When I re-initialize scm sync by removing the plugin, removing all scm-sync folders and files (in jenkins home: scm-sync-configuration*) and restart with a fresh repo even, I get this error. When I re-initialize, I need to do a manual commit and push, which is fine and can be expected. The manual step works, so there's no problem with repo access.

Oct 04, 2014 7:47:41 PM FINEST hudson.plugins.scm_sync_configuration.ScmSyncConfigurationBusiness
Queuing commit Commit hudson.plugins.scm_sync_configuration.model.Commit@7c368030 :
Author : Jenkins Admin
Comment : Jenkins configuration files updated by admin with following comment : Update scm sync config
Changeset :
A hudson.scm.SubversionSCM.xml
A hudson.maven.MavenModuleSet.xml
A hudson.tasks.Ant.xml
A hudson.plugins.git.GitSCM.xml
A hudson.triggers.SCMTrigger.xml
A hudson.plugins.git.GitTool.xml
A scm-sync-configuration.xml
A hudson.tasks.Mailer.xml
A hudson.plugins.analysis.core.GlobalSettings.xml
A config.xml
A hudson.tasks.Maven.xml
A hudson.tasks.Shell.xml
A hudson.scm.CVSSCM.xml

to SCM ...
Oct 04, 2014 7:47:41 PM FINEST hudson.plugins.scm_sync_configuration.ScmSyncConfigurationBusiness
Processing commit : Commit hudson.plugins.scm_sync_configuration.model.Commit@7c368030 :
Author : Jenkins Admin
Comment : Jenkins configuration files updated by admin with following comment : Update scm sync config
Changeset :
A hudson.scm.SubversionSCM.xml
A hudson.maven.MavenModuleSet.xml
A hudson.tasks.Ant.xml
A hudson.plugins.git.GitSCM.xml
A hudson.triggers.SCMTrigger.xml
A hudson.plugins.git.GitTool.xml
A scm-sync-configuration.xml
A hudson.tasks.Mailer.xml
A hudson.plugins.analysis.core.GlobalSettings.xml
A config.xml
A hudson.tasks.Maven.xml
A hudson.tasks.Shell.xml
A hudson.scm.CVSSCM.xml

Oct 04, 2014 7:47:41 PM FINEST hudson.plugins.scm_sync_configuration.ScmSyncConfigurationBusiness
Empty changeset to commit (no changes found on files) => commit skipped !
Oct 04, 2014 7:48:12 PM FINEST hudson.plugins.scm_sync_configuration.ScmSyncConfigurationBusiness
Queuing commit Commit hudson.plugins.scm_sync_configuration.model.Commit@60820625 :
Author : Jenkins Admin
Comment : Job [Selenium tests] configuration updated by admin
Changeset :
A jobs/Selenium tests/config.xml

to SCM ...
Oct 04, 2014 7:48:12 PM FINEST hudson.plugins.scm_sync_configuration.ScmSyncConfigurationBusiness
Processing commit : Commit hudson.plugins.scm_sync_configuration.model.Commit@60820625 :
Author : Jenkins Admin
Comment : Job [Selenium tests] configuration updated by admin
Changeset :
A jobs/Selenium tests/config.xml

