Support more of AutoCRLF

This patch introduces CRLF handling to the DirCacheCheckout and
WorkingTreeIterator supporting the AutoCRLF for add, checkout
reset and status and hopefully some other places that depende
on the underlying logic of the affected API's.

The patch includes test cases for the Status command provided by
Tomasz Zarna for bug 353867.

The core.eol and core.safecrlf options are not yet supported.

Bug: 301775
Bug: 353867
Change-Id: I2280a2dc0698829475de6a662a6c6e80b1df7663

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

@@ -110,6 +110,54 @@ public class AddCommandTest extends RepositoryTestCase {
 				indexState(CONTENT));
 	}
 
+	@Test
+	public void testAddExistingSingleFileWithNewLine() throws IOException,
+			NoFilepatternException {
+		File file = new File(db.getWorkTree(), "a.txt");
+		FileUtils.createNewFile(file);
+		PrintWriter writer = new PrintWriter(file);
+		writer.print("row1\r\nrow2");
+		writer.close();
+
+		Git git = new Git(db);
+		db.getConfig().setString("core", null, "autocrlf", "false");
+		git.add().addFilepattern("a.txt").call();
+		assertEquals("[a.txt, mode:100644, content:row1\r\nrow2]",
+				indexState(CONTENT));
+		db.getConfig().setString("core", null, "autocrlf", "true");
+		git.add().addFilepattern("a.txt").call();
+		assertEquals("[a.txt, mode:100644, content:row1\nrow2]",
+				indexState(CONTENT));
+		db.getConfig().setString("core", null, "autocrlf", "input");
+		git.add().addFilepattern("a.txt").call();
+		assertEquals("[a.txt, mode:100644, content:row1\nrow2]",
+				indexState(CONTENT));
+	}
+
+	@Test
+	public void testAddExistingSingleBinaryFile() throws IOException,
+			NoFilepatternException {
+		File file = new File(db.getWorkTree(), "a.txt");
+		FileUtils.createNewFile(file);
+		PrintWriter writer = new PrintWriter(file);
+		writer.print("row1\r\nrow2\u0000");
+		writer.close();
+
+		Git git = new Git(db);
+		db.getConfig().setString("core", null, "autocrlf", "false");
+		git.add().addFilepattern("a.txt").call();
+		assertEquals("[a.txt, mode:100644, content:row1\r\nrow2\u0000]",
+				indexState(CONTENT));
+		db.getConfig().setString("core", null, "autocrlf", "true");
+		git.add().addFilepattern("a.txt").call();
+		assertEquals("[a.txt, mode:100644, content:row1\r\nrow2\u0000]",
+				indexState(CONTENT));
+		db.getConfig().setString("core", null, "autocrlf", "input");
+		git.add().addFilepattern("a.txt").call();
+		assertEquals("[a.txt, mode:100644, content:row1\r\nrow2\u0000]",
+				indexState(CONTENT));
+	}
+
 	@Test
 	public void testAddExistingSingleFileInSubDir() throws IOException, NoFilepatternException {
 		FileUtils.mkdir(new File(db.getWorkTree(), "sub"));

