Something changed in xinit-0.99.4 and it is now looking for a APP_MAN_DIR variable . This variable (is "macro" the proper term?) is handled by aclocal.m4 that is distributed with the package, but all the libtoolization overwrites aclocal.m4 with the one on the system -- /usr/share/libtool/libltdl/aclocal.m4. And the final file knows nothing about APP_MAN... so the man pages get stuffed in $(APP_MAN_DIR)/, which is "/".
Looks like Xcursor has this problem too, otherwise we could drop the libtoolization from just apps and be done with it. I wonder if it's an autotool oops upstream... I won't have time to look at this for awhile. A patch from anyone with a sane fix would be appreciated.
Every app we run autoreconf on will be broken in the same way.
Do you have the latest util-macros installed? Which version do you have?
Aha, you're right, that's the problem...
Well, the new release of x11-misc/util-macros (referring to 0.99.2) fixed the problem in this bug. Manpages are properly installed in /usr/share/man1, etc. I am now getting collisions on /usr/share/man/man4/mouse.4.gz which is installed by both man-pages and xf86-input-mouse, though.
There's another bug open for that -- bug #29541. I've updated the eclass's util-macros dep to fix this.