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excluding sub-directories from mod_jk (mod jk) and allowing apache to execute them natively can be done with with SetEnvIf no-jk. simply add the following code to either the httpd.conf or the mod-jk.conf
DocumentRoot /var/www/html/
SetEnvIf Request_URI "/munin/*" no-jk
JkMount /* ajp13
In this case we are running munin with jboss/tomcat and want to run the perl code in the apache httpd environment at the same time forwarding all other requests to the root /* to the jboss/tomcat server