Merge branch 'stable-4.3' into stable-4.4

* stable-4.3:
  Fix computation of id in WorkingTreeIterator with autocrlf and
    smudging
  Prepare 4.3.2-SNAPSHOT builds
  JGit v4.3.1.201605051710-r
  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: I829f06699f6670e519d04c927bdba4b82df29199
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

6 files changed, 87 insertions, 24 deletions

diff --git a/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/W.patch b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/W.patch
new file mode 100644
index 0000000000..cfecb8c5c4
--- /dev/null
+++ b/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
\ No newline at end of file
diff --git a/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/W_PostImage b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/W_PostImage
new file mode 100644
index 0000000000..e69de29bb2
--- /dev/null
+++ b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/W_PostImage
diff --git a/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/W_PreImage b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/W_PreImage
new file mode 100644
index 0000000000..2e65efe2a1
--- /dev/null
+++ b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/W_PreImage
@@ -0,0 +1 @@
+a
\ No newline at end of file
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ApplyCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ApplyCommandTest.java
index 239c844c33..f2b5b3ba95 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ApplyCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ApplyCommandTest.java
@@ -147,6 +147,16 @@ public class ApplyCommandTest extends RepositoryTestCase {
 	}
 
 	@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");
 		assertEquals(1, result.getUpdatedFiles().size());
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CheckoutCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CheckoutCommandTest.java
index 8162ac4575..0bb6610a24 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CheckoutCommandTest.java
+++ b/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:*.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:bon giorno world, @version\n]",
 					indexState(CONTENT));
 
-			git2.checkout().setName("refs/heads/test").call();
+			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: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));
-			assertEquals("hello world, V1", read("filterTest.txt"));
+			assertEquals("hello world, V1\n", read("filterTest.txt"));
+
+			git2.checkout().setName(two.getName()).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));
+			assertEquals("bon giorno world, V1\n", read("filterTest.txt"));
 		}
 	}
 
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/EolRepositoryTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/EolRepositoryTest.java
index 5dd8da57c2..5f10131750 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/EolRepositoryTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/EolRepositoryTest.java
@@ -51,6 +51,7 @@ import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.NoFilepatternException;
 import org.eclipse.jgit.attributes.Attribute;
 import org.eclipse.jgit.dircache.DirCache;
+import org.eclipse.jgit.dircache.DirCacheEditor;
 import org.eclipse.jgit.dircache.DirCacheEntry;
 import org.eclipse.jgit.dircache.DirCacheIterator;
 import org.eclipse.jgit.errors.RevisionSyntaxException;
@@ -61,9 +62,11 @@ import org.eclipse.jgit.lib.CoreConfig.AutoCRLF;
 import org.eclipse.jgit.lib.CoreConfig.EOL;
 import org.eclipse.jgit.lib.FileMode;
 import org.eclipse.jgit.lib.ObjectLoader;
+import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.storage.file.FileBasedConfig;
 import org.eclipse.jgit.treewalk.FileTreeIterator;
 import org.eclipse.jgit.treewalk.TreeWalk;
+import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.IO;
 import org.junit.Assert;
 import org.junit.Test;
@@ -83,6 +86,14 @@ public class EolRepositoryTest extends RepositoryTestCase {
 	private static final FileMode F = FileMode.REGULAR_FILE;
 
 	@DataPoint
+	public static boolean doSmudgeEntries = true;
+
+	@DataPoint
+	public static boolean dontSmudgeEntries = false;
+
+	private boolean smudge;
+
+	@DataPoint
 	public static String smallContents[] = {
 			generateTestData(3, 1, true, false),
 			generateTestData(3, 1, false, true),
@@ -117,10 +128,11 @@ public class EolRepositoryTest extends RepositoryTestCase {
 		return sb.toString();
 	}
 
