Merge branch 'stable-5.3'

* stable-5.3:
  Prepare 5.3.2-SNAPSHOT builds
  JGit v5.3.1.201904271842-r
  Prepare 5.2.3-SNAPSHOT builds
  JGit v5.2.2.201904231744-r
  Revert 4678f4b and provide another solution for bug 467631
  Apache MINA sshd: make sendKexInit() work also for re-keying
  Prepare 5.1.8-SNAPSHOT builds
  JGit v5.1.7.201904200442-r
  ObjectUploadListener: Add callback interface
  Prepare 4.11.9-SNAPSHOT builds
  JGit v4.11.8.201904181247-r
  Prepare 4.9.11-SNAPSHOT builds
  JGit v4.9.10.201904181027-r
  Prepare 4.7.10-SNAPSHOT builds
  JGit v4.7.9.201904161809-r
  Prepare 4.5.8-SNAPSHOT builds
  JGit v4.5.7.201904151645-r
  Remember the cause for invalidating a packfile
  Fix API problem filters
  Fix pack files scan when filesnapshot isn't modified

Change-Id: I8a8671f7767444a77b809bd66a27d776c8332736
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

3 files changed, 96 insertions, 19 deletions

diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/diff/DiffEntryTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/diff/DiffEntryTest.java
index 73c230ac68..de768118bf 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/diff/DiffEntryTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/diff/DiffEntryTest.java
@@ -59,9 +59,12 @@ import org.eclipse.jgit.diff.DiffEntry.ChangeType;
 import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.dircache.DirCacheEditor;
 import org.eclipse.jgit.dircache.DirCacheEditor.PathEdit;
+import org.eclipse.jgit.internal.storage.file.FileRepository;
 import org.eclipse.jgit.dircache.DirCacheEntry;
+import org.eclipse.jgit.junit.JGitTestUtil;
 import org.eclipse.jgit.junit.RepositoryTestCase;
 import org.eclipse.jgit.lib.FileMode;
+import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.treewalk.EmptyTreeIterator;
 import org.eclipse.jgit.treewalk.FileTreeIterator;
@@ -417,4 +420,64 @@ public class DiffEntryTest extends RepositoryTestCase {
 			assertEquals(FileMode.REGULAR_FILE, diff.getOldMode());
 		}
 	}
+
+	@Test
+	public void shouldReportSubmoduleReplacedByFileMove() throws Exception {
+		// Create a submodule
+		FileRepository submoduleStandalone = createWorkRepository();
+		JGitTestUtil.writeTrashFile(submoduleStandalone, "fileInSubmodule",
+				"submodule");
+		Git submoduleStandaloneGit = Git.wrap(submoduleStandalone);
+		submoduleStandaloneGit.add().addFilepattern("fileInSubmodule").call();
+		submoduleStandaloneGit.commit().setMessage("add file to submodule")
+				.call();
+
+		Repository submodule_db = Git.wrap(db).submoduleAdd()
+				.setPath("modules/submodule")
+				.setURI(submoduleStandalone.getDirectory().toURI().toString())
+				.call();
+		File submodule_trash = submodule_db.getWorkTree();
+		addRepoToClose(submodule_db);
+		writeTrashFile("fileInRoot", "root");
+		Git rootGit = Git.wrap(db);
+		rootGit.add().addFilepattern("fileInRoot").call();
+		rootGit.commit().setMessage("add submodule and root file").call();
+		// Dummy change on fileInRoot
+		writeTrashFile("fileInRoot", "changed");
+		rootGit.add().addFilepattern("fileInRoot").call();
+		RevCommit firstCommit = rootGit.commit().setMessage("change root file")
+				.call();
+		// Remove the submodule again and move fileInRoot into that subfolder
+		rootGit.rm().setCached(true).addFilepattern("modules/submodule").call();
+		recursiveDelete(submodule_trash);
+		JGitTestUtil.deleteTrashFile(db, "fileInRoot");
+		// Move the fileInRoot file
+		writeTrashFile("modules/submodule/fileInRoot", "changed");
+		rootGit.rm().addFilepattern("fileInRoot").addFilepattern("modules/")
+				.call();
+		rootGit.add().addFilepattern("modules/").call();
+		RevCommit secondCommit = rootGit.commit()
+				.setMessage("remove submodule and move root file")
+				.call();
+		// Diff should report submodule having been deleted and file moved
+		// (deleted and added)
+		try (TreeWalk walk = new TreeWalk(db)) {
+			walk.addTree(firstCommit.getTree());
+			walk.addTree(secondCommit.getTree());
+			walk.setRecursive(true);
+			List<DiffEntry> diffs = DiffEntry.scan(walk);
+			assertEquals(3, diffs.size());
+			DiffEntry e = diffs.get(0);
+			assertEquals(DiffEntry.ChangeType.DELETE, e.getChangeType());
+			assertEquals("fileInRoot", e.getOldPath());
+			e = diffs.get(1);
+			assertEquals(DiffEntry.ChangeType.DELETE, e.getChangeType());
+			assertEquals("modules/submodule", e.getOldPath());
+			assertEquals(FileMode.GITLINK, e.getOldMode());
+			e = diffs.get(2);
+			assertEquals(DiffEntry.ChangeType.ADD, e.getChangeType());
+			assertEquals("modules/submodule/fileInRoot", e.getNewPath());
+		}
+
+	}
 }
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/IndexDiffSubmoduleTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/IndexDiffSubmoduleTest.java
index 93ada4f301..fa7f5ab522 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/IndexDiffSubmoduleTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/IndexDiffSubmoduleTest.java
@@ -43,12 +43,14 @@
 
 package org.eclipse.jgit.lib;
 
