/*
    * Copyright (C) 2008, Shawn O. Pearce <spearce@spearce.org>
    * 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;
  
  import java.io.BufferedReader;
  import java.io.ByteArrayInputStream;
  import java.io.File;
  import java.io.IOException;
  import java.io.InputStream;
  import java.io.InputStreamReader;
  import java.io.OutputStream;
  import java.io.PrintStream;
  import java.nio.charset.Charset;
  import java.security.AccessController;
  import java.security.PrivilegedAction;
  import java.text.MessageFormat;
  import java.util.Arrays;
  import java.util.HashMap;
  import java.util.Map;
  import java.util.Objects;
  import java.util.concurrent.ExecutorService;
  import java.util.concurrent.Executors;
  import java.util.concurrent.TimeUnit;
  import java.util.concurrent.atomic.AtomicBoolean;
  import java.util.concurrent.atomic.AtomicReference;
  
  import org.eclipse.jgit.annotations.Nullable;
  import org.eclipse.jgit.api.errors.JGitInternalException;
  import org.eclipse.jgit.errors.CommandFailedException;
  import org.eclipse.jgit.internal.JGitText;
  import org.eclipse.jgit.lib.Constants;
  import org.eclipse.jgit.lib.Repository;
  import org.eclipse.jgit.treewalk.FileTreeIterator.FileEntry;
  import org.eclipse.jgit.treewalk.FileTreeIterator.FileModeStrategy;
  import org.eclipse.jgit.treewalk.WorkingTreeIterator.Entry;
  import org.eclipse.jgit.util.ProcessResult.Status;
  import org.slf4j.Logger;
  import org.slf4j.LoggerFactory;
  
  /**
   * Abstraction to support various file system operations not in Java.
   */
  public abstract class FS {
  	private static final Logger LOG = LoggerFactory.getLogger(FS.class);
  
  	/**
  	 * An empty array of entries, suitable as a return value for
  	 * {@link #list(File, FileModeStrategy)}.
  	 *
  	 * @since 5.0
  	 */
  	protected static final Entry[] NO_ENTRIES = {};
  
  	/**
  	 * This class creates FS instances. It will be overridden by a Java7 variant
  	 * if such can be detected in {@link #detect(Boolean)}.
  	 *
  	 * @since 3.0
 	 */
 	public static class FSFactory {
 		/**
 		 * Constructor
 		 */
 		protected FSFactory() {
 			// empty
 		}
 
 		/**
 		 * Detect the file system
 		 *
 		 * @param cygwinUsed
 		 * @return FS instance
 		 */
 		public FS detect(Boolean cygwinUsed) {
 			if (SystemReader.getInstance().isWindows()) {
 				if (cygwinUsed == null)
 					cygwinUsed = Boolean.valueOf(FS_Win32_Cygwin.isCygwin());
 				if (cygwinUsed.booleanValue())
 					return new FS_Win32_Cygwin();
 				else
 					return new FS_Win32();
 			} else {
 				return new FS_POSIX();
 			}
 		}
 	}
 
 	/**
 	 * Result of an executed process. The caller is responsible to close the
 	 * contained {@link TemporaryBuffer}s
 	 *
 	 * @since 4.2
 	 */
 	public static class ExecutionResult {
 		private TemporaryBuffer stdout;
 
 		private TemporaryBuffer stderr;
 
 		private int rc;
 
 		/**
 		 * @param stdout
 		 * @param stderr
 		 * @param rc
 		 */
 		public ExecutionResult(TemporaryBuffer stdout, TemporaryBuffer stderr,
 				int rc) {
 			this.stdout = stdout;
 			this.stderr = stderr;
 			this.rc = rc;
 		}
 
 		/**
 		 * @return buffered standard output stream
 		 */
 		public TemporaryBuffer getStdout() {
 			return stdout;
 		}
 
 		/**
 		 * @return buffered standard error stream
 		 */
 		public TemporaryBuffer getStderr() {
 			return stderr;
 		}
 
