1. How do I set the email notifications to use the HTML template?
2. Can I customize the fields/content that's in the email notification?
3. Can I change the structure of the subject line?
You can fully customize body and subject of the outgoing email using our addon - Raley Email Notifications.
I have read that JIRA onDemand doesn't give ssh access. It means you won't be able to customize the existing templates or add new ones. Not sure if you can do via an Atlassian support case but I would think it is a no-no!
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As stated in OnDemand Restricted Functions : "the procedure for customising email content sent in notification messages requires editing Velocity files within the JIRA webapp. This makes it a special case of "customising source files". See JST-1791 and JRA-7266 for feature requests to allow customisation of email contents through the web UI".
The suggestion would be to vote and watch the feature requests for further updates.
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