I created a new jenkins job and then deleted it a few seconds later, after deciding I wanted to use a different name. The scm-sync-configuration plugin got into a bad state, presumably because it was trying to combine the add and delete into the same commit. Here are the logs:
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Dec 22, 2014 3:13:56 PM FINEST hudson.plugins.scm_sync_configuration.ScmSyncConfigurationBusiness

Processing commit : Commit hudson.plugins.scm_sync_configuration.model.Commit@6bdc2d06 :
Author : Craig Silverstein
Comment : Job [test-new-git] hierarchy deleted by csilvers@khanacademy.org
Changeset :
A jobs/test-new-git/config.xml
D jobs/test-new-git

Dec 22, 2014 3:13:56 PM FINE hudson.plugins.scm_sync_configuration.SCMManipulator

Deleting SCM hierarchy [/var/lib/jenkins/scm-sync-configuration/checkoutConfiguration/jobs/test-new-git] from SCM ...

Dec 22, 2014 3:13:56 PM SEVERE hudson.plugins.scm_sync_configuration.SCMManipulator deleteHierarchy

[deleteHierarchy] Problem during remove : The git command failed.
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I'm not even sure how to fix this manually. But would be great if the plugin could not get into this state to begin with.