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I work on a large software project where many vendors contribute have forks of a shared repository. Everyone has their own internal repositories and issue trackers. The problem that I'm trying to solve is to let people use the relatively common practice of including the phrase:

fixes #123

This has the awesome feature of automatically closing issues and (at least on GitHub-like servers) automatically linking issues, commits, and pull requests.

However, if we all start putting these magic phrases in our commit messages, we'll conflict with each other and start closing issues all over the place. Does anyone have suggests on ways we could mitigate the problem that don't involve just saying, "Don't do that"?

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This is covered in closing issues across repositories - the key being you need to reference the repository fully rather than use the implicit 'this repo':

fixes user/repo#42

You will still need to be careful that you don't close an issue somewhere else unless you really mean to close it.

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    This isn't a GitHub specific question. Some places use GitHub, but others use something else like Trac. – Wesley Bland Mar 16 '16 at 17:46

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