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

@@ -50,8 +50,10 @@ import java.io.IOException;
 import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.dircache.DirCacheEntry;
 import org.eclipse.jgit.errors.NoWorkTreeException;
+import org.eclipse.jgit.lib.ConfigConstants;
 import org.eclipse.jgit.lib.ObjectReader;
 import org.eclipse.jgit.lib.RepositoryTestCase;
+import org.eclipse.jgit.lib.StoredConfig;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.junit.Before;
 import org.junit.Test;
@@ -200,4 +202,35 @@ public class PathCheckoutCommandTest extends RepositoryTestCase {
 			r.release();
 		}
 	}
+
+	public void testCheckoutMixedNewlines() throws Exception {
+		// "git config core.autocrlf true"
+		StoredConfig config = git.getRepository().getConfig();
+		config.setBoolean(ConfigConstants.CONFIG_CORE_SECTION, null,
+				ConfigConstants.CONFIG_KEY_AUTOCRLF, true);
+		config.save();
+		// edit <FILE1>
+		File written = writeTrashFile(FILE1, "4\r\n4");
+		assertEquals("4\r\n4", read(written));
+		// "git add <FILE1>"
+		git.add().addFilepattern(FILE1).call();
+		// "git commit -m 'CRLF'"
+		git.commit().setMessage("CRLF").call();
+		// edit <FILE1>
+		written = writeTrashFile(FILE1, "4\n4");
+		assertEquals("4\n4", read(written));
+		// "git add <FILE1>"
+		git.add().addFilepattern(FILE1).call();
+		// "git checkout -- <FILE1>
+		git.checkout().addPath(FILE1).call();
+		// "git status" => clean
+		Status status = git.status().call();
+		assertEquals(0, status.getAdded().size());
+		assertEquals(0, status.getChanged().size());
+		assertEquals(0, status.getConflicting().size());
+		assertEquals(0, status.getMissing().size());
+		assertEquals(0, status.getModified().size());
+		assertEquals(0, status.getRemoved().size());
+		assertEquals(0, status.getUntracked().size());
+	}
 }

org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/DirCacheCheckoutTest.java

@@ -40,6 +40,7 @@
  */
 package org.eclipse.jgit.lib;
 
+import static org.junit.Assert.assertArrayEquals;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertNotNull;
@@ -878,6 +879,41 @@ public class DirCacheCheckoutTest extends RepositoryTestCase {
 		}
 	}
 
+	@Test
+	public void testCheckoutOutChangesAutoCRLFfalse() throws IOException {
+		setupCase(mk("foo"), mkmap("foo/bar", "foo\nbar"), mk("foo"));
+		checkout();
+		assertIndex(mkmap("foo/bar", "foo\nbar"));
+		assertWorkDir(mkmap("foo/bar", "foo\nbar"));
+	}
+
+	@Test
+	public void testCheckoutOutChangesAutoCRLFInput() throws IOException {
+		setupCase(mk("foo"), mkmap("foo/bar", "foo\nbar"), mk("foo"));
+		db.getConfig().setString("core", null, "autocrlf", "input");
+		checkout();
+		assertIndex(mkmap("foo/bar", "foo\nbar"));
+		assertWorkDir(mkmap("foo/bar", "foo\nbar"));
+	}
+
+	@Test
+	public void testCheckoutOutChangesAutoCRLFtrue() throws IOException {
+		setupCase(mk("foo"), mkmap("foo/bar", "foo\nbar"), mk("foo"));
+		db.getConfig().setString("core", null, "autocrlf", "true");
+		checkout();
+		assertIndex(mkmap("foo/bar", "foo\nbar"));
+		assertWorkDir(mkmap("foo/bar", "foo\r\nbar"));
+	}
+
+	@Test
+	public void testCheckoutOutChangesAutoCRLFtrueBinary() throws IOException {
+		setupCase(mk("foo"), mkmap("foo/bar", "foo\nb\u0000ar"), mk("foo"));
+		db.getConfig().setString("core", null, "autocrlf", "true");
+		checkout();
+		assertIndex(mkmap("foo/bar", "foo\nb\u0000ar"));
+		assertWorkDir(mkmap("foo/bar", "foo\nb\u0000ar"));
+	}
+
 	@Test
 	public void testCheckoutUncachedChanges() throws IOException {
 		setupCase(mk("foo"), mk("foo"), mk("foo"));
@@ -931,9 +967,8 @@ public class DirCacheCheckoutTest extends RepositoryTestCase {
 					offset += numRead;
 				}
 				is.close();
-				assertTrue("unexpected content for path " + path
+				assertArrayEquals("unexpected content for path " + path
-						+ " in workDir. Expected: <" + expectedValue + ">",
+						+ " in workDir. ", buffer, i.get(path).getBytes());
-						Arrays.equals(buffer, i.get(path).getBytes()));
 				nrFiles++;
 			}
 		}

