Here is the scenario:
The pull request on github says that there are no merge conflicts. Cloning the repo locally and merging the two branches also does not result in merge conflicts.
But, when the PR build of job on the 'Github organization' job type is run, it shows that there is a merge conflict. Here is the output:
hudson.plugins.git.GitException: Command "git merge 8b64e2f2ac7cb47ea99f267bbfa05fac17259277" returned status code 128:
stderr: error: 'merge' is not possible because you have unmerged files.
hint: Fix them up in the work tree,
hint: and then use 'git add/rm <file>' as
hint: appropriate to mark resolution and make a commit,
hint: or use 'git commit -a'.
fatal: Exiting because of an unresolved conflict.