We are planning to set up Web SSO for Jira and want to pass http headers for Jira to trust as authentication. The Jira application will be hosted behind a webproxy that injects headers. The other option would be to use a SP component like Confluence Shibboleth Authenticator directly on the Jira application to be federated with SAML2 to our IDP.
John Hare took the Confluence Shibboleth Authenticator, made some modifications, and now it should work for Jira: https://github.com/UW-Madison-DoIT/jiraRemoteUserAuth
John and I talked about merging the codebase with the Confluence Shibboleth Authenticator and at some point we might, but as of Feb. 2013 we don't have definitive plans, and for now both of us plan to keep them as separate projects.
Our home in Jira Studio is going away, so you can find the Confluence Shibboleth Authenticator renamed as Confluence HTTP Authenticator at https://marketplace.atlassian.com/plugins/shibauth.confluence.authentication.shibboleth and https://github.com/chauth/confluence_http_authenticator
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