I've stumbled on what I think is a bug of sorts.
1. Go to GH planning board.
2. New Card > Create a new epic
3. Give that epic a label under "epic/theme" field.
4. Now go to Jira, Create New Issue. Make a story and give it the same label name as you did in step 3. (It doesn't even auto-populate, showing it's totally unaware of the label you made in GH)
5. Go back to the planning board, find this new story you made in step 4.
6. Notice there is no epic assigned to it though you chose the same label as you did for the epic.
It seems to me that GH's labels for epic/theme use are separate from the labels Jira uses otherwise.
You're correct, and this is actually the intended behavior. The epic field is a separate "label-type" field, than the normal labels field itself.
thanks Tim!
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