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As per this answer https://answers.nuxeo.com/questions/6389/upgrade-from-571-to-572/6403 by @ Julien Carsique
About Shibboleth, you should use a configuration template instead of manually copying files into the server structure.
I've read this page http://doc.nuxeo.com/display/ADMINDOC56/Configuration+templates several times over the last month and can't figure out how this works. Can anyone give me some more hints about how I would go about creating a configuration template for shibboleth?