This is our experience in standing up another Avalon system on the same host to do blue-green deployment.
In Tomcat, copy webapps/fedora to webapps/fedora3.
Copy /usr/local/fedora to /usr/local/fedora3
Copy /usr/local/tomcat/conf/Catalina/localhost/fedora.xml to fedora3.xml and point "fedora.home" to /usr/local/fedora3
Clone avalon Solr core
In /usr/local/solr/solr.xml, clone core avalon and give it a new name, eg "avalon_r5"
Copy /usr/local/solr/avalon to /usr/local/solr/avalon_r5
chmod -R g+w /digitize/dropbox/are running
Give it a new name
Deploy Avalon to new folder
Make dir /var/www/avalon_r5
Copy shared folder from /var/www/avalon to avalon_r5
Edit shared yml files to reflect changes in DB, Fedora, Solr
Add new virtual host with new domain name to etc/httpd/conf.d/avalon.conf and ssl.conf
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.
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.