I'm not sure, but I have a vague memory of creating a github pull request with "Issue 4" or something in the title, and it automatically attached itself to Issue 4 in the project that I was submitting it to. I tried it again recently and it didn't work -- it just created a brand new issue instead. I don't see any options like "Attach to issue" on the new pull request page, nor "Open a new pull request for this issue" on the issue page. Is there any way to do this, to help project owners keep their Issues page clean and avoid duplication?
Edit: To clarify, I know that creating a pull request always creates a new issue. I would like to instead attach the pull request to an existing issue.
Adding a pull request to an existing upstream issue is easy assuming you forked using the normal github means.
Simply reference the issue in your commit message using any of the supported keywords:
For example: "this commit fixes #116"
The text referencing the issue does not need to appear in the subject line of your commit.
Push your commit to your github repo and the pull request will be automatically appended to the issue.
Note: While it is not required, it is strongly recommended that you commit anything that will be part of a pull request to a separate branch specific to that issue, because future commits on that branch will be appended to the pull request (automatically by github). So, if you didn't make a separate branch, left it on master, and then kept developing, then all your unrelated commits to master would get appended to your pull request.