In Centos 5.5, I've had this same experience over and over. I have no trouble installing CGI programs the old fashioned way (untar into /var/www/html and configure), but don't like un-rpm managed files floating about. So I can install, for example, phpMyAdmin, from EPEL.
That phpMyAdmin RPM drops files into a bunch of locations, the php files are under /usr/share/phpMysql
and then there are also:
/etc/httpd/conf.d/phpMyAdmin.conf /etc/phpMyAdmin /etc/phpMyAdmin/config.inc.php
and this:
/var/lib/phpMyAdmin /var/lib/phpMyAdmin/config /var/lib/phpMyAdmin/save /var/lib/phpMyAdmin/upload
In order to make this actually work on the web server, I copy the directory /usr/share/phpMyAdmin into /var/www/html and then I edit the /etc/httpd/conf.d/phpMyAdmin.conf. Then it works.
Then a new version of the phpMyAdmin RPM is released on EPEL, it gets installed, and I have no idea what I'm supposed to do to keep my thing in /var/www/html working.
I had the exact same experience with the mediawiki RPM from EPEL. It installs its files into /var/www/
var/www/mediawiki116
and
/usr/share/mediawiki116
The web server required everything to b e under /var/www/html/, so I copy files in there. The mediawiki116 documentation does not mention this problem, but I've googled long enough until I found this, which agrees with me that it is necessary to copy the files over in order to use the media wiki.
http://www.wikihow.com/Install-MediaWiki-on-Fedora
Unfortunately, now the upgrade path is obscured. When RPM updates its files (scattered over the file system), what to do?
--- Paul E. Johnson Professor, Political Science 1541 Lilac Lane, Room 504 University of Kansas