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I have a bunch of entries that say "someone referenced this issue from a commit in someone/project" that are automatically inserted by GitHub in the comments of a reported issue.

ref this issue

These are not pull requests, so what are they useful for?

Moreover, some of them are orphan commits, that appear repeatedly when someone forces a push to GitHub. Can they be removed?

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They're useful in allowing you to cross-reference from one repository to another, so that comments or issues raised elsewhere can link back and have a point of context in a way.

They're also good for those who want to use GitHub as an issue tracker for the public, who you don't want to see your source code.

For example, you have a public repo that only allows users to open Issues. And linked with that you have a private repo where the code actually sits among your team. If you push a fix, you can close the public Issue tracker and that reference will show the context/reason.

This is also part of a social coding aspect, where you can have other forks and repos reference each other to create some kind of group focus.

You cannot currently stop this cross-linking behaviour.

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