Would like stories/bugs to get automatically marked as done when the release is "released". Alll things tied to that fix version should be marked as done.
This is quite a complex one and I suspect you'll need to do some scripting or coding. I'd suggest a look at the scripting and automation apps in the marketplace to save yourself coding.
I know ScriptRunner can do this because I've done similar things (but feel free to ignore that as a recommendation as I work for Adaptavist). I think Power scripts can do it, but I've not tried, and it might be possible in Automation as well, but I'm less sure, as it's not quite scripting.
You will want to write a listener that can pick up "version released", parse over the items in that version and (this is the hard bit) for each issue, look at where it is in the workflow, and work out what sequence of transitions to push it through to get it to the "done" status you want it in.
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