Split out ApplyCommand logic to PatchApplier class

PatchApplier now routes updates through the index. This has two
results:

* we can now execute patches in-memory.

* the JGit apply command will now always update the
index to match the working tree.

Change-Id: Id60a88232f05d0367787d038d2518c670cdb543f
Co-authored-by: Han-Wen Nienhuys <hanwen@google.com>
Co-authored-by: Nitzan Gur-Furman <nitzan@google.com>

1 files changed, 14 insertions, 665 deletions

diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/ApplyCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/ApplyCommand.java
index e7f40d811b..49f225f319 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/ApplyCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/ApplyCommand.java
@@ -9,62 +9,13 @@
  */
 package org.eclipse.jgit.api;
 
-import java.io.ByteArrayInputStream;
 import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.IOException;
 import java.io.InputStream;
-import java.io.OutputStream;
-import java.nio.ByteBuffer;
-import java.nio.file.Files;
-import java.nio.file.StandardCopyOption;
-import java.text.MessageFormat;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.List;
-import java.util.zip.InflaterInputStream;
-import org.eclipse.jgit.api.errors.FilterFailedException;
 import org.eclipse.jgit.api.errors.GitAPIException;
-import org.eclipse.jgit.api.errors.PatchApplyException;
-import org.eclipse.jgit.api.errors.PatchFormatException;
-import org.eclipse.jgit.attributes.FilterCommand;
-import org.eclipse.jgit.attributes.FilterCommandRegistry;
-import org.eclipse.jgit.diff.DiffEntry.ChangeType;
-import org.eclipse.jgit.diff.RawText;
-import org.eclipse.jgit.dircache.DirCache;
-import org.eclipse.jgit.dircache.DirCacheCheckout;
-import org.eclipse.jgit.dircache.DirCacheCheckout.CheckoutMetadata;
-import org.eclipse.jgit.dircache.DirCacheIterator;
 import org.eclipse.jgit.internal.JGitText;
-import org.eclipse.jgit.lib.Constants;
-import org.eclipse.jgit.lib.CoreConfig.EolStreamType;
-import org.eclipse.jgit.lib.FileMode;
-import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.Repository;
-import org.eclipse.jgit.patch.BinaryHunk;
-import org.eclipse.jgit.patch.FileHeader;
-import org.eclipse.jgit.patch.FileHeader.PatchType;
-import org.eclipse.jgit.patch.HunkHeader;
-import org.eclipse.jgit.patch.Patch;
-import org.eclipse.jgit.treewalk.FileTreeIterator;
-import org.eclipse.jgit.treewalk.TreeWalk;
-import org.eclipse.jgit.treewalk.TreeWalk.OperationType;
-import org.eclipse.jgit.treewalk.filter.AndTreeFilter;
-import org.eclipse.jgit.treewalk.filter.NotIgnoredFilter;
-import org.eclipse.jgit.treewalk.filter.PathFilterGroup;
-import org.eclipse.jgit.util.FS;
-import org.eclipse.jgit.util.FS.ExecutionResult;
-import org.eclipse.jgit.util.FileUtils;
-import org.eclipse.jgit.util.IO;
-import org.eclipse.jgit.util.RawParseUtils;
-import org.eclipse.jgit.util.StringUtils;
-import org.eclipse.jgit.util.TemporaryBuffer;
-import org.eclipse.jgit.util.TemporaryBuffer.LocalFile;
-import org.eclipse.jgit.util.io.BinaryDeltaInputStream;
-import org.eclipse.jgit.util.io.BinaryHunkInputStream;
-import org.eclipse.jgit.util.io.EolStreamTypeUtil;
-import org.eclipse.jgit.util.sha1.SHA1;
+import org.eclipse.jgit.patch.PatchApplier;
+import org.eclipse.jgit.patch.PatchApplier.Result;
 
 /**
  * Apply a patch to files and/or to the index.
@@ -80,10 +31,13 @@ public class ApplyCommand extends GitCommand<ApplyResult> {
 	/**
 	 * Constructs the command.