-	public EolRepositoryTest(String[] testContent) {
+	public EolRepositoryTest(String[] testContent, boolean smudgeEntries) {
 		CONTENT_CRLF = testContent[0];
 		CONTENT_LF = testContent[1];
 		CONTENT_MIXED = testContent[2];
+		this.smudge = smudgeEntries;
 	}
 
 	protected String CONTENT_CRLF;
@@ -160,7 +172,7 @@ public class EolRepositoryTest extends RepositoryTestCase {
 
 	private ActualEntry entryMixed = new ActualEntry();
 
-	private DirCache dc;
+	private DirCache dirCache;
 
 	@Test
 	public void testDefaultSetup() throws Exception {
@@ -177,7 +189,9 @@ public class EolRepositoryTest extends RepositoryTestCase {
 			String indexContent) {
 		assertEquals(fileContent, entry.file);
 		assertEquals(indexContent, entry.index);
-		assertEquals(fileContent.length(), entry.indexContentLength);
+		if (entry.indexContentLength != 0) {
+			assertEquals(fileContent.length(), entry.indexContentLength);
+		}
 	}
 
 	@Test
@@ -584,6 +598,14 @@ public class EolRepositoryTest extends RepositoryTestCase {
 			dotGitattributes = null;
 		}
 
+		fileCRLF = createAndAddFile(git, "file1.txt", "a");
+
+		fileLF = createAndAddFile(git, "file2.txt", "a");
+
+		fileMixed = createAndAddFile(git, "file3.txt", "a");
+
+		RevCommit c = gitCommit(git, "create files");
+
 		fileCRLF = createAndAddFile(git, "file1.txt", CONTENT_CRLF);
 
 		fileLF = createAndAddFile(git, "file2.txt", CONTENT_LF);
@@ -593,6 +615,26 @@ public class EolRepositoryTest extends RepositoryTestCase {
 		gitCommit(git, "addFiles");
 
 		recreateWorktree(git);
+
+		if (smudge) {
+			DirCache dc = DirCache.lock(git.getRepository().getIndexFile(),
+					FS.detect());
+			DirCacheEditor editor = dc.editor();
+			for (int i = 0; i < dc.getEntryCount(); i++) {
+				editor.add(new DirCacheEditor.PathEdit(
+						dc.getEntry(i).getPathString()) {
+					public void apply(DirCacheEntry ent) {
+						ent.smudgeRacilyClean();
+					}
+				});
+			}
+			editor.commit();
+		}
+
+		// @TODO: find out why the following assertion would break the tests
+		// assertTrue(git.status().call().isClean());
+		git.checkout().setName(c.getName()).call();
+		git.checkout().setName("master").call();
 	}
 
 	private void recreateWorktree(Git git)
@@ -610,8 +652,8 @@ public class EolRepositoryTest extends RepositoryTestCase {
 		gitAdd(git, ".");
 	}
 
-	protected void gitCommit(Git git, String msg) throws GitAPIException {
-		git.commit().setMessage(msg).call();
+	protected RevCommit gitCommit(Git git, String msg) throws GitAPIException {
+		return git.commit().setMessage(msg).call();
 	}
 
 	protected void gitAdd(Git git, String path) throws GitAPIException {
@@ -644,7 +686,7 @@ public class EolRepositoryTest extends RepositoryTestCase {
 	}
 
 	private void collectRepositoryState() throws Exception {
-		dc = db.readDirCache();
+		dirCache = db.readDirCache();
 		walk = beginWalk();
 		if (dotGitattributes != null)
 			collectEntryContentAndAttributes(F, ".gitattributes", null);
@@ -680,7 +722,7 @@ public class EolRepositoryTest extends RepositoryTestCase {
 			e.attrs = e.attrs.trim();
 			e.file = new String(
 					IO.readFully(new File(db.getWorkTree(), pathName)));
-			DirCacheEntry dce = dc.getEntry(pathName);
+			DirCacheEntry dce = dirCache.getEntry(pathName);
 			ObjectLoader open = walk.getObjectReader().open(dce.getObjectId());
 			e.index = new String(open.getBytes());
 			e.indexContentLength = dce.getLength();