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After searching my logfiles I found an instance of it occurring with Jenkins 1.579 using integrity-plugin 1.25 on 09-sep-2014. At the time when the issue occurred there was no active background process like an AV scanner locking the files in the directory. I would be inclined to think that, if anything was locked at all at this time, it was locked by a thread inside the Jenkins process (or one of its plugins).
java.nio.file.DirectoryNotEmptyException: [...]
at sun.nio.fs.WindowsFileSystemProvider.implDelete(Unknown Source)
at sun.nio.fs.AbstractFileSystemProvider.delete(Unknown Source)
at java.nio.file.Files.delete(Unknown Source)
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.Util.deleteFile(Util.java:247)
at hudson.Util.deleteRecursive(Util.java:310)
at hudson.Util.deleteContentsRecursive(Util.java:212)
at hudson.Util.deleteRecursive(Util.java:301)
at hudson.Util.deleteContentsRecursive(Util.java:212)
at hudson.FilePath$13.invoke(FilePath.java:1108)
at hudson.FilePath$13.invoke(FilePath.java:1105)
at hudson.FilePath.act(FilePath.java:918)
at hudson.FilePath.act(FilePath.java:896)
at hudson.FilePath.deleteContents(FilePath.java:1105)
at hudson.scm.IntegrityCheckoutTask.invoke(IntegrityCheckoutTask.java:280)
at hudson.scm.IntegrityCheckoutTask.invoke(IntegrityCheckoutTask.java:25)
at hudson.FilePath.act(FilePath.java:918)
at hudson.FilePath.act(FilePath.java:896)
at hudson.scm.IntegritySCM.checkout(IntegritySCM.java:789)
at hudson.model.AbstractProject.checkout(AbstractProject.java:1253)
at hudson.model.AbstractBuild$AbstractBuildExecution.defaultCheckout(AbstractBuild.java:622)
at jenkins.scm.SCMCheckoutStrategy.checkout(SCMCheckoutStrategy.java:86)
at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:528)
at hudson.model.Run.execute(Run.java:1745)
at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:43)
at hudson.model.ResourceController.execute(ResourceController.java:89)
at hudson.model.Executor.run(Executor.java:240)
Retrying after 10 seconds