 	 *
-	 * @param repo
+	 * @param local
 	 */
-	ApplyCommand(Repository repo) {
-		super(repo);
+	ApplyCommand(Repository local) {
+		super(local);
+		if (local == null) {
+			throw new NullPointerException(JGitText.get().repositoryIsRequired);
+		}
 	}
 
 	/**
@@ -101,6 +55,7 @@ public class ApplyCommand extends GitCommand<ApplyResult> {
 
 	/**
 	 * {@inheritDoc}
+	 *
 	 * <p>
 	 * Executes the {@code ApplyCommand} command with all the options and
 	 * parameters collected by the setter methods (e.g.
@@ -109,621 +64,15 @@ public class ApplyCommand extends GitCommand<ApplyResult> {
 	 * method twice on an instance.
 	 */
 	@Override
-	public ApplyResult call() throws GitAPIException, PatchFormatException,
-			PatchApplyException {
+	public ApplyResult call() throws GitAPIException {
 		checkCallable();
 		setCallable(false);
 		ApplyResult r = new ApplyResult();
-		try {
-			final Patch p = new Patch();
-			try {
-				p.parse(in);
-			} finally {
-				in.close();
-			}
-			if (!p.getErrors().isEmpty()) {
-				throw new PatchFormatException(p.getErrors());
-			}
-			Repository repository = getRepository();
-			DirCache cache = repository.readDirCache();
-			for (FileHeader fh : p.getFiles()) {
-				ChangeType type = fh.getChangeType();
-				File f = null;
-				switch (type) {
-				case ADD:
-					f = getFile(fh.getNewPath(), true);
-					apply(repository, fh.getNewPath(), cache, f, fh);
-					break;
-				case MODIFY:
-					f = getFile(fh.getOldPath(), false);
-					apply(repository, fh.getOldPath(), cache, f, fh);
-					break;
-				case DELETE:
-					f = getFile(fh.getOldPath(), false);
-					if (!f.delete())
-						throw new PatchApplyException(MessageFormat.format(
-								JGitText.get().cannotDeleteFile, f));
-					break;
-				case RENAME:
-					f = getFile(fh.getOldPath(), false);
-					File dest = getFile(fh.getNewPath(), false);
-					try {
-						FileUtils.mkdirs(dest.getParentFile(), true);
-						FileUtils.rename(f, dest,
-								StandardCopyOption.ATOMIC_MOVE);
-					} catch (IOException e) {
-						throw new PatchApplyException(MessageFormat.format(
-								JGitText.get().renameFileFailed, f, dest), e);
-					}
-					apply(repository, fh.getOldPath(), cache, dest, fh);
-					r.addUpdatedFile(dest);
-					break;
-				case COPY:
-					File src = getFile(fh.getOldPath(), false);
-					f = getFile(fh.getNewPath(), false);
-					FileUtils.mkdirs(f.getParentFile(), true);
-					Files.copy(src.toPath(), f.toPath());
-					apply(repository, fh.getOldPath(), cache, f, fh);
-				}
-				r.addUpdatedFile(f);
-			}
-		} catch (IOException e) {
-			throw new PatchApplyException(MessageFormat.format(
-					JGitText.get().patchApplyException, e.getMessage()), e);
+		PatchApplier patchApplier = new PatchApplier(repo);
+		Result applyResult = patchApplier.applyPatch(in);
+		for (String p : applyResult.getPaths()) {
+			r.addUpdatedFile(new File(repo.getWorkTree(), p));
 		}
 		return r;
 	}
-
-	private File getFile(String path, boolean create)
-			throws PatchApplyException {
-		File f = new File(getRepository().getWorkTree(), path);
-		if (create) {
-			try {
-				File parent = f.getParentFile();
-				FileUtils.mkdirs(parent, true);
-				FileUtils.createNewFile(f);
-			} catch (IOException e) {
-				throw new PatchApplyException(MessageFormat.format(
-						JGitText.get().createNewFileFailed, f), e);
-			}
-		}
-		return f;
-	}
-
-	private void apply(Repository repository, String path, DirCache cache,
-			File f, FileHeader fh) throws IOException, PatchApplyException {
-		if (PatchType.BINARY.equals(fh.getPatchType())) {
-			return;
-		}
-		boolean convertCrLf = needsCrLfConversion(f, fh);
-		// Use a TreeWalk with a DirCacheIterator to pick up the correct
-		// clean/smudge filters. CR-LF handling is completely determined by
-		// whether the file or the patch have CR-LF line endings.
