Manually copied over from https://github.community/t/feature-request-prevent-issues-from-being-closed-by-merging-linked-prs/3255 (where https://github.com/akshaymankar was the original requester). I really like how the linked PRs in an issue are listed nicely on the project board as well as in the right side of the issue. It really makes discovering PRs from issues easy. In my current project, we don’t close issues until they reach production. Also, often we have multiple PRs which fix an issues (in multiple repositories). In such cases I do not want the issue to be autmatically closed, currently I just re-open them. This is not ideal because I could forget to re-open the issue and also this workflow causes a lot of notification noise in my team. It would be nice if this could somehow be configured, or if there was another keyword (instaed of fixes, closes, etc.) to signify that a PR only partially fixes an issue and the issue and the issue must not be closed auotmatically even after the PR is merged.

Users can now choose whether merging linked pull requests automatically closes the issue --check out the announcement!

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Answered by tuves