JGit warning when fetching/pruning repository

[outofcoffee]

When JGit executes a fetch with 'prune branches', it logs a warning:

12:52:46.999 [ForkJoinPool.commonPool-worker-2] WARN  o.e.j.i.s.f.RefDirectory - Unable to remove path /usr/var/clerk/git_repo/refs/heads/feature
java.nio.file.DirectoryNotEmptyException: /usr/var/clerk/git_repo/refs/heads/feature
	at sun.nio.fs.UnixFileSystemProvider.implDelete(UnixFileSystemProvider.java:242) ~[?:1.8.0_151]
	at sun.nio.fs.AbstractFileSystemProvider.delete(AbstractFileSystemProvider.java:103) ~[?:1.8.0_151]
	at java.nio.file.Files.delete(Files.java:1126) ~[?:1.8.0_151]
	at org.eclipse.jgit.internal.storage.file.RefDirectory.delete(RefDirectory.java:1289) [clerk.jar:?]
	at org.eclipse.jgit.internal.storage.file.RefDirectory.pack(RefDirectory.java:816) [clerk.jar:?]
	at org.eclipse.jgit.internal.storage.file.RefDirectory.pack(RefDirectory.java:716) [clerk.jar:?]
	at org.eclipse.jgit.internal.storage.file.PackedBatchRefUpdate.execute(PackedBatchRefUpdate.java:180) [clerk.jar:?]
	at org.eclipse.jgit.lib.BatchRefUpdate.execute(BatchRefUpdate.java:635) [clerk.jar:?]
	at org.eclipse.jgit.transport.FetchProcess.executeImp(FetchProcess.java:225) [clerk.jar:?]
	at org.eclipse.jgit.transport.FetchProcess.execute(FetchProcess.java:123) [clerk.jar:?]
	at org.eclipse.jgit.transport.Transport.fetch(Transport.java:1271) [clerk.jar:?]
	at org.eclipse.jgit.api.FetchCommand.call(FetchCommand.java:243) [clerk.jar:?]
	at io.gatehill.buildclerk.service.scm.GitScmServiceImpl.fetchRefs(GitScmServiceImpl.kt:97) [clerk.jar:?]
	at io.gatehill.buildclerk.service.scm.GitScmServiceImpl.access$fetchRefs(GitScmServiceImpl.kt:29) [clerk.jar:?]
	at io.gatehill.buildclerk.service.scm.GitScmServiceImpl$fetchUserInfoForCommit$1.invoke(GitScmServiceImpl.kt:39) [clerk.jar:?]
	at io.gatehill.buildclerk.service.scm.GitScmServiceImpl$fetchUserInfoForCommit$1.invoke(GitScmServiceImpl.kt:29) [clerk.jar:?]
	at io.gatehill.buildclerk.service.scm.GitScmServiceImpl$withGit$1.invoke(GitScmServiceImpl.kt:134) [clerk.jar:?]
	at io.gatehill.buildclerk.service.scm.GitScmServiceImpl$withGit$1.invoke(GitScmServiceImpl.kt:29) [clerk.jar:?]
	at io.gatehill.buildclerk.service.scm.GitScmServiceImpl.withRepo(GitScmServiceImpl.kt:126) [clerk.jar:?]
	at io.gatehill.buildclerk.service.scm.GitScmServiceImpl.withGit(GitScmServiceImpl.kt:133) [clerk.jar:?]
	at io.gatehill.buildclerk.service.scm.GitScmServiceImpl.fetchUserInfoForCommit(GitScmServiceImpl.kt:36) [clerk.jar:?]
	at io.gatehill.buildclerk.service.AnalysisServiceImpl$performBasicBuildAnalysis$1$fetchUserInfo$1.doResume(AnalysisServiceImpl.kt:129) [clerk.jar:?]
	at kotlin.coroutines.experimental.jvm.internal.CoroutineImpl.resume(CoroutineImpl.kt:42) [clerk.jar:?]
	at kotlinx.coroutines.experimental.DispatchedTask$DefaultImpls.run(Dispatched.kt:150) [clerk.jar:?]
	at kotlinx.coroutines.experimental.DispatchedContinuation.run(Dispatched.kt:14) [clerk.jar:?]
	at java.util.concurrent.ForkJoinTask$RunnableExecuteAction.exec(ForkJoinTask.java:1402) [?:1.8.0_151]
	at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289) [?:1.8.0_151]
	at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1056) [?:1.8.0_151]
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692) [?:1.8.0_151]
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157) [?:1.8.0_151]

This is caused by https://bugs.eclipse.org/bugs/show_bug.cgi?id=537872 and is fixed in 5.0.3 and higher. When 5.0.3+ is released we should update the dependency to grab the fix.