short term workaround is either to run jenkins with -Dorg.jenkinsci.plugins.gitclient.Git.useCLI=true, or check "clean workspace after checkout" - this option will clean workspace ...before (sic!) checkout and avoid conflict.

Could you also tell me if there is anything during your build that could have touched support/tools/relink/macholib/MachO.py ? I'm looking for a public git repository I could use to reproduce this issue.

We also experienced this issue after upgrading. We determined that our issue was due to JGit (and therefore git-plugin) not supporting symbolic links and our git repository has multiple symbolic links. We also used the workaround -Dorg.jenkinsci.plugins.gitclient.Git.useCLI=true to resolve the issue, but we're wondering what the actual implementation will be to resolve this issue.

Can you please try SNASPHOT build https://jenkins.ci.cloudbees.com/job/plugins/job/git-client-plugin/33/org.jenkins-ci.plugins$git-client/artifact/org.jenkins-ci.plugins/git-client/1.0.5-SNAPSHOT/git-client-1.0.5-SNAPSHOT.hpi ?

This one includes a possible fix to ask JGit to handle the detected conflict by itself

relates to https://bugs.eclipse.org/bugs/show_bug.cgi?id=354367

https://jenkins.ci.cloudbees.com/job/plugins/job/git-client-plugin/34/org.jenkins-ci.plugins$git-client/ provably is a better candidate to get this issue fixed : it used a patched version of JGit to include https://bugs.eclipse.org/bugs/show_bug.cgi?id=354367 proposed fix

I installed https://jenkins.ci.cloudbees.com/job/plugins/job/git-client-plugin/34/org.jenkins-ci.plugins$git-client/ and restarted Jenkins and still have this issue.

hudson.plugins.git.GitException: Could not checkout 00f6e95c8ff6cc6f7ca544fa07124dd3edaa0586
at org.jenkinsci.plugins.gitclient.JGitAPIImpl.checkout(JGitAPIImpl.java:68)
at hudson.plugins.git.GitAPI.checkout(GitAPI.java:208)
at hudson.plugins.git.GitSCM.checkout(GitSCM.java:1261)
at hudson.plugins.git.GitSCM.access$1200(GitSCM.java:57)
at hudson.plugins.git.GitSCM$4.invoke(GitSCM.java:1220)
at hudson.plugins.git.GitSCM$4.invoke(GitSCM.java:1196)
at hudson.FilePath.act(FilePath.java:865)
at hudson.FilePath.act(FilePath.java:838)
at hudson.plugins.git.GitSCM.checkout(GitSCM.java:1196)
at hudson.model.AbstractProject.checkout(AbstractProject.java:1353)
at hudson.model.AbstractBuild$AbstractBuildExecution.defaultCheckout(AbstractBuild.java:689)
at jenkins.scm.SCMCheckoutStrategy.checkout(SCMCheckoutStrategy.java:88)
at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:594)
at hudson.model.Run.execute(Run.java:1567)
at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:46)
at hudson.model.ResourceController.execute(ResourceController.java:88)
at hudson.model.Executor.run(Executor.java:237)
Caused by: org.eclipse.jgit.api.errors.CheckoutConflictException: Checkout conflict with file: Cannot delete file: ios/PorkButt/opentok-ios-sdk/Opentok.framework/Headers/OTError.h
at org.eclipse.jgit.api.CheckoutCommand.call(CheckoutCommand.java:246)
at org.jenkinsci.plugins.gitclient.JGitAPIImpl.checkout(JGitAPIImpl.java:64)
... 16 more
Caused by: org.eclipse.jgit.errors.CheckoutConflictException: Checkout conflict with file: Cannot delete file: ios/PorkButt/opentok-ios-sdk/Opentok.framework/Headers/OTError.h
at org.eclipse.jgit.dircache.DirCacheCheckout.cleanUpConflicts(DirCacheCheckout.java:1011)
at org.eclipse.jgit.dircache.DirCacheCheckout.doCheckout(DirCacheCheckout.java:413)
at org.eclipse.jgit.dircache.DirCacheCheckout.checkout(DirCacheCheckout.java:391)
at org.eclipse.jgit.api.CheckoutCommand.call(CheckoutCommand.java:242)
... 17 more

There are symlinks in there.

In our environment, this workaround doesn't solve this issue.

 -Dorg.jenkinsci.plugins.gitclient.Git.useCLI=true

However, we solved with combination below, which described at http://mrkn.hatenablog.com/entry/2013/03/18/225556 (Japanese).

• Git Plugin : 1.3.0
• Git Client Plugin : 1.0.3

If you're using a master/slave configuration you need to set the argument in your slave configuration as well.