-		try (TreeWalk walk = new TreeWalk(repository)) {
-			walk.setOperationType(OperationType.CHECKIN_OP);
-			FileTreeIterator files = new FileTreeIterator(repository);
-			int fileIdx = walk.addTree(files);
-			int cacheIdx = walk.addTree(new DirCacheIterator(cache));
-			files.setDirCacheIterator(walk, cacheIdx);
-			walk.setFilter(AndTreeFilter.create(
-					PathFilterGroup.createFromStrings(path),
-					new NotIgnoredFilter(fileIdx)));
-			walk.setRecursive(true);
-			if (walk.next()) {
-				// If the file on disk has no newline characters, convertCrLf
-				// will be false. In that case we want to honor the normal git
-				// settings.
-				EolStreamType streamType = convertCrLf ? EolStreamType.TEXT_CRLF
-						: walk.getEolStreamType(OperationType.CHECKOUT_OP);
-				String command = walk.getFilterCommand(
-						Constants.ATTR_FILTER_TYPE_SMUDGE);
-				CheckoutMetadata checkOut = new CheckoutMetadata(streamType, command);
-				FileTreeIterator file = walk.getTree(fileIdx,
-						FileTreeIterator.class);
-				if (file != null) {
-					if (PatchType.GIT_BINARY.equals(fh.getPatchType())) {
-						applyBinary(repository, path, f, fh,
-								file::openEntryStream, file.getEntryObjectId(),
-								checkOut);
-					} else {
-						command = walk.getFilterCommand(
-								Constants.ATTR_FILTER_TYPE_CLEAN);
-						RawText raw;
-						// Can't use file.openEntryStream() as it would do CR-LF
-						// conversion as usual, not as wanted by us.
-						try (InputStream input = filterClean(repository, path,
-								new FileInputStream(f), convertCrLf, command)) {
-							raw = new RawText(
-									IO.readWholeStream(input, 0).array());
-						}
-						applyText(repository, path, raw, f, fh, checkOut);
-					}
-					return;
-				}
-			}
-		}
-		// File ignored?
-		RawText raw;
-		CheckoutMetadata checkOut;
-		if (PatchType.GIT_BINARY.equals(fh.getPatchType())) {
-			checkOut = new CheckoutMetadata(EolStreamType.DIRECT, null);
-			applyBinary(repository, path, f, fh, () -> new FileInputStream(f),
-					null, checkOut);
-		} else {
-			if (convertCrLf) {
-				try (InputStream input = EolStreamTypeUtil.wrapInputStream(
-						new FileInputStream(f), EolStreamType.TEXT_LF)) {
-					raw = new RawText(IO.readWholeStream(input, 0).array());
-				}
-				checkOut = new CheckoutMetadata(EolStreamType.TEXT_CRLF, null);
-			} else {
-				raw = new RawText(f);
-				checkOut = new CheckoutMetadata(EolStreamType.DIRECT, null);
-			}
-			applyText(repository, path, raw, f, fh, checkOut);
-		}
-	}
-
-	private boolean needsCrLfConversion(File f, FileHeader fileHeader)
-			throws IOException {
-		if (PatchType.GIT_BINARY.equals(fileHeader.getPatchType())) {
-			return false;
-		}
-		if (!hasCrLf(fileHeader)) {
-			try (InputStream input = new FileInputStream(f)) {
-				return RawText.isCrLfText(input);
-			}
-		}
-		return false;
-	}
-
-	private static boolean hasCrLf(FileHeader fileHeader) {
-		if (PatchType.GIT_BINARY.equals(fileHeader.getPatchType())) {
-			return false;
-		}
-		for (HunkHeader header : fileHeader.getHunks()) {
-			byte[] buf = header.getBuffer();
-			int hunkEnd = header.getEndOffset();
-			int lineStart = header.getStartOffset();
-			while (lineStart < hunkEnd) {
-				int nextLineStart = RawParseUtils.nextLF(buf, lineStart);
-				if (nextLineStart > hunkEnd) {
-					nextLineStart = hunkEnd;
-				}
-				if (nextLineStart <= lineStart) {
-					break;
-				}
-				if (nextLineStart - lineStart > 1) {
-					char first = (char) (buf[lineStart] & 0xFF);
-					if (first == ' ' || first == '-') {
-						// It's an old line. Does it end in CR-LF?
