Fix GC.deleteEmptyRefsFolders

This method tried to iterate spurious files which may exist in the
.git/refs folder, e.g. on Mac a .DS_Store may have been created there by
inspecting the folder using the finder application. This led to a
NotDirectoryException when deleteEmptyRefsFolders tried to create an
iterator for such a file entry. Skip files contained in the refs folder
to ensure the method only tries to iterate contained folders but not
files.

Change-Id: I5f31e733072a35db1e93908a9c69a8891ae5c206
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcDeleteEmptyRefsFoldersTest.java

@@ -91,6 +91,20 @@ public class GcDeleteEmptyRefsFoldersTest extends GcTestCase {
 		assertFalse(refDir02.getParent().getParent().toFile().exists());
 	}
 
+	@Test
+	public void emptyRefFoldersSkipFiles() throws Exception {
+		FileTime fileTime = FileTime.from(Instant.now().minusSeconds(31));
+		Path refFile = Files.createFile(refsDir.resolve(".DS_Store"));
+		Path refDir01 = Files.createDirectories(heads.resolve(REF_FOLDER_01));
+		Path refDir02 = Files.createDirectories(heads.resolve(REF_FOLDER_02));
+		setLastModifiedTime(fileTime, heads, REF_FOLDER_01);
+		setLastModifiedTime(fileTime, heads, REF_FOLDER_02);
+		assertTrue(refDir01.toFile().exists());
+		assertTrue(refDir02.toFile().exists());
+		gc.gc();
+		assertTrue(Files.exists(refFile));
+	}
+
 	private void setLastModifiedTime(FileTime fileTime, Path path, String folder) throws IOException {
 		long numParents = folder.chars().filter(c -> c == '/').count();
 		Path folderPath = path.resolve(folder);

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

@@ -910,7 +910,8 @@ public class GC {
 		// Avoid deleting a folder that was created after the threshold so that concurrent
 		// operations trying to create a reference are not impacted
 		Instant threshold = Instant.now().minus(30, ChronoUnit.SECONDS);
-		try (Stream<Path> entries = Files.list(refs)) {
+		try (Stream<Path> entries = Files.list(refs)
+				.filter(Files::isDirectory)) {
 			Iterator<Path> iterator = entries.iterator();
 			while (iterator.hasNext()) {
 				try (Stream<Path> s = Files.list(iterator.next())) {