org.eclipse.jgit.test/tst/org/eclipse/jgit/util/io/AutoCRLFOutputStreamTest.java

@@ -0,0 +1,123 @@
+/*
+ * Copyright (C) 2011, Robin Rosenberg
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * 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
+ *
+ * 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.
+ */
+
+package org.eclipse.jgit.util.io;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+
+import org.junit.Assert;
+import org.junit.Test;
+
+public class AutoCRLFOutputStreamTest {
+
+	@Test
+	public void test() throws IOException {
+		assertNoCrLf("", "");
+		assertNoCrLf("\r", "\r");
+		assertNoCrLf("\r\n", "\n");
+		assertNoCrLf("\r\n", "\r\n");
+		assertNoCrLf("\r\r", "\r\r");
+		assertNoCrLf("\r\n\r", "\n\r");
+		assertNoCrLf("\r\n\r\r", "\r\n\r\r");
+		assertNoCrLf("\r\n\r\n", "\r\n\r\n");
+		assertNoCrLf("\r\n\r\n\r", "\n\r\n\r");
+	}
+
+	private void assertNoCrLf(String string, String string2) throws IOException {
+		assertNoCrLfHelper(string, string2);
+		// \u00e5 = LATIN SMALL LETTER A WITH RING ABOVE
+		// the byte value is negative
+		assertNoCrLfHelper("\u00e5" + string, "\u00e5" + string2);
+		assertNoCrLfHelper("\u00e5" + string + "\u00e5", "\u00e5" + string2
+				+ "\u00e5");
+		assertNoCrLfHelper(string + "\u00e5", string2 + "\u00e5");
+	}
+
+	private void assertNoCrLfHelper(String expect, String input)
+			throws IOException {
+		byte[] inbytes = input.getBytes();
+		byte[] expectBytes = expect.getBytes();
+		for (int i = 0; i < 5; ++i) {
+			byte[] buf = new byte[i];
+			InputStream in = new ByteArrayInputStream(inbytes);
+			ByteArrayOutputStream bos = new ByteArrayOutputStream();
+			OutputStream out = new AutoCRLFOutputStream(bos);
+			if (i > 0) {
+				int n;
+				while ((n = in.read(buf)) >= 0) {
+					out.write(buf, 0, n);
+				}
+			} else {
+				int c;
+				while ((c = in.read()) != -1)
+					out.write(c);
+			}
+			out.flush();
+			in.close();
+			out.close();
+			byte[] actualBytes = bos.toByteArray();
+			Assert.assertEquals("bufsize=" + i, encode(expectBytes),
+					encode(actualBytes));
+		}
+	}
+
+	String encode(byte[] in) {
+		StringBuilder str = new StringBuilder();
+		for (byte b : in) {
+			if (b < 32)
+				str.append(0xFF & b);
+			else {
+				str.append("'");
+				str.append((char) b);
+				str.append("'");
+			}
+			str.append(' ');
+		}
+		return str.toString();
+	}
+
+}

org.eclipse.jgit.test/tst/org/eclipse/jgit/util/io/EolCanonicalizingInputStreamTest.java

@@ -77,6 +77,12 @@ public class EolCanonicalizingInputStreamTest {
 		test(bytes, bytes);
 	}
 
+	@Test
+	public void testEmpty() throws IOException {
+		final byte[] bytes = asBytes("");
+		test(bytes, bytes);
+	}
+
 	private void test(byte[] input, byte[] expected) throws IOException {
 		final InputStream bis1 = new ByteArrayInputStream(input);
 		final InputStream cis1 = new EolCanonicalizingInputStream(bis1);

