I just upgraded to git plugin and Jenkins. I wiped out my workspace and then tried to run a build and got the messages below. I tried turning on the option to wipe out the workspace and force a clone and that didn't help either.

15:56:31 Started by user Jon Schewe
15:56:31 Building in workspace /home/hudson/.hudson/jobs/fll-release/workspace
15:56:31 Pruning obsolete local branches
15:56:31 FATAL: Command "config --get remote.origin.url" returned status code 1:
15:56:31 stdout:
15:56:31 stderr:
15:56:31 hudson.plugins.git.GitException: Command "config --get remote.origin.url" returned status code 1:
15:56:31 stdout:
15:56:31 stderr:
15:56:31 at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommandIn(CliGitAPIImpl.java:940)
15:56:31 at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommandIn(CliGitAPIImpl.java:921)
15:56:31 at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommand(CliGitAPIImpl.java:865)
15:56:31 at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommand(CliGitAPIImpl.java:875)
15:56:31 at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.getRemoteUrl(CliGitAPIImpl.java:603)
15:56:31 at hudson.plugins.git.GitAPI.getRemoteUrl(GitAPI.java:61)
15:56:31 at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.prune(CliGitAPIImpl.java:393)
15:56:31 at hudson.plugins.git.extensions.impl.PruneStaleBranch.beforeCheckout(PruneStaleBranch.java:31)
15:56:31 at hudson.plugins.git.GitSCM.checkout(GitSCM.java:858)
15:56:31 at hudson.model.AbstractProject.checkout(AbstractProject.java:1376)
15:56:31 at hudson.model.AbstractBuild$AbstractBuildExecution.defaultCheckout(AbstractBuild.java:655)
15:56:31 at jenkins.scm.SCMCheckoutStrategy.checkout(SCMCheckoutStrategy.java:88)
15:56:31 at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:560)
15:56:31 at hudson.model.Run.execute(Run.java:1592)
15:56:31 at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:46)
15:56:31 at hudson.model.ResourceController.execute(ResourceController.java:88)
15:56:31 at hudson.model.Executor.run(Executor.java:237)

Eventually I got my job to build, here is what I did.

1) Delete configured repository
2) Delete configured branches
3) Select "None" as SCM
4) Save
5) Configure git repository

Perhaps some data isn't getting properly migrated? I was running Jenkins 1.509.1 and git plugin 1.4.0 with git client plugin 1.4.5.