diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/EolStreamTypeUtilTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/EolStreamTypeUtilTest.java
index 1e3a39aad..2a553ce1a 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/EolStreamTypeUtilTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/EolStreamTypeUtilTest.java
@@ -1,43 +1,11 @@
 /*
- * Copyright (C) 2015, Ivan Motsch <ivan.motsch@bsiag.com>
+ * Copyright (C) 2015, 2020 Ivan Motsch <ivan.motsch@bsiag.com> and others
  *
- * This program and the accompanying materials are made available
- * under the terms of the Eclipse Distribution License v1.0 which
- * accompanies this distribution, is reproduced below, and is
- * available at http://www.eclipse.org/org/documents/edl-v10.php
+ * This program and the accompanying materials are made available under the
+ * terms of the Eclipse Distribution License v. 1.0 which is available at
+ * https://www.eclipse.org/org/documents/edl-v10.php.
  *
- * All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or
- * without modification, are permitted provided that the following
- * conditions are met:
- *
- * - Redistributions of source code must retain the above copyright
- *   notice, this list of conditions and the following disclaimer.
- *
- * - Redistributions in binary form must reproduce the above
- *   copyright notice, this list of conditions and the following
- *   disclaimer in the documentation and/or other materials provided
- *   with the distribution.
- *
- * - Neither the name of the Eclipse Foundation, Inc. nor the
- *   names of its contributors may be used to endorse or promote
- *   products derived from this software without specific prior
- *   written permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
- * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
- * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
- * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
- * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
- * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
- * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
- * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ * SPDX-License-Identifier: BSD-3-Clause
  */
 
 package org.eclipse.jgit.api;
@@ -90,16 +58,20 @@ public void testCheckoutLF() throws Exception {
 		testCheckout(TEXT_LF, AUTO_LF, "\r", "\r");
 		testCheckout(TEXT_LF, AUTO_LF, "\n", "\n");
 
-		testCheckout(TEXT_LF, AUTO_LF, "\r\n", "\n");
+		testCheckout(TEXT_LF, null, "\r\n", "\n");
+		testCheckout(null, AUTO_LF, "\r\n", "\r\n");
 		testCheckout(TEXT_LF, AUTO_LF, "\n\r", "\n\r");
 
-		testCheckout(TEXT_LF, AUTO_LF, "\n\r\n", "\n\n");
-		testCheckout(TEXT_LF, AUTO_LF, "\r\n\r", "\n\r");
+		testCheckout(TEXT_LF, null, "\n\r\n", "\n\n");
+		testCheckout(null, AUTO_LF, "\n\r\n", "\n\r\n");
+		testCheckout(TEXT_LF, null, "\r\n\r", "\n\r");
+		testCheckout(null, AUTO_LF, "\r\n\r", "\r\n\r");
 
 		testCheckout(TEXT_LF, AUTO_LF, "a\nb\n", "a\nb\n");
 		testCheckout(TEXT_LF, AUTO_LF, "a\rb\r", "a\rb\r");
 		testCheckout(TEXT_LF, AUTO_LF, "a\n\rb\n\r", "a\n\rb\n\r");
-		testCheckout(TEXT_LF, AUTO_LF, "a\r\nb\r\n", "a\nb\n");
+		testCheckout(TEXT_LF, null, "a\r\nb\r\n", "a\nb\n");
+		testCheckout(null, AUTO_LF, "a\r\nb\r\n", "a\r\nb\r\n");
 	}
 
 	@Test
@@ -153,45 +125,49 @@ private void testCheckout(EolStreamType streamTypeText,
 		byte[] outputBytes = output.getBytes(UTF_8);
 		byte[] expectedConversionBytes = expectedConversion.getBytes(UTF_8);
 
-		// test using output text and assuming it was declared TEXT
-		b = new ByteArrayOutputStream();
-		try (OutputStream out = EolStreamTypeUtil.wrapOutputStream(b,
-				streamTypeText)) {
-			out.write(outputBytes);
+		if (streamTypeText != null) {
+			// test using output text and assuming it was declared TEXT
+			b = new ByteArrayOutputStream();
+			try (OutputStream out = EolStreamTypeUtil.wrapOutputStream(b,
+					streamTypeText)) {
+				out.write(outputBytes);
+			}
+			assertArrayEquals(expectedConversionBytes, b.toByteArray());
 		}
-		assertArrayEquals(expectedConversionBytes, b.toByteArray());
-
-		// test using ouput text and assuming it was declared AUTO, using binary
-		// detection
-		b = new ByteArrayOutputStream();
-		try (OutputStream out = EolStreamTypeUtil.wrapOutputStream(b,
-				streamTypeWithBinaryCheck)) {
-			out.write(outputBytes);
+		if (streamTypeWithBinaryCheck != null) {
+			// test using output text and assuming it was declared AUTO, using
+			// binary detection
+			b = new ByteArrayOutputStream();
+			try (OutputStream out = EolStreamTypeUtil.wrapOutputStream(b,
+					streamTypeWithBinaryCheck)) {
+				out.write(outputBytes);
+			}
+			assertArrayEquals(expectedConversionBytes, b.toByteArray());
 		}
-		assertArrayEquals(expectedConversionBytes, b.toByteArray());
-
 		// now pollute output text with some binary bytes
 		outputBytes = extendWithBinaryData(outputBytes);
 		expectedConversionBytes = extendWithBinaryData(expectedConversionBytes);
 
