Merge branch 'stable-4.3'

* stable-4.3:
  Scan loose ref before packed in case gc about to remove the loose
  Fix possible NPEs when reporting transport errors
  Fix calling of clean/smudge filters from Checkout,MergeCommands
  Fix ApplyCommand when result of patch is an empty file

Change-Id: I0dc76b7a8c87ce8e0386a1b9e0fa92a3aa62abf7
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/W.patch

@@ -0,0 +1,7 @@
+diff --git a/W b/W
+index a3648a1..2d44096 100644
+--- a/W
++++ b/W
+@@ -1 +0,0 @@
+-a
+\ No newline at end of file

org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/W_PreImage

@@ -0,0 +1 @@
+a

org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ApplyCommandTest.java

@@ -146,6 +146,16 @@ public class ApplyCommandTest extends RepositoryTestCase {
 				b.getString(0, b.size(), false));
 	}
 
+	@Test
+	public void testModifyW() throws Exception {
+		ApplyResult result = init("W");
+		assertEquals(1, result.getUpdatedFiles().size());
+		assertEquals(new File(db.getWorkTree(), "W"),
+				result.getUpdatedFiles().get(0));
+		checkFile(new File(db.getWorkTree(), "W"),
+				b.getString(0, b.size(), false));
+	}
+
 	@Test
 	public void testModifyX() throws Exception {
 		ApplyResult result = init("X");

org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CheckoutCommandTest.java

@@ -88,7 +88,6 @@ import org.eclipse.jgit.transport.RemoteConfig;
 import org.eclipse.jgit.transport.URIish;
 import org.eclipse.jgit.util.FileUtils;
 import org.junit.Before;
-import org.junit.Ignore;
 import org.junit.Test;
 
 public class CheckoutCommandTest extends RepositoryTestCase {
@@ -740,11 +739,9 @@ public class CheckoutCommandTest extends RepositoryTestCase {
 	}
 
 	@Test
-	@Ignore
-	public void testSmudgeAndClean() throws IOException, GitAPIException {
-		// @TODO: fix this test
-		File clean_filter = writeTempFile("sed s/V1/@version/g -");
-		File smudge_filter = writeTempFile("sed s/@version/V1/g -");
+	public void testSmudgeAndClean() throws Exception {
+		File clean_filter = writeTempFile("sed s/V1/@version/g");
+		File smudge_filter = writeTempFile("sed s/@version/V1/g");
 
 		try (Git git2 = new Git(db)) {
 			StoredConfig config = git.getRepository().getConfig();
@@ -753,33 +750,39 @@ public class CheckoutCommandTest extends RepositoryTestCase {
 			config.setString("filter", "tstFilter", "clean",
 					"sh " + slashify(clean_filter.getPath()));
 			config.save();
-			writeTrashFile(".gitattributes", "*.txt filter=tstFilter");
+			writeTrashFile(".gitattributes", "filterTest.txt filter=tstFilter");
 			git2.add().addFilepattern(".gitattributes").call();
 			git2.commit().setMessage("add attributes").call();
 
-			writeTrashFile("filterTest.txt", "hello world, V1");
+			fsTick(writeTrashFile("filterTest.txt", "hello world, V1\n"));
 			git2.add().addFilepattern("filterTest.txt").call();
-			git2.commit().setMessage("add filterText.txt").call();
+			RevCommit one = git2.commit().setMessage("add filterText.txt").call();
 			assertEquals(
-					"[.gitattributes, mode:100644, content:*.txt filter=tstFilter][Test.txt, mode:100644, content:Some other change][filterTest.txt, mode:100644, content:hello world, @version]",
+					"[.gitattributes, mode:100644, content:filterTest.txt filter=tstFilter][Test.txt, mode:100644, content:Some change][filterTest.txt, mode:100644, content:hello world, @version\n]",
 					indexState(CONTENT));
 