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

@@ -45,6 +45,7 @@ package org.eclipse.jgit.dircache;
 import java.io.File;
 import java.io.FileOutputStream;
 import java.io.IOException;
+import java.io.OutputStream;
 import java.text.MessageFormat;
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -62,6 +63,7 @@ import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.ObjectLoader;
 import org.eclipse.jgit.lib.ObjectReader;
 import org.eclipse.jgit.lib.Repository;
+import org.eclipse.jgit.lib.CoreConfig.AutoCRLF;
 import org.eclipse.jgit.treewalk.AbstractTreeIterator;
 import org.eclipse.jgit.treewalk.CanonicalTreeParser;
 import org.eclipse.jgit.treewalk.EmptyTreeIterator;
@@ -73,6 +75,7 @@ import org.eclipse.jgit.treewalk.WorkingTreeOptions;
 import org.eclipse.jgit.treewalk.filter.PathFilter;
 import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.FileUtils;
+import org.eclipse.jgit.util.io.AutoCRLFOutputStream;
 
 /**
  * This class handles checking out one or two trees merging with the index.
@@ -926,14 +929,19 @@ public class DirCacheCheckout {
 		ObjectLoader ol = or.open(entry.getObjectId());
 		File parentDir = f.getParentFile();
 		File tmpFile = File.createTempFile("._" + f.getName(), null, parentDir);
-		FileOutputStream channel = new FileOutputStream(tmpFile);
+		WorkingTreeOptions opt = repo.getConfig().get(WorkingTreeOptions.KEY);
+		FileOutputStream rawChannel = new FileOutputStream(tmpFile);
+		OutputStream channel;
+		if (opt.getAutoCRLF() == AutoCRLF.TRUE)
+			channel = new AutoCRLFOutputStream(rawChannel);
+		else
+			channel = rawChannel;
 		try {
 			ol.copyTo(channel);
 		} finally {
 			channel.close();
 		}
 		FS fs = repo.getFS();
-		WorkingTreeOptions opt = repo.getConfig().get(WorkingTreeOptions.KEY);
 		if (opt.isFileMode() && fs.supportsExecute()) {
 			if (FileMode.EXECUTABLE_FILE.equals(entry.getRawMode())) {
 				if (!fs.canExecute(tmpFile))
@@ -954,6 +962,9 @@ public class DirCacheCheckout {
 			}
 		}
 		entry.setLastModified(f.lastModified());
-		entry.setLength((int) ol.getSize());
+		if (opt.getAutoCRLF() != AutoCRLF.FALSE)
+			entry.setLength(f.length()); // AutoCRLF wants on-disk-size
+		else
+			entry.setLength((int) ol.getSize());
 	}
 }

org.eclipse.jgit/src/org/eclipse/jgit/storage/file/ObjectDirectoryInserter.java

@@ -97,8 +97,8 @@ class ObjectDirectoryInserter extends ObjectInserter {
 			throws IOException {
 		if (len <= buffer().length) {
 			byte[] buf = buffer();
-			IO.readFully(is, buf, 0, (int) len);
+			int actLen = IO.readFully(is, buf, 0);
-			return insert(type, buf, 0, (int) len);
+			return insert(type, buf, 0, actLen);
 
 		} else {
 			MessageDigest md = digest();

org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeIterator.java

@@ -72,6 +72,7 @@ import org.eclipse.jgit.ignore.IgnoreNode;
 import org.eclipse.jgit.ignore.IgnoreRule;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.CoreConfig;
+import org.eclipse.jgit.lib.CoreConfig.AutoCRLF;
 import org.eclipse.jgit.lib.FileMode;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.Repository;
@@ -402,7 +403,7 @@ public abstract class WorkingTreeIterator extends AbstractTreeIterator {
 		}
 	}
 
-	private InputStream filterClean(InputStream in) {
+	private InputStream filterClean(InputStream in) throws IOException {
 		return new EolCanonicalizingInputStream(in);
 	}
 