 		/**
 		 * @return the return code of the process
 		 */
 		public int getRc() {
 			return rc;
 		}
 	}
 
 	/** The auto-detected implementation selected for this operating system and JRE. */
 	public static final FS DETECTED = detect();
 
 	private volatile static FSFactory factory;
 
 	/**
 	 * Auto-detect the appropriate file system abstraction.
 	 *
 	 * @return detected file system abstraction
 	 */
 	public static FS detect() {
 		return detect(null);
 	}
 
 	/**
 	 * Auto-detect the appropriate file system abstraction, taking into account
 	 * the presence of a Cygwin installation on the system. Using jgit in
 	 * combination with Cygwin requires a more elaborate (and possibly slower)
 	 * resolution of file system paths.
 	 *
 	 * @param cygwinUsed
 	 *            <ul>
 	 *            <li><code>Boolean.TRUE</code> to assume that Cygwin is used in
 	 *            combination with jgit</li>
 	 *            <li><code>Boolean.FALSE</code> to assume that Cygwin is
 	 *            <b>not</b> used with jgit</li>
 	 *            <li><code>null</code> to auto-detect whether a Cygwin
 	 *            installation is present on the system and in this case assume
 	 *            that Cygwin is used</li>
 	 *            </ul>
 	 *
 	 *            Note: this parameter is only relevant on Windows.
 	 * @return detected file system abstraction
 	 */
 	public static FS detect(Boolean cygwinUsed) {
 		if (factory == null) {
 			factory = new FS.FSFactory();
 		}
 		return factory.detect(cygwinUsed);
 	}
 
 	private volatile Holder<File> userHome;
 
 	private volatile Holder<File> gitSystemConfig;
 
 	/**
 	 * Constructs a file system abstraction.
 	 */
 	protected FS() {
 		// Do nothing by default.
 	}
 
 	/**
 	 * Initialize this FS using another's current settings.
 	 *
 	 * @param src
 	 *            the source FS to copy from.
 	 */
 	protected FS(FS src) {
 		userHome = src.userHome;
 		gitSystemConfig = src.gitSystemConfig;
 	}
 
 	/**
 	 * Create a new instance of the same type of FS.
 	 *
 	 * @return a new instance of the same type of FS.
 	 */
 	public abstract FS newInstance();
 
 	/**
 	 * Does this operating system and JRE support the execute flag on files?
 	 *
 	 * @return true if this implementation can provide reasonably accurate
 	 *         executable bit information; false otherwise.
 	 */
 	public abstract boolean supportsExecute();
 
 	/**
 	 * Does this file system support atomic file creation via
 	 * java.io.File#createNewFile()? In certain environments (e.g. on NFS) it is
 	 * not guaranteed that when two file system clients run createNewFile() in
 	 * parallel only one will succeed. In such cases both clients may think they
 	 * created a new file.
 	 *
 	 * @return true if this implementation support atomic creation of new Files
 	 *         by {@link java.io.File#createNewFile()}
 	 * @since 4.5
 	 */
 	public boolean supportsAtomicCreateNewFile() {
 		return true;
 	}
 
 	/**
 	 * Does this operating system and JRE supports symbolic links. The
 	 * capability to handle symbolic links is detected at runtime.
 	 *
 	 * @return true if symbolic links may be used
 	 * @since 3.0
 	 */
 	public boolean supportsSymlinks() {
 		return false;
 	}
 
 	/**
 	 * Is this file system case sensitive
 	 *
 	 * @return true if this implementation is case sensitive
 	 */
 	public abstract boolean isCaseSensitive();
 
 	/**
 	 * Determine if the file is executable (or not).
 	 * <p>
 	 * Not all platforms and JREs support executable flags on files. If the
 	 * feature is unsupported this method will always return false.
 	 * <p>
 	 * <em>If the platform supports symbolic links and <code>f</code> is a symbolic link
 	 * this method returns false, rather than the state of the executable flags
 	 * on the target file.</em>
 	 *
 	 * @param f
 	 *            abstract path to test.
 	 * @return true if the file is believed to be executable by the user.
 	 */
 	public abstract boolean canExecute(File f);
 