-		// again, test using output text and assuming it was declared TEXT
-		b = new ByteArrayOutputStream();
-		try (OutputStream out = EolStreamTypeUtil.wrapOutputStream(b,
-				streamTypeText)) {
-			out.write(outputBytes);
+		if (streamTypeText != null) {
+			// again, test using output text and assuming it was declared TEXT
+			b = new ByteArrayOutputStream();
+			try (OutputStream out = EolStreamTypeUtil.wrapOutputStream(b,
+					streamTypeText)) {
+				out.write(outputBytes);
+			}
+			assertArrayEquals(expectedConversionBytes, b.toByteArray());
 		}
-		assertArrayEquals(expectedConversionBytes, b.toByteArray());
-
-		// again, test using ouput text and assuming it was declared AUTO, using
-		// binary
-		// detection
-		b = new ByteArrayOutputStream();
-		try (OutputStream out = EolStreamTypeUtil.wrapOutputStream(b,
-				streamTypeWithBinaryCheck)) {
-			out.write(outputBytes);
+		if (streamTypeWithBinaryCheck != null) {
+			// again, test using output text and assuming it was declared AUTO,
+			// using binary detection
+			b = new ByteArrayOutputStream();
+			try (OutputStream out = EolStreamTypeUtil.wrapOutputStream(b,
+					streamTypeWithBinaryCheck)) {
+				out.write(outputBytes);
+			}
+			// expect no conversion
+			assertArrayEquals(outputBytes, b.toByteArray());
 		}
-		// expect no conversion
-		assertArrayEquals(outputBytes, b.toByteArray());
 	}
 
 	@Test
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/DirCacheCheckoutTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/DirCacheCheckoutTest.java
index a272c8f2e..b943486b1 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/DirCacheCheckoutTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/DirCacheCheckoutTest.java
@@ -2,41 +2,13 @@
  * Copyright (C) 2007, Dave Watson <dwatson@mimvista.com>
  * Copyright (C) 2008-2011, Shawn O. Pearce <spearce@spearce.org>
  * Copyright (C) 2008-2011, Robin Rosenberg <robin.rosenberg@dewire.com>
- * Copyright (C) 2010-2011, Christian Halstrick <christian.halstrick@sap.com>
- * and other copyright owners as documented in the project's IP log.
+ * Copyright (C) 2010, 2020 Christian Halstrick <christian.halstrick@sap.com> and others
  *
  * This program and the accompanying materials are made available under the
- * terms of the Eclipse Distribution License v1.0 which accompanies this
- * distribution, is reproduced below, and is available at
- * http://www.eclipse.org/org/documents/edl-v10.php
+ * terms of the Eclipse Distribution License v. 1.0 which is available at
+ * https://www.eclipse.org/org/documents/edl-v10.php.
  *
- * All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- *
- * - Redistributions of source code must retain the above copyright notice, this
- * list of conditions and the following disclaimer.
- *
- * - Redistributions in binary form must reproduce the above copyright notice,
- * this list of conditions and the following disclaimer in the documentation
- * and/or other materials provided with the distribution.
- *
- * - Neither the name of the Eclipse Foundation, Inc. nor the names of its
- * contributors may be used to endorse or promote products derived from this
- * software without specific prior written permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
- * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
- * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
- * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
- * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
- * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
- * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- * POSSIBILITY OF SUCH DAMAGE.
+ * SPDX-License-Identifier: BSD-3-Clause
  */
 package org.eclipse.jgit.lib;
 
@@ -85,6 +57,7 @@
 import org.eclipse.jgit.treewalk.WorkingTreeIterator;
 import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.FileUtils;
+import org.eclipse.jgit.util.StringUtils;
 import org.junit.Assume;
 import org.junit.Test;
 
@@ -284,6 +257,86 @@ public void testInitialCheckout() throws Exception {
 		}
 	}
 