-						if (buf[nextLineStart - 2] == '\r') {
-							return true;
-						}
-					}
-				}
-				lineStart = nextLineStart;
-			}
-		}
-		return false;
-	}
-
-	private InputStream filterClean(Repository repository, String path,
-			InputStream fromFile, boolean convertCrLf, String filterCommand)
-			throws IOException {
-		InputStream input = fromFile;
-		if (convertCrLf) {
-			input = EolStreamTypeUtil.wrapInputStream(input,
-					EolStreamType.TEXT_LF);
-		}
-		if (StringUtils.isEmptyOrNull(filterCommand)) {
-			return input;
-		}
-		if (FilterCommandRegistry.isRegistered(filterCommand)) {
-			LocalFile buffer = new TemporaryBuffer.LocalFile(null);
-			FilterCommand command = FilterCommandRegistry.createFilterCommand(
-					filterCommand, repository, input, buffer);
-			while (command.run() != -1) {
-				// loop as long as command.run() tells there is work to do
-			}
-			return buffer.openInputStreamWithAutoDestroy();
-		}
-		FS fs = repository.getFS();
-		ProcessBuilder filterProcessBuilder = fs.runInShell(filterCommand,
-				new String[0]);
-		filterProcessBuilder.directory(repository.getWorkTree());
-		filterProcessBuilder.environment().put(Constants.GIT_DIR_KEY,
-				repository.getDirectory().getAbsolutePath());
-		ExecutionResult result;
-		try {
-			result = fs.execute(filterProcessBuilder, in);
-		} catch (IOException | InterruptedException e) {
-			throw new IOException(
-					new FilterFailedException(e, filterCommand, path));
-		}
-		int rc = result.getRc();
-		if (rc != 0) {
-			throw new IOException(new FilterFailedException(rc, filterCommand,
-					path, result.getStdout().toByteArray(4096), RawParseUtils
-							.decode(result.getStderr().toByteArray(4096))));
-		}
-		return result.getStdout().openInputStreamWithAutoDestroy();
-	}
-
-	private void initHash(SHA1 hash, long size) {
-		hash.update(Constants.encodedTypeString(Constants.OBJ_BLOB));
-		hash.update((byte) ' ');
-		hash.update(Constants.encodeASCII(size));
-		hash.update((byte) 0);
-	}
-
-	private ObjectId hash(File f) throws IOException {
-		SHA1 hash = SHA1.newInstance();
-		initHash(hash, f.length());
-		try (InputStream input = new FileInputStream(f)) {
-			byte[] buf = new byte[8192];
-			int n;
-			while ((n = input.read(buf)) >= 0) {
-				hash.update(buf, 0, n);
-			}
-		}
-		return hash.toObjectId();
-	}
-
-	private void checkOid(ObjectId baseId, ObjectId id, ChangeType type, File f,
-			String path)
-			throws PatchApplyException, IOException {
-		boolean hashOk = false;
-		if (id != null) {
-			hashOk = baseId.equals(id);
-			if (!hashOk && ChangeType.ADD.equals(type)
-					&& ObjectId.zeroId().equals(baseId)) {
-				// We create the file first. The OID of an empty file is not the
-				// zero id!
-				hashOk = Constants.EMPTY_BLOB_ID.equals(id);
-			}
-		} else {
-			if (ObjectId.zeroId().equals(baseId)) {
-				// File empty is OK.
