Although I had defined "net-www/apache doc" in /etc/portage/package.use (which was changed by portage to "www-servers/apache doc") the directory '/manual' is now gone after an world update :-( Reproducible: Always
BTW: After an n22 /var/log/portage # emerge --nospinner --newuse --update --ask --verbose --deep --tree world now the manual directory is back - w/o any changes from my side.
Sorry, we forgot to move the package initially, so your /etc/portage/package.use got out of sync with the tree.