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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.