I would like to manage functional requirements by functional area and have traceability from high level functional requirements through to associated stories, development and then implementation. At the the moment it is all at an EPIC and issue level. There is much detail (technical, testing etc) I can't see what we are supposed to be delivering (I.e.what the client is paying for.) Can an EPIC belong to a Project Area that would belong to a Project that would belong to a Programme?
JIRA doesn't have relationships above the project level. You can imitate that with naming conventions, but I don't think that is what you're looking for. It sounds like you want a parent to child to grandchild type relationship, correct?
To add to what Joe said, I'd be taking a look at the Portfolio add-on, and maybe Tempo's Folio and Planner as well - these introduce more layers aimed at programme management.
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