Oct 04, 2014 7:48:12 PM FINE hudson.plugins.scm_sync_configuration.SCMManipulator
Checking in SCM files ...
Oct 04, 2014 7:48:12 PM FINER org.apache.maven.scm.manager.ScmManager checkIn
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.checkin(AbstractGitScmProvider.java:217)
at org.apache.maven.scm.provider.AbstractScmProvider.checkIn(AbstractScmProvider.java:415)
at org.apache.maven.scm.provider.AbstractScmProvider.checkIn(AbstractScmProvider.java:397)
at org.apache.maven.scm.manager.AbstractScmManager.checkIn(AbstractScmManager.java:423)
at hudson.plugins.scm_sync_configuration.SCMManipulator.checkinFiles(SCMManipulator.java:242)
at hudson.plugins.scm_sync_configuration.ScmSyncConfigurationBusiness.processCommitsQueue(ScmSyncConfigurationBusiness.java:208)
at hudson.plugins.scm_sync_configuration.ScmSyncConfigurationBusiness.access$000(ScmSyncConfigurationBusiness.java:29)
at hudson.plugins.scm_sync_configuration.ScmSyncConfigurationBusiness$1.call(ScmSyncConfigurationBusiness.java:143)
at hudson.plugins.scm_sync_configuration.ScmSyncConfigurationBusiness$1.call(ScmSyncConfigurationBusiness.java:141)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$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:122)
at org.apache.maven.scm.provider.git.gitexe.command.checkin.GitCheckInCommand.executeCheckInCommand(GitCheckInCommand.java:129)
at org.apache.maven.scm.command.checkin.AbstractCheckInCommand.executeCommand(AbstractCheckInCommand.java:54)
at org.apache.maven.scm.command.AbstractCommand.execute(AbstractCommand.java:59)
... 14 more
Caused by: org.codehaus.plexus.util.cli.CommandLineException: Error inside systemOut parser
at org.codehaus.plexus.util.cli.CommandLineUtils$1.call(CommandLineUtils.java:188)
at org.codehaus.plexus.util.cli.CommandLineUtils.executeCommandLine(CommandLineUtils.java:107)
at org.codehaus.plexus.util.cli.CommandLineUtils.executeCommandLine(CommandLineUtils.java:74)
at org.apache.maven.scm.provider.git.gitexe.command.GitCommandLineUtils.execute(GitCommandLineUtils.java:118)
... 17 more
Caused by: java.lang.IllegalArgumentException: Illegal character in path at index 0: "jobs/Selenium%20tests/config.xml"
at java.net.URI.create(URI.java:859)
at org.apache.maven.scm.provider.git.gitexe.command.status.GitStatusConsumer.resolveURI(GitStatusConsumer.java:251)
at org.apache.maven.scm.provider.git.gitexe.command.status.GitStatusConsumer.resolvePath(GitStatusConsumer.java:232)
at org.apache.maven.scm.provider.git.gitexe.command.status.GitStatusConsumer.consumeLine(GitStatusConsumer.java:138)
at org.codehaus.plexus.util.cli.StreamPumper.consumeLine(StreamPumper.java:190)
at org.codehaus.plexus.util.cli.StreamPumper.run(StreamPumper.java:135)
Caused by: java.net.URISyntaxException: Illegal character in path at index 0: "jobs/Selenium%20tests/config.xml"
at java.net.URI$Parser.fail(URI.java:2829)
at java.net.URI$Parser.checkChars(URI.java:3002)
at java.net.URI$Parser.parseHierarchical(URI.java:3086)
at java.net.URI$Parser.parse(URI.java:3044)
at java.net.URI.<init>(URI.java:595)
at java.net.URI.create(URI.java:857)
... 5 more

Oct 04, 2014 7:48:12 PM SEVERE hudson.plugins.scm_sync_configuration.SCMManipulator checkinFiles
[checkinFiles] Error while checkin : Exception while executing SCM command.
Oct 04, 2014 7:48:12 PM FINER hudson.plugins.scm_sync_configuration.SCMManipulator checkinFiles
THROW
hudson.plugins.scm_sync_configuration.exceptions.LoggableException: Error while checking in file to scm repository
at hudson.plugins.scm_sync_configuration.ScmSyncConfigurationBusiness.processCommitsQueue(ScmSyncConfigurationBusiness.java:214)
at hudson.plugins.scm_sync_configuration.ScmSyncConfigurationBusiness.access$000(ScmSyncConfigurationBusiness.java:29)
at hudson.plugins.scm_sync_configuration.ScmSyncConfigurationBusiness$1.call(ScmSyncConfigurationBusiness.java:143)
at hudson.plugins.scm_sync_configuration.ScmSyncConfigurationBusiness$1.call(ScmSyncConfigurationBusiness.java:141)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)

Oct 04, 2014 7:48:12 PM SEVERE hudson.plugins.scm_sync_configuration.ScmSyncConfigurationBusiness processCommitsQueue
Error while processing commit queue : Error while checking in file to scm repository