+import static org.junit.Assert.assertArrayEquals;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertTrue;
 
 import java.io.File;
 import java.io.IOException;
+import java.util.Arrays;
 import java.util.Set;
 
 import org.eclipse.jgit.api.CloneCommand;
@@ -128,7 +130,8 @@ public class IndexDiffSubmoduleTest extends RepositoryTestCase {
 		IndexDiff indexDiff = new IndexDiff(db2, Constants.HEAD,
 				new FileTreeIterator(db2));
 		indexDiff.setIgnoreSubmoduleMode(mode);
-		assertFalse(indexDiff.diff());
+		boolean changed = indexDiff.diff();
+		assertFalse(changed);
 	}
 
 	@Theory
@@ -263,4 +266,33 @@ public class IndexDiffSubmoduleTest extends RepositoryTestCase {
 		assertDiff(indexDiff, mode, IgnoreSubmoduleMode.ALL,
 				IgnoreSubmoduleMode.DIRTY, IgnoreSubmoduleMode.UNTRACKED);
 	}
+
+	@Theory
+	public void testSubmoduleReplacedByMovedFile(IgnoreSubmoduleMode mode)
+			throws Exception {
+		Git git = Git.wrap(db);
+		git.rm().setCached(true).addFilepattern("modules/submodule").call();
+		recursiveDelete(submodule_trash);
+		JGitTestUtil.deleteTrashFile(db, "fileInRoot");
+		// Move the fileInRoot file
+		writeTrashFile("modules/submodule/fileInRoot", "root");
+		git.rm().addFilepattern("fileInRoot").addFilepattern("modules/").call();
+		git.add().addFilepattern("modules/").call();
+		IndexDiff indexDiff = new IndexDiff(db, Constants.HEAD,
+				new FileTreeIterator(db));
+		indexDiff.setIgnoreSubmoduleMode(mode);
+		assertTrue(indexDiff.diff());
+		String[] removed = indexDiff.getRemoved().toArray(new String[0]);
+		Arrays.sort(removed);
+		if (IgnoreSubmoduleMode.ALL.equals(mode)) {
+			assertArrayEquals(new String[] { "fileInRoot" }, removed);
+		} else {
+			assertArrayEquals(
+					new String[] { "fileInRoot", "modules/submodule" },
+					removed);
+		}
+		assertEquals("[modules/submodule/fileInRoot]",
+				indexDiff.getAdded().toString());
+	}
+
 }
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/PathsTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/PathsTest.java
index f78cbe2601..7542ec8910 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/PathsTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/PathsTest.java
@@ -89,29 +89,14 @@ public class PathsTest {
 				a, 0, a.length, FileMode.TREE.getBits(),
 				b, 0, b.length, FileMode.TREE.getBits()));
 		assertEquals(0, compare(
-				a, 0, a.length, FileMode.TREE.getBits(),
-				b, 0, b.length, FileMode.GITLINK.getBits()));
-		assertEquals(0, compare(
-				a, 0, a.length, FileMode.GITLINK.getBits(),
-				b, 0, b.length, FileMode.GITLINK.getBits()));
-		assertEquals(0, compare(
-				a, 0, a.length, FileMode.GITLINK.getBits(),
-				b, 0, b.length, FileMode.TREE.getBits()));
-		assertEquals(0, compare(
 				a, 0, a.length, FileMode.REGULAR_FILE.getBits(),
 				b, 0, b.length, FileMode.REGULAR_FILE.getBits()));
 		assertEquals(-47, compare(
 				a, 0, a.length, FileMode.REGULAR_FILE.getBits(),
 				b, 0, b.length, FileMode.TREE.getBits()));
-		assertEquals(0, compare(
-				a, 0, a.length, FileMode.REGULAR_FILE.getBits(),
-				b, 0, b.length, FileMode.GITLINK.getBits()));
 		assertEquals(47, compare(
 				a, 0, a.length, FileMode.TREE.getBits(),
 				b, 0, b.length, FileMode.REGULAR_FILE.getBits()));
-		assertEquals(0, compare(
-				a, 0, a.length, FileMode.GITLINK.getBits(),
-				b, 0, b.length, FileMode.REGULAR_FILE.getBits()));
 
 		assertEquals(0, compareSameName(
 				a, 0, a.length,
@@ -119,9 +104,6 @@ public class PathsTest {
 		assertEquals(0, compareSameName(
 				a, 0, a.length,
 				b, 0, b.length, FileMode.REGULAR_FILE.getBits()));
-		assertEquals(0, compareSameName(
-				a, 0, a.length,
-				b, 0, b.length, FileMode.GITLINK.getBits()));
 
 		a = Constants.encode("a.c");
 		b = Constants.encode("a");