@@ -498,7 +499,13 @@ public abstract class WorkingTreeIterator extends AbstractTreeIterator {
 	 *             the file could not be opened for reading.
 	 */
 	public InputStream openEntryStream() throws IOException {
-		return current().openInputStream();
+		InputStream rawis = current().openInputStream();
+		InputStream is;
+		if (getOptions().getAutoCRLF() != AutoCRLF.FALSE)
+			is = new EolCanonicalizingInputStream(rawis);
+		else
+			is = rawis;
+		return is;
 	}
 
 	/**

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

@@ -142,7 +142,13 @@ public class IO {
 				throw new IOException(MessageFormat.format(
 						JGitText.get().fileIsTooLarge, path));
 			final byte[] buf = new byte[(int) sz];
-			IO.readFully(in, buf, 0, buf.length);
+			int actSz = IO.readFully(in, buf, 0);
+
+			if (actSz == sz) {
+				byte[] ret = new byte[actSz];
+				System.arraycopy(buf, 0, ret, 0, actSz);
+				return ret;
+			}
 			return buf;
 		} finally {
 			try {
@@ -253,6 +259,31 @@ public class IO {
 		return cnt != 0 ? cnt : -1;
 	}
 
+	/**
+	 * Read the entire byte array into memory, unless input is shorter
+	 *
+	 * @param fd
+	 *            input stream to read the data from.
+	 * @param dst
+	 *            buffer that must be fully populated, [off, off+len).
+	 * @param off
+	 *            position within the buffer to start writing to.
+	 * @return number of bytes in buffer or stream, whichever is shortest
+	 * @throws IOException
+	 *             there was an error reading from the stream.
+	 */
+	public static int readFully(InputStream fd, byte[] dst, int off)
+			throws IOException {
+		int r;
+		int len = 0;
+		while ((r = fd.read(dst, off, dst.length - off)) >= 0
+				&& len < dst.length) {
+			off += r;
+			len += r;
+		}
+		return len;
+	}
+
 	/**
 	 * Skip an entire region of an input stream.
 	 * <p>