+	private void checkoutLineEndings(String inIndex, String expected,
+			String attributes) throws Exception {
+		try (Git git = new Git(db);
+				TestRepository<Repository> db_t = new TestRepository<>(db)) {
+			BranchBuilder master = db_t.branch("master");
+			master.commit().add("f", inIndex).message("m0").create();
+			if (!StringUtils.isEmptyOrNull(attributes)) {
+				master.commit().add(".gitattributes", attributes)
+						.message("attributes").create();
+			}
+			File f = new File(db.getWorkTree(), "f");
+			assertFalse(f.exists());
+			git.checkout().setName("master").call();
+			assertTrue(f.exists());
+			checkFile(f, expected);
+		}
+	}
+
+	@Test
+	public void testCheckoutWithCRLF() throws Exception {
+		checkoutLineEndings("first line\r\nsecond line\r\n",
+				"first line\r\nsecond line\r\n", null);
+	}
+
+	@Test
+	public void testCheckoutWithCRLFAuto() throws Exception {
+		checkoutLineEndings("first line\r\nsecond line\r\n",
+				"first line\r\nsecond line\r\n", "f text=auto");
+	}
+
+	@Test
+	public void testCheckoutWithCRLFAutoEolLf() throws Exception {
+		checkoutLineEndings("first line\r\nsecond line\r\n",
+				"first line\r\nsecond line\r\n", "f text=auto eol=lf");
+	}
+
+	@Test
+	public void testCheckoutWithCRLFAutoEolNative() throws Exception {
+		checkoutLineEndings("first line\r\nsecond line\r\n",
+				"first line\r\nsecond line\r\n", "f text=auto eol=native");
+	}
+
+	@Test
+	public void testCheckoutWithCRLFAutoEolCrLf() throws Exception {
+		checkoutLineEndings("first line\r\nsecond line\r\n",
+				"first line\r\nsecond line\r\n", "f text=auto eol=crlf");
+	}
+
+	@Test
+	public void testCheckoutWithLF() throws Exception {
+		checkoutLineEndings("first line\nsecond line\n",
+				"first line\nsecond line\n", null);
+	}
+
+	@Test
+	public void testCheckoutWithLFAuto() throws Exception {
+		checkoutLineEndings("first line\nsecond line\n",
+				"first line\nsecond line\n", "f text=auto");
+	}
+
+	@Test
+	public void testCheckoutWithLFAutoEolLf() throws Exception {
+		checkoutLineEndings("first line\nsecond line\n",
+				"first line\nsecond line\n", "f text=auto eol=lf");
+	}
+
+	@Test
+	public void testCheckoutWithLFAutoEolNative() throws Exception {
+		checkoutLineEndings(
+				"first line\nsecond line\n", "first line\nsecond line\n"
+						.replaceAll("\n", System.lineSeparator()),
+				"f text=auto eol=native");
+	}
+
+	@Test
+	public void testCheckoutWithLFAutoEolCrLf() throws Exception {
+		checkoutLineEndings("first line\nsecond line\n",
+				"first line\r\nsecond line\r\n", "f text=auto eol=crlf");
+	}
+
 	private DirCacheCheckout resetHard(RevCommit commit)
 			throws NoWorkTreeException,
 			CorruptObjectException, IOException {
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/merge/MergerTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/merge/MergerTest.java
index 7a244e1d8..e2ac89be9 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/merge/MergerTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/merge/MergerTest.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2012, Robin Stocker <robin@nibor.org> and others
+ * Copyright (C) 2012, 2020 Robin Stocker <robin@nibor.org> and others
  *
  * This program and the accompanying materials are made available under the
  * terms of the Eclipse Distribution License v. 1.0 which is available at
@@ -366,6 +366,48 @@ public void mergeWithCrlfInWT(MergeStrategy strategy) throws IOException,
 				mergeResult.getMergeStatus());
 	}
 
