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In summary, the directories containing configuration files which need to be modified are:

/opt/shrine/tomcat/** ← Tomcat homeconf/ ← Tomcat configuration files

/opt/shrine/tomcat/lib/ ← Shrine config files

/etc/shibboleth ← / ← Shibboleth configuration files

/etc/httpd/** ← Apache configuration files

/var/www/html/ ← Apache static content as set in, for instance, /etc/httpd/conf/httpd.conf

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