-			git2.checkout().setCreateBranch(true).setName("test2").call();
-			writeTrashFile("filterTest.txt", "bon giorno world, V1");
+			fsTick(writeTrashFile("filterTest.txt", "bon giorno world, V1\n"));
 			git2.add().addFilepattern("filterTest.txt").call();
-			git2.commit().setMessage("modified filterText.txt").call();
+			RevCommit two = git2.commit().setMessage("modified filterTest.txt").call();
+
+			assertTrue(git2.status().call().isClean());
+			assertEquals(
+					"[.gitattributes, mode:100644, content:filterTest.txt filter=tstFilter][Test.txt, mode:100644, content:Some change][filterTest.txt, mode:100644, content:bon giorno world, @version\n]",
+					indexState(CONTENT));
 
+			git2.checkout().setName(one.getName()).call();
 			assertTrue(git2.status().call().isClean());
 			assertEquals(
-					"[.gitattributes, mode:100644, content:*.txt filter=tstFilter][Test.txt, mode:100644, content:Some other change][filterTest.txt, mode:100644, content:bon giorno world, @version]",
+					"[.gitattributes, mode:100644, content:filterTest.txt filter=tstFilter][Test.txt, mode:100644, content:Some change][filterTest.txt, mode:100644, content:hello world, @version\n]",
 					indexState(CONTENT));
+			assertEquals("hello world, V1\n", read("filterTest.txt"));
 
-			git2.checkout().setName("refs/heads/test").call();
+			git2.checkout().setName(two.getName()).call();
 			assertTrue(git2.status().call().isClean());
 			assertEquals(
-					"[.gitattributes, mode:100644, content:*.txt filter=tstFilter][Test.txt, mode:100644, content:Some other change][filterTest.txt, mode:100644, content:hello world, @version]",
+					"[.gitattributes, mode:100644, content:filterTest.txt filter=tstFilter][Test.txt, mode:100644, content:Some change][filterTest.txt, mode:100644, content:bon giorno world, @version\n]",
 					indexState(CONTENT));
-			assertEquals("hello world, V1", read("filterTest.txt"));
+			assertEquals("bon giorno world, V1\n", read("filterTest.txt"));
 		}
 	}
 

org.eclipse.jgit/src/org/eclipse/jgit/api/ApplyCommand.java

@@ -223,12 +223,16 @@ public class ApplyCommand extends GitCommand<ApplyResult> {
 					pos++;
 					break;
 				case '-':
-					if (!newLines.get(hh.getNewStartLine() - 1 + pos).equals(
-							hunkLine.substring(1))) {
+					if (hh.getNewStartLine() == 0) {
+						newLines.clear();
+					} else {
+						if (!newLines.get(hh.getNewStartLine() - 1 + pos)
+								.equals(hunkLine.substring(1))) {
 							throw new PatchApplyException(MessageFormat.format(
 									JGitText.get().patchApplyException, hh));
 						}
 						newLines.remove(hh.getNewStartLine() - 1 + pos);
+					}
 					break;
 				case '+':
 					newLines.add(hh.getNewStartLine() - 1 + pos,
@@ -250,7 +254,9 @@ public class ApplyCommand extends GitCommand<ApplyResult> {
 			// still there!
 			sb.append(l).append('\n');
 		}
+		if (sb.length() > 0) {
 			sb.deleteCharAt(sb.length() - 1);
+		}
 		FileWriter fw = new FileWriter(f);
 		fw.write(sb.toString());
 		fw.close();

org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheCheckout.java

@@ -280,8 +280,9 @@ public class DirCacheCheckout {
 
 		addTree(walk, headCommitTree);
 		addTree(walk, mergeCommitTree);
-		walk.addTree(new DirCacheBuildIterator(builder));
+		int dciPos = walk.addTree(new DirCacheBuildIterator(builder));
 		walk.addTree(workingTree);
+		workingTree.setDirCacheIterator(walk, dciPos);
 
 		while (walk.next()) {
 			processEntry(walk.getTree(0, CanonicalTreeParser.class),
@@ -320,8 +321,9 @@ public class DirCacheCheckout {
 
