I am using scm-sync-configuration plugin with github. I have a nice README.md telling people not to edit the configurations directly as they are managed by scm-sync-configuration.

The bug is even when I modify the README.md, scm-sync-configuration fails. This is because the remote repository is ahead of the local checkout by 1 commit.

This is actually not a problem as the README.md is not a conflicting change! In git a pull will update your local checkout without issue.

Repo case:

1. Already have scm-sync-configuration syncing with github
2. Modify the README.md
3. Change a job

Expected result:
The change to the job is pushed up to github

Actual result:
Sync fails.

How to fix

1. On Jenkins master go to $JENKINS_HOME/scm-sync-configuration/checkoutConfiguration/
2. git pull
3. git commit --amend --author 'Jenkins Continuous Build server <jenkins@localhost.localdomain>'
4. git push
5. clear the scm sync error at bottom of Jenkins page
6. restart Jenkins master (I use http://JENKINS_URL/restart)

The last step is needed as this is another bug with scm-sync-plugin where if you modify the scm repository on disk, its internal in-memory data structures are out of sync. So you restart Jenkins to clear the in-memory state.