We are interested in On Demand JIRA Agile and Confluence. Is there a way that we can link Shibboleth authenication methods to the ON DEMAND versions of this software?
No, OnDemand uses it's own authentication system (based on Crowd) and you can't connect other authentication systems into it.
Actually, none of the Atlassian stuff directly supports Shibboleth, but I'm sure I saw a Crowd plugin that enables Crowd to do it (which means all the Atlassian apps hooked into a Crowd can then use it). Not for OnDemand, obviously.
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