 		walk = new NameConflictTreeWalk(repo);
 		addTree(walk, mergeCommitTree);
-		walk.addTree(new DirCacheBuildIterator(builder));
+		int dciPos = walk.addTree(new DirCacheBuildIterator(builder));
 		walk.addTree(workingTree);
+		workingTree.setDirCacheIterator(walk, dciPos);
 
 		while (walk.next()) {
 			processEntry(walk.getTree(0, CanonicalTreeParser.class),
@@ -1093,8 +1095,10 @@ public class DirCacheCheckout {
 	private boolean isModifiedSubtree_IndexWorkingtree(String path)
 			throws CorruptObjectException, IOException {
 		try (NameConflictTreeWalk tw = new NameConflictTreeWalk(repo)) {
-			tw.addTree(new DirCacheIterator(dc));
-			tw.addTree(new FileTreeIterator(repo));
+			int dciPos = tw.addTree(new DirCacheIterator(dc));
+			FileTreeIterator fti = new FileTreeIterator(repo);
+			tw.addTree(fti);
+			fti.setDirCacheIterator(tw, dciPos);
 			tw.setRecursive(true);
 			tw.setFilter(PathFilter.create(path));
 			DirCacheIterator dcIt;

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

@@ -312,11 +312,10 @@ public class RefDirectory extends RefDatabase {
 
 	@Override
 	public Map<String, Ref> getRefs(String prefix) throws IOException {
-		final RefList<Ref> packed = getPackedRefs();
 		final RefList<LooseRef> oldLoose = looseRefs.get();
-
 		LooseScanner scan = new LooseScanner(oldLoose);
 		scan.scan(prefix);
+		final RefList<Ref> packed = getPackedRefs();
 
 		RefList<LooseRef> loose;
 		if (scan.newLoose != null) {

org.eclipse.jgit/src/org/eclipse/jgit/merge/ResolveMerger.java

@@ -1005,13 +1005,14 @@ public class ResolveMerger extends ThreeWayMerger {
 		builder = dircache.builder();
 		DirCacheBuildIterator buildIt = new DirCacheBuildIterator(builder);
 
-		tw = new NameConflictTreeWalk(reader);
+		tw = new NameConflictTreeWalk(db, reader);
 		tw.addTree(baseTree);
 		tw.addTree(headTree);
 		tw.addTree(mergeTree);
-		tw.addTree(buildIt);
+		int dciPos = tw.addTree(buildIt);
 		if (workingTreeIterator != null) {
 			tw.addTree(workingTreeIterator);
+			workingTreeIterator.setDirCacheIterator(tw, dciPos);
 		} else {
 			tw.setFilter(TreeFilter.ANY_DIFF);
 		}

org.eclipse.jgit/src/org/eclipse/jgit/merge/StrategySimpleTwoWayInCore.java

@@ -106,7 +106,7 @@ public class StrategySimpleTwoWayInCore extends ThreeWayMergeStrategy {
 
 		InCoreMerger(final Repository local) {
 			super(local);
-			tw = new NameConflictTreeWalk(reader);
+			tw = new NameConflictTreeWalk(local, reader);
 			cache = DirCache.newInCore();
 		}
 

org.eclipse.jgit/src/org/eclipse/jgit/util/HttpSupport.java

@@ -189,7 +189,8 @@ public class HttpSupport {
 		try {
 			return c.getResponseCode();
 		} catch (ConnectException ce) {
-			final String host = c.getURL().getHost();
+			final URL url = c.getURL();
+			final String host = (url == null) ? "<null>" : url.getHost();
 			// The standard J2SE error message is not very useful.
 			//
 			if ("Connection timed out: connect".equals(ce.getMessage())) //$NON-NLS-1$
@@ -216,7 +217,8 @@ public class HttpSupport {
 		try {
 			return c.getResponseCode();
 		} catch (ConnectException ce) {
-			final String host = c.getURL().getHost();
+			final URL url = c.getURL();
+			final String host = (url == null) ? "<null>" : url.getHost();
 			// The standard J2SE error message is not very useful.
 			//
 			if ("Connection timed out: connect".equals(ce.getMessage())) //$NON-NLS-1$