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Why do new projects automatically create a new Workflow Scheme????? It makes no sense.
They also create a new Workflow by the way, so you can repeat the “delete all the things” exercise in the Workflow menu of Jira → Settings → Issues.
Finally the answer to the original problem statement can be found in the Workflow editor (same location). When you create a new status it asks you which category you want to associate it with. If you chose “Done“ then it gives you the tickmark.
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