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I believe I've figured out why all of the changes appear in each build changelog rather than just the actual changes in the pull request. In the `if` block at https://github.com/jenkinsci/git-plugin/blob/master/src/main/java/hudson/plugins/git/GitSCM.java#L1128 the merge is performed with the specified branch. However, as far as I can tell, nowhere in that block is the merge branch updated from `origin` so the merge is always on top of, potentially, an out of date copy of the branch. Therefore `git whatchanged` is looking at an old rev as the starting point.