This is our experience in standing up another Avalon system on the same host to do red black blue-green deployment.
Clone Fedora
In Tomcat, copy webapps/fedora to webapps/fedora3.
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Copy /usr/local/solr/avalon to /usr/local/solr/avalon_r5Unload and clean out Solr index: http://localhost:8983/solr/admin/cores?action=UNLOAD&core=avalon_r5&deleteIndex=trueRecreate core
Clone Matterhorn
Copy matterhorn and opencast folder to a new location.
Edit links and paths in /usr/local/matterhorn/etc/config.properties
Clone database
Give it a new name
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Cap deploy from your local machine to server. For really large repo, you may want to migrate and reindex separately in a screen/tmux session.
Make sure your background jobs are running and pointing to new Avalon location.
Reindex Solr
Manually kick off rake avalon:reindex. This can take a very long time if you have a large collection, better run it in a tmux session.