Fix NoSuchFileException during directory cleanup in RefDirectory

Bug: 538285
Change-Id: Iab5c381a412cb2c2176af55189668c267ed29fbc
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java

 		File dir = file.getParentFile();
 		for (int i = 0; i < depth; ++i) {
 			try {
-				Files.delete(dir.toPath());
+				Files.deleteIfExists(dir.toPath());
 			} catch (DirectoryNotEmptyException e) {
 				// Don't log; normal case when there are other refs with the
 				// same prefix