+	@Theory
+	public void mergeConflictWithCrLfTextAuto(MergeStrategy strategy)
+			throws IOException, GitAPIException {
+		Git git = Git.wrap(db);
+		writeTrashFile("crlf.txt", "a crlf file\r\n");
+		git.add().addFilepattern("crlf.txt").call();
+		git.commit().setMessage("base").call();
+		assertEquals("[crlf.txt, mode:100644, content:a crlf file\r\n]",
+				indexState(CONTENT));
+		writeTrashFile(".gitattributes", "crlf.txt text=auto");
+		git.add().addFilepattern(".gitattributes").call();
+		git.commit().setMessage("attributes").call();
+
+		git.branchCreate().setName("brancha").call();
+
+		writeTrashFile("crlf.txt", "a crlf file\r\na second line\r\n");
+		git.add().addFilepattern("crlf.txt").call();
+		git.commit().setMessage("on master").call();
+		assertEquals(
+				"[.gitattributes, mode:100644, content:crlf.txt text=auto]"
+						+ "[crlf.txt, mode:100644, content:a crlf file\r\na second line\r\n]",
+				indexState(CONTENT));
+
+		git.checkout().setName("brancha").call();
+		File testFile = writeTrashFile("crlf.txt",
+				"a crlf file\r\nanother line\r\n");
+		git.add().addFilepattern("crlf.txt").call();
+		git.commit().setMessage("on brancha").call();
+
+		MergeResult mergeResult = git.merge().setStrategy(strategy)
+				.include(db.resolve("master")).call();
+		assertEquals(MergeResult.MergeStatus.CONFLICTING,
+				mergeResult.getMergeStatus());
+		checkFile(testFile,
+				"a crlf file\r\n" //
+						+ "<<<<<<< HEAD\n" //
+						+ "another line\r\n" //
+						+ "=======\n" //
+						+ "a second line\r\n" //
+						+ ">>>>>>> 8e9e704742f1bc8a41eac88aac4aeefd338b7384\n");
+	}
+
 	@Theory
 	public void mergeWithCrlfAutoCrlfTrue(MergeStrategy strategy)
 			throws IOException, GitAPIException {
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/io/AutoLFInputStreamTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/io/AutoLFInputStreamTest.java
index fb90461e1..c391694fb 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/io/AutoLFInputStreamTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/io/AutoLFInputStreamTest.java
@@ -1,6 +1,6 @@
 /*
  * Copyright (C) 2010, Marc Strapetz <marc.strapetz@syntevo.com>
- * Copyright (C) 2015, Ivan Motsch <ivan.motsch@bsiag.com> and others
+ * Copyright (C) 2015, 2020 Ivan Motsch <ivan.motsch@bsiag.com> and others
  *
  * This program and the accompanying materials are made available under the
  * terms of the Eclipse Distribution License v. 1.0 which is available at
@@ -17,7 +17,9 @@
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.io.InputStream;
+import java.util.function.Function;
 
+import org.eclipse.jgit.util.io.AutoLFInputStream.StreamFlag;
 import org.junit.Test;
 
 public class AutoLFInputStreamTest {
@@ -25,47 +27,65 @@ public class AutoLFInputStreamTest {
 	@Test
 	public void testLF() throws IOException {
 		final byte[] bytes = asBytes("1\n2\n3");
-		test(bytes, bytes, false);
+		test(bytes, bytes);
 	}
 
 	@Test
 	public void testCR() throws IOException {
 		final byte[] bytes = asBytes("1\r2\r3");
-		test(bytes, bytes, false);
+		test(bytes, bytes);
 	}
 
 	@Test
 	public void testCRLF() throws IOException {
-		test(asBytes("1\r\n2\r\n3"), asBytes("1\n2\n3"), false);
+		test(asBytes("1\r\n2\r\n3"), asBytes("1\n2\n3"));
 	}
 
 	@Test
 	public void testLFCR() throws IOException {
 		final byte[] bytes = asBytes("1\n\r2\n\r3");
-		test(bytes, bytes, false);
+		test(bytes, bytes);
 	}
 
 	@Test
 	public void testEmpty() throws IOException {
 		final byte[] bytes = asBytes("");
-		test(bytes, bytes, false);
+		test(bytes, bytes);
 	}
 
 	@Test
 	public void testBinaryDetect() throws IOException {
 		final byte[] bytes = asBytes("1\r\n2\r\n3\0");
-		test(bytes, bytes, true);
+		test(bytes, bytes, StreamFlag.DETECT_BINARY);
 	}
 
 	@Test
 	public void testBinaryDontDetect() throws IOException {
-		test(asBytes("1\r\n2\r\n3\0"), asBytes("1\n2\n3\0"), false);
+		test(asBytes("1\r\n2\r\n3\0"), asBytes("1\n2\n3\0"));
+	}
+
+	@Test
+	public void testCrLf() throws IOException {
+		byte[] bytes = asBytes("1\r\n2\n3\r\n\r");
+		test(bytes, bytes, in -> AutoLFInputStream.create(in,
+				StreamFlag.DETECT_BINARY, StreamFlag.FOR_CHECKOUT));
+	}
+
+	@Test
+	public void testCrLfDontDetect() throws IOException {
+		test(asBytes("1\r\n2\r\n"), asBytes("1\n2\n"),
+				in -> AutoLFInputStream.create(in, StreamFlag.DETECT_BINARY));
+	}
+
+	private static void test(byte[] input, byte[] expected, StreamFlag... flags)
+			throws IOException {
+		test(input, expected, in -> AutoLFInputStream.create(in, flags));
 	}
 
