The problem is defiantly not with the theme or any specific plugin. The problem is the fatal error thrown anytime an include or require is seen.
My only other suggestion is to open your php.ini file and find the line
include_path=".:/usr/local/lib/php"
and comment it out by placing a ; infront of it so it looks like this:
;include_path=".:/usr/local/lib/php"
This will cause php to use the default include path which might fix the problem.
After you make the change restart apache $ /etc/init.d/apache2 restart
or $ /etc/init.d/httpd restart
or $ service httpd restart
depending on what distro of linux your running.
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