-				hashOk = !f.exists() || f.length() == 0;
-			} else {
-				hashOk = baseId.equals(hash(f));
-			}
-		}
-		if (!hashOk) {
-			throw new PatchApplyException(MessageFormat
-					.format(JGitText.get().applyBinaryBaseOidWrong, path));
-		}
-	}
-
-	private void applyBinary(Repository repository, String path, File f,
-			FileHeader fh, DirCacheCheckout.StreamSupplier loader, ObjectId id,
-			CheckoutMetadata checkOut)
-			throws PatchApplyException, IOException {
-		if (!fh.getOldId().isComplete() || !fh.getNewId().isComplete()) {
-			throw new PatchApplyException(MessageFormat
-					.format(JGitText.get().applyBinaryOidTooShort, path));
-		}
-		BinaryHunk hunk = fh.getForwardBinaryHunk();
-		// A BinaryHunk has the start at the "literal" or "delta" token. Data
-		// starts on the next line.
-		int start = RawParseUtils.nextLF(hunk.getBuffer(),
-				hunk.getStartOffset());
-		int length = hunk.getEndOffset() - start;
-		SHA1 hash = SHA1.newInstance();
-		// Write to a buffer and copy to the file only if everything was fine
-		TemporaryBuffer buffer = new TemporaryBuffer.LocalFile(null);
-		try {
-			switch (hunk.getType()) {
-			case LITERAL_DEFLATED:
-				// This just overwrites the file. We need to check the hash of
-				// the base.
-				checkOid(fh.getOldId().toObjectId(), id, fh.getChangeType(), f,
-						path);
-				initHash(hash, hunk.getSize());
-				try (OutputStream out = buffer;
-						InputStream inflated = new SHA1InputStream(hash,
-								new InflaterInputStream(
-										new BinaryHunkInputStream(
-												new ByteArrayInputStream(
-														hunk.getBuffer(), start,
-														length))))) {
-					DirCacheCheckout.getContent(repository, path, checkOut,
-							() -> inflated, null, out);
-					if (!fh.getNewId().toObjectId().equals(hash.toObjectId())) {
-						throw new PatchApplyException(MessageFormat.format(
-								JGitText.get().applyBinaryResultOidWrong,
-								path));
-					}
-				}
-				try (InputStream bufIn = buffer.openInputStream()) {
-					Files.copy(bufIn, f.toPath(),
-							StandardCopyOption.REPLACE_EXISTING);
-				}
-				break;
-			case DELTA_DEFLATED:
-				// Unfortunately delta application needs random access to the
-				// base to construct the result.
-				byte[] base;
-				try (InputStream input = loader.load()) {
-					base = IO.readWholeStream(input, 0).array();
-				}
-				// At least stream the result!
-				try (BinaryDeltaInputStream input = new BinaryDeltaInputStream(
-						base,
-						new InflaterInputStream(new BinaryHunkInputStream(
-								new ByteArrayInputStream(hunk.getBuffer(),
-										start, length))))) {
-					long finalSize = input.getExpectedResultSize();
-					initHash(hash, finalSize);
-					try (OutputStream out = buffer;
-							SHA1InputStream hashed = new SHA1InputStream(hash,
-									input)) {
-						DirCacheCheckout.getContent(repository, path, checkOut,
-								() -> hashed, null, out);
-						if (!fh.getNewId().toObjectId()
-								.equals(hash.toObjectId())) {
-							throw new PatchApplyException(MessageFormat.format(
-									JGitText.get().applyBinaryResultOidWrong,
-									path));
-						}
-					}
-				}
-				try (InputStream bufIn = buffer.openInputStream()) {
-					Files.copy(bufIn, f.toPath(),
-							StandardCopyOption.REPLACE_EXISTING);
-				}
-				break;
-			default:
-				break;
-			}
-		} finally {
-			buffer.destroy();
-		}
-	}
-
-	private void applyText(Repository repository, String path, RawText rt,
-			File f, FileHeader fh, CheckoutMetadata checkOut)