 	/**
 	 * Set a file to be executable by the user.
 	 * <p>
 	 * Not all platforms and JREs support executable flags on files. If the
 	 * feature is unsupported this method will always return false and no
 	 * changes will be made to the file specified.
 	 *
 	 * @param f
 	 *            path to modify the executable status of.
 	 * @param canExec
 	 *            true to enable execution; false to disable it.
 	 * @return true if the change succeeded; false otherwise.
 	 */
 	public abstract boolean setExecute(File f, boolean canExec);
 
 	/**
 	 * Get the last modified time of a file system object. If the OS/JRE support
 	 * symbolic links, the modification time of the link is returned, rather
 	 * than that of the link target.
 	 *
 	 * @param f
 	 *            a {@link java.io.File} object.
 	 * @return last modified time of f
 	 * @throws java.io.IOException
 	 * @since 3.0
 	 */
 	public long lastModified(File f) throws IOException {
 		return FileUtils.lastModified(f);
 	}
 
 	/**
 	 * Set the last modified time of a file system object. If the OS/JRE support
 	 * symbolic links, the link is modified, not the target,
 	 *
 	 * @param f
 	 *            a {@link java.io.File} object.
 	 * @param time
 	 *            last modified time
 	 * @throws java.io.IOException
 	 * @since 3.0
 	 */
 	public void setLastModified(File f, long time) throws IOException {
 		FileUtils.setLastModified(f, time);
 	}
 
 	/**
 	 * Get the length of a file or link, If the OS/JRE supports symbolic links
 	 * it's the length of the link, else the length of the target.
 	 *
 	 * @param path
 	 *            a {@link java.io.File} object.
 	 * @return length of a file
 	 * @throws java.io.IOException
 	 * @since 3.0
 	 */
 	public long length(File path) throws IOException {
 		return FileUtils.getLength(path);
 	}
 
 	/**
 	 * Delete a file. Throws an exception if delete fails.
 	 *
 	 * @param f
 	 *            a {@link java.io.File} object.
 	 * @throws java.io.IOException
 	 *             this may be a Java7 subclass with detailed information
 	 * @since 3.3
 	 */
 	public void delete(File f) throws IOException {
 		FileUtils.delete(f);
 	}
 
 	/**
 	 * Resolve this file to its actual path name that the JRE can use.
 	 * <p>
 	 * This method can be relatively expensive. Computing a translation may
 	 * require forking an external process per path name translated. Callers
 	 * should try to minimize the number of translations necessary by caching
 	 * the results.
 	 * <p>
 	 * Not all platforms and JREs require path name translation. Currently only
 	 * Cygwin on Win32 require translation for Cygwin based paths.
 	 *
 	 * @param dir
 	 *            directory relative to which the path name is.
 	 * @param name
 	 *            path name to translate.
 	 * @return the translated path. <code>new File(dir,name)</code> if this
 	 *         platform does not require path name translation.
 	 */
 	public File resolve(File dir, String name) {
 		final File abspn = new File(name);
 		if (abspn.isAbsolute())
 			return abspn;
 		return new File(dir, name);
 	}
 
 	/**
 	 * Determine the user's home directory (location where preferences are).
 	 * <p>
 	 * This method can be expensive on the first invocation if path name
 	 * translation is required. Subsequent invocations return a cached result.
 	 * <p>
 	 * Not all platforms and JREs require path name translation. Currently only
 	 * Cygwin on Win32 requires translation of the Cygwin HOME directory.
 	 *
 	 * @return the user's home directory; null if the user does not have one.
 	 */
 	public File userHome() {
 		Holder<File> p = userHome;
 		if (p == null) {
 			p = new Holder<>(userHomeImpl());
 			userHome = p;
 		}
 		return p.value;
 	}
 
