Fix possible NPE in IndexDiff when not all submodules are cloned

The latest changes to IndexDiff just assumed that all configured
submodules are allways cloned. If a configured submodule did not exist
an exception was thrown. This is fixed by this commit.

Bug: 450567
Change-Id: Iabe3b196d998c19483082e5720038ebddaeb1890

org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleWalkTest.java

@@ -56,11 +56,15 @@ import java.io.File;
 import java.io.FileWriter;
 import java.io.IOException;
 
+import org.eclipse.jgit.api.Git;
+import org.eclipse.jgit.api.Status;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.dircache.DirCacheEditor;
 import org.eclipse.jgit.dircache.DirCacheEditor.PathEdit;
 import org.eclipse.jgit.dircache.DirCacheEntry;
 import org.eclipse.jgit.errors.ConfigInvalidException;
+import org.eclipse.jgit.errors.NoWorkTreeException;
 import org.eclipse.jgit.junit.RepositoryTestCase;
 import org.eclipse.jgit.junit.TestRepository;
 import org.eclipse.jgit.lib.Config;
@@ -98,7 +102,7 @@ public class SubmoduleWalkTest extends RepositoryTestCase {
 
 	@Test
 	public void repositoryWithRootLevelSubmodule() throws IOException,
-			ConfigInvalidException {
+			ConfigInvalidException, NoWorkTreeException, GitAPIException {
 		final ObjectId id = ObjectId
 				.fromString("abcd1234abcd1234abcd1234abcd1234abcd1234");
 		final String path = "sub";
@@ -124,6 +128,8 @@ public class SubmoduleWalkTest extends RepositoryTestCase {
 		assertNull(gen.getModulesUpdate());
 		assertNull(gen.getModulesUrl());
 		assertNull(gen.getRepository());
+		Status status = Git.wrap(db).status().call();
+		assertTrue(!status.isClean());
 		assertFalse(gen.next());
 	}
 

org.eclipse.jgit/src/org/eclipse/jgit/lib/IndexDiff.java

@@ -532,6 +532,7 @@ public class IndexDiff {
 					throw e1;
 				}
 				Repository subRepo = smw.getRepository();
+				if (subRepo != null) {
 					ObjectId subHead = subRepo.resolve("HEAD"); //$NON-NLS-1$
 					if (subHead != null && !subHead.equals(smw.getObjectId()))
 						modified.add(smw.getPath());
@@ -556,6 +557,7 @@ public class IndexDiff {
 						}
 					}
 				}
+			}
 
 		}