova ~ # equery files baselayout | grep X /usr/X11R6 /usr/X11R6/share /usr/X11R6/share/info -> ../../share/info /usr/include/GL -> /usr/X11R6/include/GL None of that stuff should be installed by baselayout, nor should anything else related to X. It just gets in the way of when X is setting stuff up.
Created attachment 50045 [details, diff] baselayout-1.11.8-r3.ebuild.patch For your convenience, here's a patch deleting all references to X11R6.
1.11.9-r1 does this now