 	/**
 	 * Set the user's home directory location.
 	 *
 	 * @param path
 	 *            the location of the user's preferences; null if there is no
 	 *            home directory for the current user.
 	 * @return {@code this}.
 	 */
 	public FS setUserHome(File path) {
 		userHome = new Holder<>(path);
 		return this;
 	}
 
 	/**
 	 * Does this file system have problems with atomic renames?
 	 *
 	 * @return true if the caller should retry a failed rename of a lock file.
 	 */
 	public abstract boolean retryFailedLockFileCommit();
 
 	/**
 	 * Determine the user's home directory (location where preferences are).
 	 *
 	 * @return the user's home directory; null if the user does not have one.
 	 */
 	protected File userHomeImpl() {
 		final String home = AccessController
 				.doPrivileged(new PrivilegedAction<String>() {
 					@Override
 					public String run() {
 						return System.getProperty("user.home"); //$NON-NLS-1$
 					}
 				});
 		if (home == null || home.length() == 0)
 			return null;
 		return new File(home).getAbsoluteFile();
 	}
 
 	/**
 	 * Searches the given path to see if it contains one of the given files.
 	 * Returns the first it finds. Returns null if not found or if path is null.
 	 *
 	 * @param path
 	 *            List of paths to search separated by File.pathSeparator
 	 * @param lookFor
 	 *            Files to search for in the given path
 	 * @return the first match found, or null
 	 * @since 3.0
 	 */
 	protected static File searchPath(String path, String... lookFor) {
 		if (path == null)
 			return null;
 
 		for (String p : path.split(File.pathSeparator)) {
 			for (String command : lookFor) {
 				final File e = new File(p, command);
 				if (e.isFile())
 					return e.getAbsoluteFile();
 			}
 		}
 		return null;
 	}
 
 	/**
 	 * Execute a command and return a single line of output as a String
 	 *
 	 * @param dir
 	 *            Working directory for the command
 	 * @param command
 	 *            as component array
 	 * @param encoding
 	 *            to be used to parse the command's output
 	 * @return the one-line output of the command or {@code null} if there is
 	 *         none
 	 * @throws org.eclipse.jgit.errors.CommandFailedException
 	 *             thrown when the command failed (return code was non-zero)
 	 */
 	@Nullable
 	protected static String readPipe(File dir, String[] command,
 			String encoding) throws CommandFailedException {
 		return readPipe(dir, command, encoding, null);
 	}
 
 	/**
 	 * Execute a command and return a single line of output as a String
 	 *
 	 * @param dir
 	 *            Working directory for the command
 	 * @param command
 	 *            as component array
 	 * @param encoding
 	 *            to be used to parse the command's output
 	 * @param env
 	 *            Map of environment variables to be merged with those of the
 	 *            current process
 	 * @return the one-line output of the command or {@code null} if there is
 	 *         none
 	 * @throws org.eclipse.jgit.errors.CommandFailedException
 	 *             thrown when the command failed (return code was non-zero)
 	 * @since 4.0
 	 */
 	@Nullable
 	protected static String readPipe(File dir, String[] command,
 			String encoding, Map<String, String> env)
 			throws CommandFailedException {
 		final boolean debug = LOG.isDebugEnabled();
 		try {
 			if (debug) {
 				LOG.debug("readpipe " + Arrays.asList(command) + "," //$NON-NLS-1$ //$NON-NLS-2$
 						+ dir);
 			}
 			ProcessBuilder pb = new ProcessBuilder(command);
 			pb.directory(dir);
 			if (env != null) {
 				pb.environment().putAll(env);
 			}
 			Process p;
 			try {
 				p = pb.start();
 			} catch (IOException e) {
 				// Process failed to start
 				throw new CommandFailedException(-1, e.getMessage(), e);
 			}
 			p.getOutputStream().close();
 			GobblerThread gobbler = new GobblerThread(p, command, dir);
 			gobbler.start();
 			String r = null;
 			try (BufferedReader lineRead = new BufferedReader(
 					new InputStreamReader(p.getInputStream(), encoding))) {
 				r = lineRead.readLine();
 				if (debug) {
 					LOG.debug("readpipe may return '" + r + "'"); //$NON-NLS-1$ //$NON-NLS-2$
 					LOG.debug("remaining output:\n"); //$NON-NLS-1$
 					String l;
 					while ((l = lineRead.readLine()) != null) {
 						LOG.debug(l);
 					}
 				}
 			}
 