 	private static void test(byte[] input, byte[] expected,
-			boolean detectBinary) throws IOException {
+			Function<InputStream, InputStream> factory) throws IOException {
 		try (InputStream bis1 = new ByteArrayInputStream(input);
-				InputStream cis1 = new AutoLFInputStream(bis1, detectBinary)) {
+				InputStream cis1 = factory.apply(bis1)) {
 			int index1 = 0;
 			for (int b = cis1.read(); b != -1; b = cis1.read()) {
 				assertEquals(expected[index1], (byte) b);
@@ -77,8 +97,7 @@ private static void test(byte[] input, byte[] expected,
 			for (int bufferSize = 1; bufferSize < 10; bufferSize++) {
 				final byte[] buffer = new byte[bufferSize];
 				try (InputStream bis2 = new ByteArrayInputStream(input);
-						InputStream cis2 = new AutoLFInputStream(bis2,
-								detectBinary)) {
+						InputStream cis2 = factory.apply(bis2)) {
 
 					int read = 0;
 					for (int readNow = cis2.read(buffer, 0,
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/io/AutoLFOutputStreamTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/io/AutoLFOutputStreamTest.java
new file mode 100644
index 000000000..1b7e55e45
--- /dev/null
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/io/AutoLFOutputStreamTest.java
@@ -0,0 +1,84 @@
+/*
+ * Copyright (C) 2020, Thomas Wolf <thomas.wolf@paranor.ch> and others
+ *
+ * This program and the accompanying materials are made available under the
+ * terms of the Eclipse Distribution License v. 1.0 which is available at
+ * https://www.eclipse.org/org/documents/edl-v10.php.
+ *
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
+package org.eclipse.jgit.util.io;
+
+import static java.nio.charset.StandardCharsets.UTF_8;
+import static org.junit.Assert.assertArrayEquals;
+
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.OutputStream;
+
+import org.junit.Test;
+
+public class AutoLFOutputStreamTest {
+
+	@Test
+	public void testLF() throws IOException {
+		final byte[] bytes = asBytes("1\n2\n3");
+		test(bytes, bytes, false);
+	}
+
+	@Test
+	public void testCR() throws IOException {
+		final byte[] bytes = asBytes("1\r2\r3");
+		test(bytes, bytes, false);
+	}
+
+	@Test
+	public void testCRLFNoDetect() throws IOException {
+		test(asBytes("1\r\n2\r\n3"), asBytes("1\n2\n3"), false);
+	}
+
+	@Test
+	public void testLFCR() throws IOException {
+		final byte[] bytes = asBytes("1\n\r2\n\r3");
+		test(bytes, bytes, false);
+	}
+
+	@Test
+	public void testEmpty() throws IOException {
+		final byte[] bytes = asBytes("");
+		test(bytes, bytes, false);
+	}
+
+	@Test
+	public void testBinaryDetect() throws IOException {
+		final byte[] bytes = asBytes("1\r\n2\r\n3\0");
+		test(bytes, bytes, true);
+	}
+
+	@Test
+	public void testBinaryDontDetect() throws IOException {
+		test(asBytes("1\r\n2\r\n3\0"), asBytes("1\n2\n3\0"), false);
+	}
+
+	@Test
+	public void testCrLfDetect() throws IOException {
+		byte[] bytes = asBytes("1\r\n2\n3\r\n\r");
+		test(bytes, bytes, true);
+	}
+
+	private static void test(byte[] input, byte[] expected,
+			boolean detectBinary) throws IOException {
+		try (ByteArrayOutputStream result = new ByteArrayOutputStream();
+				OutputStream out = new AutoLFOutputStream(result,
+						detectBinary)) {
+			out.write(input);
+			out.close();
+			assertArrayEquals(expected, result.toByteArray());
+		}
+	}
+
+	private static byte[] asBytes(String in) {
+		return in.getBytes(UTF_8);
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/io/AutoLFInputStream.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/io/AutoLFInputStream.java
index 8c9b1bf5c..0e335a9dc 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/io/AutoLFInputStream.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/io/AutoLFInputStream.java
@@ -1,6 +1,6 @@
 /*
  * Copyright (C) 2010, 2013 Marc Strapetz <marc.strapetz@syntevo.com>
- * Copyright (C) 2015, Ivan Motsch <ivan.motsch@bsiag.com> and others
+ * Copyright (C) 2015, 2020 Ivan Motsch <ivan.motsch@bsiag.com> and others
  *
  * This program and the accompanying materials are made available under the
  * terms of the Eclipse Distribution License v. 1.0 which is available at
@@ -13,26 +13,58 @@
 
 import java.io.IOException;
 import java.io.InputStream;
+import java.util.Arrays;
+import java.util.EnumSet;
+import java.util.Set;
 
 import org.eclipse.jgit.diff.RawText;
 
