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Hi,
Workaround for job renames is :
In last resort, you can switch in the global config page : Git SCM => No SCM + save => Git SCM + save
This will result in :
Initial sync has a drawback : if you have checkoutConfiguration/foo and JENKINS_HOME/foo doesn't exist, foo won't be removed from your repository (I prefer not to remove such files due to "reload files from repo" feature)