 			for (;;) {
 				try {
 					int rc = p.waitFor();
 					gobbler.join();
 					if (rc == 0 && !gobbler.fail.get()) {
 						return r;
 					} else {
 						if (debug) {
 							LOG.debug("readpipe rc=" + rc); //$NON-NLS-1$
 						}
 						throw new CommandFailedException(rc,
 								gobbler.errorMessage.get(),
 								gobbler.exception.get());
 					}
 				} catch (InterruptedException ie) {
 					// Stop bothering me, I have a zombie to reap.
 				}
 			}
 		} catch (IOException e) {
 			LOG.error("Caught exception in FS.readPipe()", e); //$NON-NLS-1$
 		}
 		if (debug) {
 			LOG.debug("readpipe returns null"); //$NON-NLS-1$
 		}
 		return null;
 	}
 
 	private static class GobblerThread extends Thread {
 
 		/* The process has 5 seconds to exit after closing stderr */
 		private static final int PROCESS_EXIT_TIMEOUT = 5;
 
 		private final Process p;
 		private final String desc;
 		private final String dir;
 		final AtomicBoolean fail = new AtomicBoolean();
 		final AtomicReference<String> errorMessage = new AtomicReference<>();
 		final AtomicReference<Throwable> exception = new AtomicReference<>();
 
 		GobblerThread(Process p, String[] command, File dir) {
 			this.p = p;
 			this.desc = Arrays.toString(command);
 			this.dir = Objects.toString(dir);
 		}
 
 		@Override
 		public void run() {
 			StringBuilder err = new StringBuilder();
 			try (InputStream is = p.getErrorStream()) {
 				int ch;
 				while ((ch = is.read()) != -1) {
 					err.append((char) ch);
 				}
 			} catch (IOException e) {
 				if (waitForProcessCompletion(e) && p.exitValue() != 0) {
 					setError(e, e.getMessage(), p.exitValue());
 					fail.set(true);
 				} else {
 					// ignore. command terminated faster and stream was just closed
 					// or the process didn't terminate within timeout
 				}
 			} finally {
 				if (waitForProcessCompletion(null) && err.length() > 0) {
 					setError(null, err.toString(), p.exitValue());
 					if (p.exitValue() != 0) {
 						fail.set(true);
 					}
 				}
 			}
 		}
 
 		@SuppressWarnings("boxing")
 		private boolean waitForProcessCompletion(IOException originalError) {
 			try {
 				if (!p.waitFor(PROCESS_EXIT_TIMEOUT, TimeUnit.SECONDS)) {
 					setError(originalError, MessageFormat.format(
 							JGitText.get().commandClosedStderrButDidntExit,
 							desc, PROCESS_EXIT_TIMEOUT), -1);
 					fail.set(true);
 				}
 			} catch (InterruptedException e) {
 				LOG.error(MessageFormat.format(
 						JGitText.get().threadInterruptedWhileRunning, desc), e);
 			}
 			return false;
 		}
 
 		private void setError(IOException e, String message, int exitCode) {
 			exception.set(e);
 			errorMessage.set(MessageFormat.format(
 					JGitText.get().exceptionCaughtDuringExecutionOfCommand,
 					desc, dir, Integer.valueOf(exitCode), message));
 		}
 	}
 
 	/**
 	 * Discover the path to the Git executable.
 	 *
 	 * @return the path to the Git executable or {@code null} if it cannot be
 	 *         determined.
 	 * @since 4.0
 	 */
 	protected abstract File discoverGitExe();
 
