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In case of "upstream" remote, it takes precedence over "origin" remote (this was a highly requested feature). Pull requests are always created against the canonical ("main") version of this project, which is pointed to by "upstream" remote. Is it an option for you to swap the names of your remotes?
Also, you can try hub pull-request -b OWNER:master, where "OWNER" is the username/org name of the repo against which the PR should be opened on.
Have an edge case here, I think, where the "upstream" remote repo has a different repo name from the "origin" repo.
I haven't found a way to make a pull request into the "origin" repo without removing the "upstream" remote.
Is there a way of doing it?
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