Ian,
We do online backup of the DB
for the indexes we do a quick TAR when the server is offline
Find the best practices from jazz.net here or join us during Innovate 2014
https://jazz.net/wiki/bin/view/Deployment/
Ian Wark selected this answer as the correct answer
you can find a comprehensive guide to CLM backups here:
http://pic.dhe.ibm.com/infocenter/clmhelp/v4r0m6/index.jsp?topic=%2Fcom.ibm.jazz.repository.web.admin.doc%2Ftopics%2Ft_jfs_backup.html&resultof%3D%2522%2562%2561%2563%256b%2575%2570%2522%2520
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