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.
The hub project can do this.
In the repository and branch that you want to send a pull request from:
$ hub pull-request -i 4
This uses the GitHub API, and attaches a pull request for the current branch to the existing issue number 4.
EDIT: Comment by @atomicules: To expand on the answer by @MichaelMior a full example is:
$ hub pull-request -i 4 -b USERNAME_OF_UPSTREAM_OWNER:UPSTREAM_BRANCH -h YOUR_USERNAME:YOUR_BRANCH URL_TO_ISSUE