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 5dd8da5..5f10131 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.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.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 @@
 	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 @@
 		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 @@
 
 	private ActualEntry entryMixed = new ActualEntry();
 
-	private DirCache dc;
+	private DirCache dirCache;
 
 	@Test
 	public void testDefaultSetup() throws Exception {
@@ -177,7 +189,9 @@
 			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 @@
 			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 @@
 		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 @@
 		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 @@
 	}
 
 	private void collectRepositoryState() throws Exception {
-		dc = db.readDirCache();
+		dirCache = db.readDirCache();
 		walk = beginWalk();
 		if (dotGitattributes != null)
 			collectEntryContentAndAttributes(F, ".gitattributes", null);
@@ -680,7 +722,7 @@
 			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();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/TreeWalk.java b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/TreeWalk.java
index 501d676..7dac50a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/TreeWalk.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/TreeWalk.java
@@ -580,16 +580,30 @@
 	}
 
 	/**
+	 * @param opType
+	 *            the operationtype (checkin/checkout) which should be used
+	 * @return the EOL stream type of the current entry using the config and
+	 *         {@link #getAttributes()} Note that this method may return null if
+	 *         the {@link TreeWalk} is not based on a working tree
+	 */
+	// TODO(msohn) make this method public in 4.4
+	@Nullable
+	EolStreamType getEolStreamType(OperationType opType) {
+			if (attributesNodeProvider == null || config == null)
+				return null;
+		return EolStreamTypeUtil.detectStreamType(opType,
+					config.get(WorkingTreeOptions.KEY), getAttributes());
+	}
+
+	/**
 	 * @return the EOL stream type of the current entry using the config and
 	 *         {@link #getAttributes()} Note that this method may return null if
 	 *         the {@link TreeWalk} is not based on a working tree
 	 * @since 4.3
 	 */
+	// TODO(msohn) deprecate this method in 4.4
 	public @Nullable EolStreamType getEolStreamType() {
-			if (attributesNodeProvider == null || config == null)
-				return null;
-			return EolStreamTypeUtil.detectStreamType(operationType,
-					config.get(WorkingTreeOptions.KEY), getAttributes());
+		return (getEolStreamType(operationType));
 	}
 
 	/** Reset this walker so new tree iterators can be added to it. */
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeIterator.java b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeIterator.java
index 39176c6..c8de3de 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeIterator.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeIterator.java
@@ -86,6 +86,7 @@
 import org.eclipse.jgit.lib.ObjectReader;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.submodule.SubmoduleWalk;
+import org.eclipse.jgit.treewalk.TreeWalk.OperationType;
 import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.FS.ExecutionResult;
 import org.eclipse.jgit.util.Holder;
@@ -361,7 +362,8 @@
 				state.initializeDigestAndReadBuffer();
 
 				final long len = e.getLength();
-				InputStream filteredIs = possiblyFilteredInputStream(e, is, len);
+				InputStream filteredIs = possiblyFilteredInputStream(e, is, len,
+						OperationType.CHECKIN_OP);
 				return computeHash(filteredIs, canonLen);
 			} finally {
 				safeClose(is);
@@ -374,8 +376,15 @@
 
 	private InputStream possiblyFilteredInputStream(final Entry e,
 			final InputStream is, final long len) throws IOException {
+		return possiblyFilteredInputStream(e, is, len, null);
+
+	}
+
+	private InputStream possiblyFilteredInputStream(final Entry e,
+			final InputStream is, final long len, OperationType opType)
+			throws IOException {
 		if (getCleanFilterCommand() == null
-				&& getEolStreamType() == EolStreamType.DIRECT) {
+				&& getEolStreamType(opType) == EolStreamType.DIRECT) {
 			canonLen = len;
 			return is;
 		}
@@ -385,7 +394,7 @@
 			byte[] raw = rawbuf.array();
 			int n = rawbuf.limit();
 			if (!isBinary(raw, n)) {
-				rawbuf = filterClean(raw, n);
+				rawbuf = filterClean(raw, n, opType);
 				raw = rawbuf.array();
 				n = rawbuf.limit();
 			}
@@ -398,13 +407,14 @@
 				return is;
 			}
 
-		final InputStream lenIs = filterClean(e.openInputStream());
+		final InputStream lenIs = filterClean(e.openInputStream(),
+				opType);
 		try {
 			canonLen = computeLength(lenIs);
 		} finally {
 			safeClose(lenIs);
 		}
-		return filterClean(is);
+		return filterClean(is, opType);
 	}
 
 	private static void safeClose(final InputStream in) {
@@ -430,17 +440,23 @@
 		}
 	}
 
-	private ByteBuffer filterClean(byte[] src, int n) throws IOException {
+	private ByteBuffer filterClean(byte[] src, int n, OperationType opType)
+			throws IOException {
 		InputStream in = new ByteArrayInputStream(src);
 		try {
-			return IO.readWholeStream(filterClean(in), n);
+			return IO.readWholeStream(filterClean(in, opType), n);
 		} finally {
 			safeClose(in);
 		}
 	}
 
 	private InputStream filterClean(InputStream in) throws IOException {
-		in = handleAutoCRLF(in);
+		return filterClean(in, null);
+	}
+
+	private InputStream filterClean(InputStream in, OperationType opType)
+			throws IOException {
+		in = handleAutoCRLF(in, opType);
 		String filterCommand = getCleanFilterCommand();
 		if (filterCommand != null) {
 			FS fs = repository.getFS();
@@ -469,8 +485,9 @@
 		return in;
 	}
 
-	private InputStream handleAutoCRLF(InputStream in) throws IOException {
-		return EolStreamTypeUtil.wrapInputStream(in, getEolStreamType());
+	private InputStream handleAutoCRLF(InputStream in, OperationType opType)
+			throws IOException {
+		return EolStreamTypeUtil.wrapInputStream(in, getEolStreamType(opType));
 	}
 
 	/**
@@ -1332,10 +1349,28 @@
 	 * @since 4.3
 	 */
 	public EolStreamType getEolStreamType() throws IOException {
+		return getEolStreamType(null);
+	}
+
+	/**
+	 * @param opType
+	 *            The operationtype (checkin/checkout) which should be used
+	 * @return the eol stream type for the current entry or <code>null</code> if
+	 *         it cannot be determined. When state or state.walk is null or the
+	 *         {@link TreeWalk} is not based on a {@link Repository} then null
+	 *         is returned.
+	 * @throws IOException
+	 */
+	private EolStreamType getEolStreamType(OperationType opType)
+			throws IOException {
 		if (eolStreamTypeHolder == null) {
 			EolStreamType type=null;
 			if (state.walk != null) {
-				type=state.walk.getEolStreamType();
+				if (opType != null) {
+					type = state.walk.getEolStreamType(opType);
+				} else {
+					type=state.walk.getEolStreamType();
+				}
 			} else {
 				switch (getOptions().getAutoCRLF()) {
 				case FALSE:
diff --git a/tools/release.sh b/tools/release.sh
index 7adb375..d180bdf 100755
--- a/tools/release.sh
+++ b/tools/release.sh
@@ -47,6 +47,5 @@
 git tag -sf -m "$MSG" $1
 
 # run the build
-mvn clean install
+mvn clean install -T 1C
 mvn clean install -f org.eclipse.jgit.packaging/pom.xml
-