Bug 213436 has cropped up again: app-admin/webapp-config-1.50.16-r1 collides with app-portage/eclass-manpages-20091209 on the file /usr/share/man/man5/webapp.eclass.5.bz2 The collision was introduced in revision 1.14 of app-admin/webapp-config/webapp-config-1.50.16-r1.ebuild. View diff at: http://sources.gentoo.org/cgi-bin/viewvc.cgi/gentoo-x86/app-admin/webapp-config/webapp-config-1.50.16-r1.ebuild?r1=1.13&r2=1.14 (specifically line 47)
This problem is resolved in app-admin/webapp-config-1.50.16-r3 with rm -f doc/webapp.eclass.5{,.html} , which is ~arch-masked. Please consider stabilizing app-admin/webapp-config-1.50.16-r3.
Just an FYI here, -r3 *does* have the collision too.
@Jeremy Apparently you're the victim of bug 294266 and you have all required dependencies installed to get webapp.eclass manpage actually generated.
It should be fixed now.