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If you're looking for agile power-ups to GitHub Issues, there's a few great options in the ecosystem. Check out ZenHub if you're looking for things like issue dependencies, epics, multi-repo boards, etc. and want to stay in GitHub. GitKraken Boards are also a great option and integrate with their Git GUI.

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My team uses ZenHub extensively, but it's not that great for OSS projects IMO. The extra metadata and organization that ZenHub allows isn't visible via GitHub issues, so it's basically just for the core team.

Issue dependencies should be part of the core issue tracker. And GitHub has multi-repo boards, but only for repose in the same org.

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