 /**
  * An InputStream that normalizes CRLF to LF.
- *
- * Existing single CR are not changed to LF, but retained as is.
- *
- * Optionally, a binary check on the first 8000 bytes is performed and in case
- * of binary files, canonicalization is turned off (for the complete file).
  * <p>
- * This is the former EolCanonicalizingInputStream with a new name in order to
- * have same naming for all LF / CRLF streams
+ * Existing single CR are not changed to LF but are retained as is.
+ * </p>
+ * <p>
+ * Optionally, a binary check on the first 8kB is performed and in case of
+ * binary files, canonicalization is turned off (for the complete file). If
+ * binary checking determines that the input is CR/LF-delimited text and the
+ * stream has been created for checkout, canonicalization is also turned off.
+ * </p>
  *
  * @since 4.3
  */
 public class AutoLFInputStream extends InputStream {
+
+	// This is the former EolCanonicalizingInputStream with a new name in order
+	// to have same naming for all LF / CRLF streams.
+
+	/**
+	 * Flags for controlling auto-detection of binary vs. text content (for
+	 * text=auto).
+	 *
+	 * @since 5.9
+	 */
+	public enum StreamFlag {
+		/**
+		 * Check the first 8kB for binary content and switch off
+		 * canonicalization off for the whole file if so.
+		 */
+		DETECT_BINARY,
+		/**
+		 * If {@link #DETECT_BINARY} is set, throw an {@link IsBinaryException}
+		 * if binary content is detected.
+		 */
+		ABORT_IF_BINARY,
+		/**
+		 * If {@link #DETECT_BINARY} is set and content is found to be CR-LF
+		 * delimited text, switch off canonicalization.
+		 */
+		FOR_CHECKOUT
+	}
+
 	private final byte[] single = new byte[1];
 
-	private final byte[] buf = new byte[8096];
+	private final byte[] buf = new byte[8 * 1024];
 
 	private final InputStream in;
 
@@ -40,11 +72,23 @@ public class AutoLFInputStream extends InputStream {
 
 	private int ptr;
 
+	/**
+	 * Set to {@code true} if no CR/LF processing is to be done: if the input is
+	 * binary data, or CR/LF-delimited text and {@link StreamFlag#FOR_CHECKOUT}
+	 * was given.
+	 */
+	private boolean passAsIs;
+
+	/**
+	 * Set to {@code true} if the input was detected to be binary data.
+	 */
 	private boolean isBinary;
 
 	private boolean detectBinary;
 
-	private boolean abortIfBinary;
+	private final boolean abortIfBinary;
+
+	private final boolean forCheckout;
 
 	/**
 	 * A special exception thrown when {@link AutoLFInputStream} is told to
@@ -62,20 +106,64 @@ public static class IsBinaryException extends IOException {
 	}
 
 	/**
-	 * Creates a new InputStream, wrapping the specified stream
+	 * Factory method for creating an {@link AutoLFInputStream} with the
+	 * specified {@link StreamFlag flags}.
+	 *
+	 * @param in
+	 *            raw input stream
+	 * @param flags
+	 *            {@link StreamFlag}s controlling the stream behavior
+	 * @return a new {@link AutoLFInputStream}
+	 * @since 5.9
+	 */
+	public static AutoLFInputStream create(InputStream in,
+			StreamFlag... flags) {
+		if (flags == null) {
+			return new AutoLFInputStream(in, null);
+		}
+		EnumSet<StreamFlag> set = EnumSet.noneOf(StreamFlag.class);
+		set.addAll(Arrays.asList(flags));
+		return new AutoLFInputStream(in, set);
+	}
+
+	/**
+	 * Creates a new InputStream, wrapping the specified stream.
+	 *
+	 * @param in
+	 *            raw input stream
+	 * @param flags
+	 *            {@link StreamFlag}s controlling the stream behavior;
+	 *            {@code null} is treated as an empty set
+	 * @since 5.9
+	 */
+	public AutoLFInputStream(InputStream in, Set<StreamFlag> flags) {
+		this.in = in;
+		this.detectBinary = flags != null
+				&& flags.contains(StreamFlag.DETECT_BINARY);
+		this.abortIfBinary = flags != null
+				&& flags.contains(StreamFlag.ABORT_IF_BINARY);
+		this.forCheckout = flags != null
+				&& flags.contains(StreamFlag.FOR_CHECKOUT);
+	}
+
+	/**
+	 * Creates a new InputStream, wrapping the specified stream.
 	 *
 	 * @param in
 	 *            raw input stream
 	 * @param detectBinary
 	 *            whether binaries should be detected
 	 * @since 2.0
+	 * @deprecated since 5.9, use {@link #create(InputStream, StreamFlag...)}
+	 *             instead
 	 */
+	@Deprecated
 	public AutoLFInputStream(InputStream in, boolean detectBinary) {
 		this(in, detectBinary, false);
 	}
 
