When I add new stories inmy backlog, I assign them the "affected version" I target this story to be part of.
The Version panel on the left hand side actually filters on the "Fix Version", which is of no use to me. When the story is completed, the "Fix Version" is actually filled-in by the team of developers. I would make more sense to me to be able to filter my stories by "affected version" instead of "fix version", since anyways my stories are removed off my backlog one "Resolved" (or Completed)...
How could I do this?
I think that the only way for you to do that is to build a quick filter and activate it while in the "Active Sprint" view.
However, most people use the Fix Version to plan their releases. If your team is in control of the Fix version, it is most likely because they assign the exact release version at the end of the sprint. Since JIRA allows many Fix Version simultaneously, you could still take control of the Fix Version. As a product owner, you are in control of the Major and Minor versions. So you could create a version called "3.1.x" or simply "3.1" and plan your release accordingly. When the team builds the functionality of a story, they add another version with the fix and/or build version (e.g. "3.1.21" or "220.127.116.11"). So, you can still use the Agile Version Reports to track the progress of your release.
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