Fix calling of clean/smudge filters from Checkout,MergeCommands

When CheckoutCommand or MergeCommand is called then not in all situation
the treewalks have been prepared to support clean/smudge filters. Fix
this

Bug: 491505
Change-Id: Iab5608049221c46d06812552ab97299e44d59e64

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/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/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();
 		}