This repo reproduces a problem with GitHub's "resolve conflicts" feature. The issue occurs when merging into a non-master branch from the master branch of a fork.

The result is that a merge commit is created, but conflicts still exist fo the pull-request.

Steps:

  1. Create a new repository on GitHub, adding a dummy file foo.

  2. Check-out a new branch updated-upstream.

  3. Commit and push an edit on foo to origin/updated-upstream.

  4. Switch to a different GitHub account and fork the repository.

  5. On the fork, edit foo in a conflicting way on the master branch.

  6. Create a pull request from master to updated-upstream.

  7. Resolve conflicts via GitHub. This will create a merge commit from updated-upstream to master, when the merge ought to be from master to updated-upstream.

See #1 for the result.