i'm using the multi-branch-project plugin.
I get the following errors and there are no commits in the local git repository.
these errors appear for every configuration change in jenkins.

also, when I browse /var/lib/jenkins/jobs/my-feature-branches there is a folder named branches, and underneath it there are multiple folders which contain config.xml files.
when I browse /var/lib/jenkins/scm-sync-configuration/checkoutConfiguration/my-feature-branches, there is only config.xml and no further folders or files.

Aug 16, 2016 9:41:13 AM FINEST hudson.plugins.scm_sync_configuration.ScmSyncConfigurationBusiness
Processing commit : Commit hudson.plugins.scm_sync_configuration.model.Commit@2076693a :
Author : SYSTEM
Comment : SYSTEM: File hierarchy deleted

Change performed by SYSTEM

Changeset :
D jobs/My-feature-branches/branches/my-branch-name

Aug 16, 2016 9:41:13 AM FINE hudson.plugins.scm_sync_configuration.SCMManipulator
Deleting SCM hierarchy [/var/lib/jenkins/scm-sync-configuration/checkoutConfiguration/jobs/My-feature-branches/branches/my-branch-name] from SCM ...

Aug 16, 2016 9:41:13 AM FINER org.apache.maven.scm.manager.ScmManager remove

THROW
org.apache.maven.scm.ScmException: Exception while executing SCM command.
at org.apache.maven.scm.command.AbstractCommand.execute(AbstractCommand.java:63)
at org.apache.maven.scm.provider.git.AbstractGitScmProvider.executeCommand(AbstractGitScmProvider.java:291)
at org.apache.maven.scm.provider.git.AbstractGitScmProvider.remove(AbstractGitScmProvider.java:255)
at org.apache.maven.scm.provider.AbstractScmProvider.remove(AbstractScmProvider.java:773)
at org.apache.maven.scm.manager.AbstractScmManager.remove(AbstractScmManager.java:553)
at hudson.plugins.scm_sync_configuration.SCMManipulator.deleteHierarchy(SCMManipulator.java:127)
at hudson.plugins.scm_sync_configuration.ScmSyncConfigurationBusiness.deleteHierarchy(ScmSyncConfigurationBusiness.java:117)
at hudson.plugins.scm_sync_configuration.ScmSyncConfigurationBusiness.processCommitsQueue(ScmSyncConfigurationBusiness.java:214)
at hudson.plugins.scm_sync_configuration.ScmSyncConfigurationBusiness.access$000(ScmSyncConfigurationBusiness.java:32)
at hudson.plugins.scm_sync_configuration.ScmSyncConfigurationBusiness$1.call(ScmSyncConfigurationBusiness.java:148)
at hudson.plugins.scm_sync_configuration.ScmSyncConfigurationBusiness$1.call(ScmSyncConfigurationBusiness.java:145)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.apache.maven.scm.ScmException: Error while executing command.
at org.apache.maven.scm.provider.git.gitexe.command.GitCommandLineUtils.execute(GitCommandLineUtils.java:150)
at org.apache.maven.scm.provider.git.gitexe.command.remove.GitRemoveCommand.executeRemoveCommand(GitRemoveCommand.java:65)
at org.apache.maven.scm.command.remove.AbstractRemoveCommand.executeCommand(AbstractRemoveCommand.java:49)
at org.apache.maven.scm.command.AbstractCommand.execute(AbstractCommand.java:59)
... 14 more
Caused by: org.codehaus.plexus.util.cli.CommandLineException: Working directory "/var/lib/jenkins/scm-sync-configuration/checkoutConfiguration/jobs/My-feature-branches/branches/my-branch-name" does not exist!
at org.codehaus.plexus.util.cli.Commandline.execute(Commandline.java:661)
at org.codehaus.plexus.util.cli.CommandLineUtils.executeCommandLineAsCallable(CommandLineUtils.java:134)
at org.codehaus.plexus.util.cli.CommandLineUtils.executeCommandLine(CommandLineUtils.java:105)
at org.codehaus.plexus.util.cli.CommandLineUtils.executeCommandLine(CommandLineUtils.java:74)
at org.apache.maven.scm.provider.git.gitexe.command.GitCommandLineUtils.execute(GitCommandLineUtils.java:146)
... 17 more

Aug 16, 2016 9:41:13 AM SEVERE hudson.plugins.scm_sync_configuration.SCMManipulator deleteHierarchy

[deleteHierarchy] Hierarchy deletion aborted : Exception while executing SCM command.