If I use the jgit implementation in a job which should merge from multiple branches, the merge result is not pushed back to origin. Merge result is pushed if I use the command line implementation in the same job.

Steps to duplicate the problem (with apologies for the number of steps)

1. Create a bare git repo on the master node as Jenkins user
   1. rm -rf /tmp/changes.git /tmp/changes
   2. git init --bare /tmp/changes.git
   3. echo "#! /bin/sh" > /tmp/changes.git/hooks/post-receive
   4. echo "curl --silent http://127.0.0.1:8080/git/notifyCommit?url=/tmp/changes.git" >> /tmp/changes.git/hooks/post-receive
   5. chmod a+x /tmp/changes.git/hooks/post-receive
   6. cd /tmp
   7. git clone changes.git
   8. cd changes
   9. echo "Git plugin 2.0 no longer shows changes from merges" > README
   10. git add README
   11. git commit -m "Add README to describe this repository" README
   12. git push origin master
2. Create a Jenkins merge job using that bare git repo
   1. Create a new free-style software project "merge-changes"
   2. Restrict where this project can be run
      1. Label Expression: master
   3. Git source code management settings
      1. Use jgit rather than default
      2. Repository URL: /tmp/changes.git
      3. Branches to build: */master*
   4. Additional behaviors: Merge before build
      1. Name of repository: origin
         1. (error on merge if this is blank - help says should use default, but didn't)
      2. Branch to merge to: master
   5. Poll SCM (for convenience with the git hook installed earlier)
      1. H * * * *
   6. Add post-build action: Git Publisher
      1. Git Publisher settings
         1. Merge results: Yes
         2. Branches:
            1. Branches to push: master
            2. Target remote name: origin
   7. Save the job
3. Build Jenkins job
   1. curl --silent http://127.0.0.1:8080/job/merge-changes/build?delay=0sec
4. Create new master-add-timestamp branch and commit from it
   1. git checkout -b master-add-timestamp
   2. date >> timestamp
   3. git add timestamp
   4. git commit -m "Add timestamp" timestamp
   5. git push origin master-add-timestamp
5. Jenkins job runs
6. Confirm master branch did not receive the merge result
   1. git checkout master
   2. git pull
   3. git log