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In the future, I believe it's better to identify the issue by the GitHub issue rather than a commit. Otherwise, it requires extra navigation which may not always work (e.g. if commit gets rebased or processed in some other way).
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I advise this because the commit view allows to see which tags/branches it is on. I wonder if that works in case of "Rebase and merge" / "squash"
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You can always navigate from issue to commit, not sure the opposite is true?
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In most cases you can, I'm not sure if there are exceptions. Anyway, the PR does not contain information about branches and tags, only the commit does AFAIK
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The exception is when a PR gets rebased (effectively, excluded from the tree). If the navigation works from the commit to the PR, it will work the other way around as well. At the same time, a PR or a commit not always exists (it can be just an issue), so from the consistency standpoint, it's better to link to issues and PRs instead of issues and commits. Additionally, issues usually contain more context, discussions, labels, etc.