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If you want to make changes to the upstream, I suggest adding an extra mirror in between the upstream and the repo you want to add the submodule in. That way, you can maintain your version without worrying about how your other code is affected. Only after it is tested do you then merge it into your other repo.

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The projects I add as submodules are all hosted on Github. For those that require modification, I would fork (mirror) the project, commit the changes to my fork, and add the fork as a submodule to the parent project I'm working on. So, yes, I do add an extra mirror in between but it's really because I lack contributor permission to the main repository.

Also, if repository A and B reference repository C as a submodule and I update repository C for A, B would not be affected since submodule references are just commit IDs. There's no need to create two additional mirrors (C-for-A and C-for-B) if that's what you meant.

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