-			throws IOException, PatchApplyException {
-		List<ByteBuffer> oldLines = new ArrayList<>(rt.size());
-		for (int i = 0; i < rt.size(); i++) {
-			oldLines.add(rt.getRawString(i));
-		}
-		List<ByteBuffer> newLines = new ArrayList<>(oldLines);
-		int afterLastHunk = 0;
-		int lineNumberShift = 0;
-		int lastHunkNewLine = -1;
-		for (HunkHeader hh : fh.getHunks()) {
-
-			// We assume hunks to be ordered
-			if (hh.getNewStartLine() <= lastHunkNewLine) {
-				throw new PatchApplyException(MessageFormat
-						.format(JGitText.get().patchApplyException, hh));
-			}
-			lastHunkNewLine = hh.getNewStartLine();
-
-			byte[] b = new byte[hh.getEndOffset() - hh.getStartOffset()];
-			System.arraycopy(hh.getBuffer(), hh.getStartOffset(), b, 0,
-					b.length);
-			RawText hrt = new RawText(b);
-
-			List<ByteBuffer> hunkLines = new ArrayList<>(hrt.size());
-			for (int i = 0; i < hrt.size(); i++) {
-				hunkLines.add(hrt.getRawString(i));
-			}
-
-			if (hh.getNewStartLine() == 0) {
-				// Must be the single hunk for clearing all content
-				if (fh.getHunks().size() == 1
-						&& canApplyAt(hunkLines, newLines, 0)) {
-					newLines.clear();
-					break;
-				}
-				throw new PatchApplyException(MessageFormat
-						.format(JGitText.get().patchApplyException, hh));
-			}
-			// Hunk lines as reported by the hunk may be off, so don't rely on
-			// them.
-			int applyAt = hh.getNewStartLine() - 1 + lineNumberShift;
-			// But they definitely should not go backwards.
-			if (applyAt < afterLastHunk && lineNumberShift < 0) {
-				applyAt = hh.getNewStartLine() - 1;
-				lineNumberShift = 0;
-			}
-			if (applyAt < afterLastHunk) {
-				throw new PatchApplyException(MessageFormat
-						.format(JGitText.get().patchApplyException, hh));
-			}
-			boolean applies = false;
-			int oldLinesInHunk = hh.getLinesContext()
-					+ hh.getOldImage().getLinesDeleted();
-			if (oldLinesInHunk <= 1) {
-				// Don't shift hunks without context lines. Just try the
-				// position corrected by the current lineNumberShift, and if
-				// that fails, the position recorded in the hunk header.
-				applies = canApplyAt(hunkLines, newLines, applyAt);
-				if (!applies && lineNumberShift != 0) {
-					applyAt = hh.getNewStartLine() - 1;
-					applies = applyAt >= afterLastHunk
-							&& canApplyAt(hunkLines, newLines, applyAt);
-				}
-			} else {
-				int maxShift = applyAt - afterLastHunk;
-				for (int shift = 0; shift <= maxShift; shift++) {
-					if (canApplyAt(hunkLines, newLines, applyAt - shift)) {
-						applies = true;
-						applyAt -= shift;
-						break;
-					}
-				}
-				if (!applies) {
-					// Try shifting the hunk downwards
-					applyAt = hh.getNewStartLine() - 1 + lineNumberShift;
-					maxShift = newLines.size() - applyAt - oldLinesInHunk;
-					for (int shift = 1; shift <= maxShift; shift++) {
-						if (canApplyAt(hunkLines, newLines, applyAt + shift)) {
-							applies = true;
-							applyAt += shift;
-							break;
-						}
-					}
-				}
-			}
-			if (!applies) {
-				throw new PatchApplyException(MessageFormat
-						.format(JGitText.get().patchApplyException, hh));
-			}
-			// Hunk applies at applyAt. Apply it, and update afterLastHunk and
-			// lineNumberShift
-			lineNumberShift = applyAt - hh.getNewStartLine() + 1;
-			int sz = hunkLines.size();
-			for (int j = 1; j < sz; j++) {
-				ByteBuffer hunkLine = hunkLines.get(j);
-				if (!hunkLine.hasRemaining()) {
-					// Completely empty line; accept as empty context line
-					applyAt++;
-					continue;
-				}
-				switch (hunkLine.array()[hunkLine.position()]) {