 	/**
-	 * Creates a new InputStream, wrapping the specified stream
+	 * Creates a new InputStream, wrapping the specified stream.
 	 *
 	 * @param in
 	 *            raw input stream
@@ -84,12 +172,16 @@ public AutoLFInputStream(InputStream in, boolean detectBinary) {
 	 * @param abortIfBinary
 	 *            throw an IOException if the file is binary
 	 * @since 3.3
+	 * @deprecated since 5.9, use {@link #create(InputStream, StreamFlag...)}
+	 *             instead
 	 */
+	@Deprecated
 	public AutoLFInputStream(InputStream in, boolean detectBinary,
 			boolean abortIfBinary) {
 		this.in = in;
 		this.detectBinary = detectBinary;
 		this.abortIfBinary = abortIfBinary;
+		this.forCheckout = false;
 	}
 
 	/** {@inheritDoc} */
@@ -118,7 +210,7 @@ public int read(byte[] bs, int off, int len)
 			}
 
 			byte b = buf[ptr++];
-			if (isBinary || b != '\r') {
+			if (passAsIs || b != '\r') {
 				// Logic for binary files ends here
 				bs[i++] = b;
 				continue;
@@ -170,9 +262,14 @@ private boolean fillBuffer() throws IOException {
 		}
 		if (detectBinary) {
 			isBinary = RawText.isBinary(buf, cnt);
+			passAsIs = isBinary;
 			detectBinary = false;
-			if (isBinary && abortIfBinary)
+			if (isBinary && abortIfBinary) {
 				throw new IsBinaryException();
+			}
+			if (!passAsIs && forCheckout) {
+				passAsIs = RawText.isCrLfText(buf, cnt);
+			}
 		}
 		ptr = 0;
 		return true;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/io/AutoLFOutputStream.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/io/AutoLFOutputStream.java
index e235aa0ed..195fdb421 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/io/AutoLFOutputStream.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/io/AutoLFOutputStream.java
@@ -1,43 +1,12 @@
 /*
  * Copyright (C) 2015, Ivan Motsch <ivan.motsch@bsiag.com>
+ * Copyright (C) 2020, Thomas Wolf <thomas.wolf@paranor.ch> and others
  *
- * This program and the accompanying materials are made available
- * under the terms of the Eclipse Distribution License v1.0 which
- * accompanies this distribution, is reproduced below, and is
- * available at http://www.eclipse.org/org/documents/edl-v10.php
+ * This program and the accompanying materials are made available under the
+ * terms of the Eclipse Distribution License v. 1.0 which is available at
+ * https://www.eclipse.org/org/documents/edl-v10.php.
  *
- * All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or
- * without modification, are permitted provided that the following
- * conditions are met:
- *
- * - Redistributions of source code must retain the above copyright
- *   notice, this list of conditions and the following disclaimer.
- *
- * - Redistributions in binary form must reproduce the above
- *   copyright notice, this list of conditions and the following
- *   disclaimer in the documentation and/or other materials provided
- *   with the distribution.
- *
- * - Neither the name of the Eclipse Foundation, Inc. nor the
- *   names of its contributors may be used to endorse or promote
- *   products derived from this software without specific prior
- *   written permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
- * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
- * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
- * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
- * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
- * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
- * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
- * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ * SPDX-License-Identifier: BSD-3-Clause
  */
 
 package org.eclipse.jgit.util.io;
@@ -49,11 +18,15 @@
 
 /**
  * An OutputStream that reduces CRLF to LF.
- *
+ * <p>
  * Existing single CR are not changed to LF, but retained as is.
- *
+ * </p>
+ * <p>
  * A binary check on the first 8000 bytes is performed and in case of binary
- * files, canonicalization is turned off (for the complete file).
+ * files, canonicalization is turned off (for the complete file). If the binary
+ * check determines that the input is not binary but text with CR/LF,
+ * canonicalization is also turned off.
+ * </p>
  *
  * @since 4.3
  */
@@ -76,9 +49,7 @@ public class AutoLFOutputStream extends OutputStream {
 	private boolean isBinary;
 
 	/**
-	 * <p>
 	 * Constructor for AutoLFOutputStream.
-	 * </p>
 	 *
 	 * @param out
 	 *            an {@link java.io.OutputStream} object.
@@ -88,9 +59,7 @@ public AutoLFOutputStream(OutputStream out) {
 	}
 
