If you are having problems with permissions on RHEL, Fedora or other RHEL workalike, check /var/log/messages for issues with SELinux permissions.

Because cmmlwiki installs by default outside the normal /var/www tree, you need to use chcon to change the types of objects to satisfy SELinux.

The CGI needs to be of type httpd_sys_script_t. The CMMLWIKI directories need to be of type httpd_sys_content_t.

There is another gotcha. libannodex seems to access the source directories, I'm guessing because of compilation with -g. So all the directories on the path to annodex-core/libannodex/src/importers and all the contents of that directory have to be of type httpd_sys_content_t to satisfy SELinux.

When you have no more messages in /var/log/messages from SELinux, then permission problems are just plain Linux/Unix permission problems.