After several successful builds with the Git plugin 2.0 beta, one of my jobs failed to complete the checkout. It failed with a CheckoutConflictException and a stack trace.

When I switched the job back to the command line git, with no intervening change to the central repository and with no change to the slave or its workspace, the job completed successfully.

The console log shows:

selected Git installation does not exists. Using Default
Fetching changes from the remote Git repository
Checking out Revision 3e9743ae51b0c098a3e484af09670c7b65801bff (origin/port-linux)
FATAL: Could not checkout 3e9743ae51b0c098a3e484af09670c7b65801bff
hudson.plugins.git.GitException: Could not checkout 3e9743ae51b0c098a3e484af09670c7b65801bff
at org.jenkinsci.plugins.gitclient.JGitAPIImpl.checkout(JGitAPIImpl.java:164)
at org.jenkinsci.plugins.gitclient.JGitAPIImpl.checkoutBranch(JGitAPIImpl.java:194)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at hudson.remoting.RemoteInvocationHandler$RPCRequest.perform(RemoteInvocationHandler.java:275)
at hudson.remoting.RemoteInvocationHandler$RPCRequest.call(RemoteInvocationHandler.java:256)
at hudson.remoting.RemoteInvocationHandler$RPCRequest.call(RemoteInvocationHandler.java:215)
at hudson.remoting.UserRequest.perform(UserRequest.java:118)
at hudson.remoting.UserRequest.perform(UserRequest.java:48)
at hudson.remoting.Request$2.run(Request.java:326)
at hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:72)
at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at hudson.remoting.Engine$1$1.run(Engine.java:58)
at java.lang.Thread.run(Unknown Source)
Caused by: org.eclipse.jgit.api.errors.CheckoutConflictException: Checkout conflict with files:
README-port-linux.org
at org.eclipse.jgit.api.CheckoutCommand.call(CheckoutCommand.java:244)
at org.jenkinsci.plugins.gitclient.JGitAPIImpl.checkout(JGitAPIImpl.java:162)
... 18 more
Caused by: org.eclipse.jgit.errors.CheckoutConflictException: Checkout conflict with files:
README-port-linux.org
at org.eclipse.jgit.dircache.DirCacheCheckout.doCheckout(DirCacheCheckout.java:411)
at org.eclipse.jgit.dircache.DirCacheCheckout.checkout(DirCacheCheckout.java:391)
at org.eclipse.jgit.api.CheckoutCommand.call(CheckoutCommand.java:240)
... 19 more