 	/**
-	 * <p>
 	 * Constructor for AutoLFOutputStream.
-	 * </p>
 	 *
 	 * @param out
 	 *            an {@link java.io.OutputStream} object.
@@ -123,14 +92,11 @@ public void write(byte[] b) throws IOException {
 	public void write(byte[] b, int startOff, int startLen)
 			throws IOException {
 		final int overflow = buffer(b, startOff, startLen);
-		if (overflow < 0) {
+		if (overflow <= 0) {
 			return;
 		}
 		final int off = startOff + startLen - overflow;
 		final int len = overflow;
-		if (len == 0) {
-			return;
-		}
 		int lastw = off;
 		if (isBinary) {
 			out.write(b, off, len);
@@ -190,6 +156,9 @@ private int buffer(byte[] b, int off, int len) throws IOException {
 	private void decideMode() throws IOException {
 		if (detectBinary) {
 			isBinary = RawText.isBinary(binbuf, binbufcnt);
+			if (!isBinary) {
+				isBinary = RawText.isCrLfText(binbuf, binbufcnt);
+			}
 			detectBinary = false;
 		}
 		int cachedLen = binbufcnt;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/io/EolStreamTypeUtil.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/io/EolStreamTypeUtil.java
index c33c869b6..88ee2aee8 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/io/EolStreamTypeUtil.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/io/EolStreamTypeUtil.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2015, Ivan Motsch <ivan.motsch@bsiag.com> and others
+ * Copyright (C) 2015, 2020 Ivan Motsch <ivan.motsch@bsiag.com> and others
  *
  * This program and the accompanying materials are made available under the
  * terms of the Eclipse Distribution License v. 1.0 which is available at
@@ -12,12 +12,14 @@
 
 import java.io.InputStream;
 import java.io.OutputStream;
+import java.util.EnumSet;
 
 import org.eclipse.jgit.attributes.Attributes;
 import org.eclipse.jgit.lib.CoreConfig.EolStreamType;
 import org.eclipse.jgit.treewalk.TreeWalk.OperationType;
 import org.eclipse.jgit.treewalk.WorkingTreeOptions;
 import org.eclipse.jgit.util.SystemReader;
+import org.eclipse.jgit.util.io.AutoLFInputStream.StreamFlag;
 
 /**
  * Utility used to create input and output stream wrappers for
@@ -71,7 +73,7 @@ public static EolStreamType detectStreamType(OperationType op,
 
 	/**
 	 * Wrap the input stream depending on
-	 * {@link org.eclipse.jgit.lib.CoreConfig.EolStreamType}
+	 * {@link org.eclipse.jgit.lib.CoreConfig.EolStreamType}.
 	 *
 	 * @param in
 	 *            original stream
@@ -82,15 +84,38 @@ public static EolStreamType detectStreamType(OperationType op,
 	 */
 	public static InputStream wrapInputStream(InputStream in,
 			EolStreamType conversion) {
+		return wrapInputStream(in, conversion, false);
+	}
+
+	/**
+	 * Wrap the input stream depending on
+	 * {@link org.eclipse.jgit.lib.CoreConfig.EolStreamType}.
+	 *
+	 * @param in
+	 *            original stream
+	 * @param conversion
+	 *            to be performed
+	 * @param forCheckout
+	 *            whether the stream is for checking out from the repository
+	 * @return the converted stream depending on
+	 *         {@link org.eclipse.jgit.lib.CoreConfig.EolStreamType}
+	 * @since 5.9
+	 */
+	public static InputStream wrapInputStream(InputStream in,
+			EolStreamType conversion, boolean forCheckout) {
 		switch (conversion) {
 		case TEXT_CRLF:
 			return new AutoCRLFInputStream(in, false);
 		case TEXT_LF:
-			return new AutoLFInputStream(in, false);
+			return AutoLFInputStream.create(in);
 		case AUTO_CRLF:
 			return new AutoCRLFInputStream(in, true);
 		case AUTO_LF:
-			return new AutoLFInputStream(in, true);
+			EnumSet<StreamFlag> flags = forCheckout
+					? EnumSet.of(StreamFlag.DETECT_BINARY,
+							StreamFlag.FOR_CHECKOUT)
+					: EnumSet.of(StreamFlag.DETECT_BINARY);
+			return new AutoLFInputStream(in, flags);
 		default:
 			return in;
 		}
@@ -98,7 +123,7 @@ public static InputStream wrapInputStream(InputStream in,
 
 	/**
 	 * Wrap the output stream depending on
-	 * {@link org.eclipse.jgit.lib.CoreConfig.EolStreamType}
+	 * {@link org.eclipse.jgit.lib.CoreConfig.EolStreamType}.
 	 *
 	 * @param out
 	 *            original stream