org.eclipse.jgit/src/org/eclipse/jgit/util/io/AutoCRLFOutputStream.java

@@ -0,0 +1,187 @@
+/*
+ * Copyright (C) 2011, Robin Rosenberg
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * 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
+ *
+ * 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.
+ */
+
+package org.eclipse.jgit.util.io;
+
+import java.io.IOException;
+import java.io.OutputStream;
+
+import org.eclipse.jgit.diff.RawText;
+
+/**
+ * An OutputStream that expands LF to CRLF.
+ * <p>
+ * Existing CRLF are not expanded to CRCRLF, but retained as is.
+ */
+public class AutoCRLFOutputStream extends OutputStream {
+
+	private final OutputStream out;
+
+	private int buf = -1;
+
+	private byte[] binbuf = new byte[8000];
+
+	private int binbufcnt = 0;
+
+	private boolean isBinary;
+
+	/**
+	 * @param out
+	 */
+	public AutoCRLFOutputStream(OutputStream out) {
+		this.out = out;
+	}
+
+	@Override
+	public void write(int b) throws IOException {
+		int overflow = buffer((byte) b);
+		if (overflow >= 0)
+			return;
+		if (isBinary) {
+			out.write(b);
+			return;
+		}
+		if (b == '\n') {
+			if (buf == '\r') {
+				out.write('\n');
+				buf = -1;
+			} else if (buf == -1) {
+				out.write('\r');
+				out.write('\n');
+				buf = -1;
+			}
+		} else if (b == '\r') {
+			out.write(b);
+			buf = '\r';
+		} else {
+			out.write(b);
+			buf = -1;
+		}
+	}
+
+	@Override
+	public void write(byte[] b) throws IOException {
+		int overflow = buffer(b, 0, b.length);
+		if (overflow > 0)
+			write(b, b.length - overflow, overflow);
+	}
+
+	@Override
+	public void write(byte[] b, int off, int len) throws IOException {
+		int overflow = buffer(b, off, len);
+		if (overflow < 0)
+			return;
+		off = off + len - overflow;
+		len = overflow;
+		if (len == 0)
+			return;
+		int lastw = off;
+		if (isBinary) {
+			out.write(b, off, len);
+			return;
+		}
+		for (int i = off; i < off + len; ++i) {
+			byte c = b[i];
+			if (c == '\r') {
+				buf = '\r';
+			} else if (c == '\n') {
+				if (buf != '\r') {
+					if (lastw < i) {
+						out.write(b, lastw, i - lastw);
+					}
+					out.write('\r');
+					lastw = i;
+				}
+				buf = -1;
+			} else {
+				buf = -1;
+			}
+		}
+		if (lastw < off + len) {
+			out.write(b, lastw, off + len - lastw);
+		}
+		if (b[off + len - 1] == '\r')
+			buf = '\r';
+	}
+
+	private int buffer(byte b) throws IOException {
+		if (binbufcnt > binbuf.length)
+			return 1;
+		binbuf[binbufcnt++] = b;
+		if (binbufcnt == binbuf.length)
+			decideMode();
+		return 0;
+	}
+
+	private int buffer(byte[] b, int off, int len) throws IOException {
+		if (binbufcnt > binbuf.length)
+			return len;
+		int copy = Math.min(binbuf.length - binbufcnt, len);
+		System.arraycopy(b, off, binbuf, binbufcnt, copy);
+		binbufcnt += copy;
+		int remaining = len - copy;
+		if (remaining > 0)
+			decideMode();
+		return remaining;
+	}
+
+	private void decideMode() throws IOException {
+		isBinary = RawText.isBinary(binbuf, binbufcnt);
+		int cachedLen = binbufcnt;
+		binbufcnt = binbuf.length + 1; // full!
+		write(binbuf, 0, cachedLen);
+	}
+
+	@Override
+	public void flush() throws IOException {
+		if (binbufcnt < binbuf.length)
+			decideMode();
+		buf = -1;
+	}
+
+	@Override
+	public void close() throws IOException {
+		flush();
+		super.close();
+	}
+}

org.eclipse.jgit/src/org/eclipse/jgit/util/io/EolCanonicalizingInputStream.java

@@ -46,8 +46,11 @@ package org.eclipse.jgit.util.io;
 import java.io.IOException;
 import java.io.InputStream;
 
+import org.eclipse.jgit.diff.RawText;
+
 /**
- * An input stream which canonicalizes EOLs bytes on the fly to '\n'.
+ * An input stream which canonicalizes EOLs bytes on the fly to '\n', unless the
+ * first 8000 bytes indicate the stream is binary.
  *
  * Note: Make sure to apply this InputStream only to text files!
  */
@@ -62,6 +65,10 @@ public class EolCanonicalizingInputStream extends InputStream {
 
 	private int ptr;
 
+	private boolean isBinary;
+
+	private boolean modeDetected;
+
 	/**
 	 * Creates a new InputStream, wrapping the specified stream
 	 *
@@ -95,7 +102,8 @@ public class EolCanonicalizingInputStream extends InputStream {
 			}
 
 			byte b = buf[ptr++];
-			if (b != '\r') {
+			if (isBinary || b != '\r') {
+				// Logic for binary files ends here
 				bs[off++] = b;
 				continue;
 			}
@@ -124,6 +132,10 @@ public class EolCanonicalizingInputStream extends InputStream {
 		cnt = in.read(buf, 0, buf.length);
 		if (cnt < 1)
 			return false;
+		if (!modeDetected) {
+			isBinary = RawText.isBinary(buf, cnt);
+			modeDetected = true;
+		}
 		ptr = 0;
 		return true;
 	}