-				case ' ':
-					applyAt++;
-					break;
-				case '-':
-					newLines.remove(applyAt);
-					break;
-				case '+':
-					newLines.add(applyAt++, slice(hunkLine, 1));
-					break;
-				default:
-					break;
-				}
-			}
-			afterLastHunk = applyAt;
-		}
-		if (!isNoNewlineAtEndOfFile(fh)) {
-			newLines.add(null);
-		}
-		if (!rt.isMissingNewlineAtEnd()) {
-			oldLines.add(null);
-		}
-		if (oldLines.equals(newLines)) {
-			return; // Unchanged; don't touch the file
-		}
-
-		TemporaryBuffer buffer = new TemporaryBuffer.LocalFile(null);
-		try {
-			try (OutputStream out = buffer) {
-				for (Iterator<ByteBuffer> l = newLines.iterator(); l
-						.hasNext();) {
-					ByteBuffer line = l.next();
-					if (line == null) {
-						// Must be the marker for the final newline
-						break;
-					}
-					out.write(line.array(), line.position(), line.remaining());
-					if (l.hasNext()) {
-						out.write('\n');
-					}
-				}
-			}
-			try (OutputStream output = new FileOutputStream(f)) {
-				DirCacheCheckout.getContent(repository, path, checkOut,
-						buffer::openInputStream, null, output);
-			}
-		} finally {
-			buffer.destroy();
-		}
-		repository.getFS().setExecute(f,
-				fh.getNewMode() == FileMode.EXECUTABLE_FILE);
-	}
-
-	private boolean canApplyAt(List<ByteBuffer> hunkLines,
-			List<ByteBuffer> newLines, int line) {
-		int sz = hunkLines.size();
-		int limit = newLines.size();
-		int pos = line;
-		for (int j = 1; j < sz; j++) {
-			ByteBuffer hunkLine = hunkLines.get(j);
-			if (!hunkLine.hasRemaining()) {
-				// Empty line. Accept as empty context line.
-				if (pos >= limit || newLines.get(pos).hasRemaining()) {
-					return false;
-				}
-				pos++;
-				continue;
-			}
-			switch (hunkLine.array()[hunkLine.position()]) {
-			case ' ':
-			case '-':
-				if (pos >= limit
-						|| !newLines.get(pos).equals(slice(hunkLine, 1))) {
-					return false;
-				}
-				pos++;
-				break;
-			default:
-				break;
-			}
-		}
-		return true;
-	}
-
-	private ByteBuffer slice(ByteBuffer b, int off) {
-		int newOffset = b.position() + off;
-		return ByteBuffer.wrap(b.array(), newOffset, b.limit() - newOffset);
-	}
-
-	private boolean isNoNewlineAtEndOfFile(FileHeader fh) {
-		List<? extends HunkHeader> hunks = fh.getHunks();
-		if (hunks == null || hunks.isEmpty()) {
-			return false;
-		}
-		HunkHeader lastHunk = hunks.get(hunks.size() - 1);
-		byte[] buf = new byte[lastHunk.getEndOffset()
-				- lastHunk.getStartOffset()];
-		System.arraycopy(lastHunk.getBuffer(), lastHunk.getStartOffset(), buf,
-				0, buf.length);
-		RawText lhrt = new RawText(buf);
-		return lhrt.getString(lhrt.size() - 1)
-				.equals("\\ No newline at end of file"); //$NON-NLS-1$
-	}
-
-	/**
-	 * An {@link InputStream} that updates a {@link SHA1} on every byte read.
-	 * The hash is supposed to have been initialized before reading starts.
-	 */
-	private static class SHA1InputStream extends InputStream {
-
-		private final SHA1 hash;
-
-		private final InputStream in;
-
-		SHA1InputStream(SHA1 hash, InputStream in) {
-			this.hash = hash;
-			this.in = in;
-		}
-
-		@Override
-		public int read() throws IOException {
-			int b = in.read();
-			if (b >= 0) {
-				hash.update((byte) b);
-			}
-			return b;
-		}
-
-		@Override
-		public int read(byte[] b, int off, int len) throws IOException {
-			int n = in.read(b, off, len);
-			if (n > 0) {
-				hash.update(b, off, n);
-			}
-			return n;
-		}
-
-		@Override
-		public void close() throws IOException {
-			in.close();
-		}
-	}
 }