i was using 'yum upgrade'. the doxygen issue is that a new package must have been made, but the addons directory didn't get updated. it's not obvious what should be done in that case. the php-manual issue is just that php-manual isn't built anymore. i was hoping that there was a way to tell yum (via the repositories) that a package was obsoleted by "nothing" and would just get removed. i guess that a dummy package that has no new files but obsoletes all the old packages could do that. kinda funky but might be helpful.