When enabling builds for Pull Requests in the GitHub Branch Source plugin and selecting the option to merge with head of target branch, the plugin will check out on the master to perform a merge and push a new commit.
This is slow when dealing with large repositories (especially with large numbers of PRs) and causes massive load of the Jenkins master with no guarantee of the mergability. The GitHub API offers a merge commit SHA that gets automatically calculated for each PR. Using this instead of merging manually is far more efficient.
More details about the `merge_commit_sha` are available at https://developer.github.com/v3/pulls/#get-a-single-pull-request