 	/**
 	 * Discover the path to the system-wide Git configuration file
 	 *
 	 * @return the path to the system-wide Git configuration file or
 	 *         {@code null} if it cannot be determined.
 	 * @since 4.0
 	 */
 	protected File discoverGitSystemConfig() {
 		File gitExe = discoverGitExe();
 		if (gitExe == null) {
 			return null;
 		}
 
 		// Bug 480782: Check if the discovered git executable is JGit CLI
 		String v;
 		try {
 			v = readPipe(gitExe.getParentFile(),
 				new String[] { "git", "--version" }, //$NON-NLS-1$ //$NON-NLS-2$
 				Charset.defaultCharset().name());
 		} catch (CommandFailedException e) {
 			LOG.warn(e.getMessage());
 			return null;
 		}
 		if (StringUtils.isEmptyOrNull(v)
 				|| (v != null && v.startsWith("jgit"))) { //$NON-NLS-1$
 			return null;
 		}
 
 		// Trick Git into printing the path to the config file by using "echo"
 		// as the editor.
 		Map<String, String> env = new HashMap<>();
 		env.put("GIT_EDITOR", "echo"); //$NON-NLS-1$ //$NON-NLS-2$
 
 		String w;
 		try {
 			w = readPipe(gitExe.getParentFile(),
 				new String[] { "git", "config", "--system", "--edit" }, //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ //$NON-NLS-4$
 				Charset.defaultCharset().name(), env);
 		} catch (CommandFailedException e) {
 			LOG.warn(e.getMessage());
 			return null;
 		}
 		if (StringUtils.isEmptyOrNull(w)) {
 			return null;
 		}
 
 		return new File(w);
 	}
 
 	/**
 	 * Get the currently used path to the system-wide Git configuration file.
 	 *
 	 * @return the currently used path to the system-wide Git configuration file
 	 *         or {@code null} if none has been set.
 	 * @since 4.0
 	 */
 	public File getGitSystemConfig() {
 		if (gitSystemConfig == null) {
 			gitSystemConfig = new Holder<>(discoverGitSystemConfig());
 		}
 		return gitSystemConfig.value;
 	}
 
 	/**
 	 * Set the path to the system-wide Git configuration file to use.
 	 *
 	 * @param configFile
 	 *            the path to the config file.
 	 * @return {@code this}
 	 * @since 4.0
 	 */
 	public FS setGitSystemConfig(File configFile) {
 		gitSystemConfig = new Holder<>(configFile);
 		return this;
 	}
 
 	/**
 	 * Get the parent directory of this file's parent directory
 	 *
 	 * @param grandchild
 	 *            a {@link java.io.File} object.
 	 * @return the parent directory of this file's parent directory or
 	 *         {@code null} in case there's no grandparent directory
 	 * @since 4.0
 	 */
 	protected static File resolveGrandparentFile(File grandchild) {
 		if (grandchild != null) {
 			File parent = grandchild.getParentFile();
 			if (parent != null)
 				return parent.getParentFile();
 		}
 		return null;
 	}
 
 	/**
 	 * Check if a file is a symbolic link and read it
 	 *
 	 * @param path
 	 *            a {@link java.io.File} object.
 	 * @return target of link or null
 	 * @throws java.io.IOException
 	 * @since 3.0
 	 */
 	public String readSymLink(File path) throws IOException {
 		return FileUtils.readSymLink(path);
 	}
 
 	/**
 	 * Whether the path is a symbolic link (and we support these).
 	 *
 	 * @param path
 	 *            a {@link java.io.File} object.
 	 * @return true if the path is a symbolic link (and we support these)
 	 * @throws java.io.IOException
 	 * @since 3.0
 	 */
 	public boolean isSymLink(File path) throws IOException {
 		return FileUtils.isSymlink(path);
 	}
 
 	/**
 	 * Tests if the path exists, in case of a symbolic link, true even if the
 	 * target does not exist
 	 *
 	 * @param path
 	 *            a {@link java.io.File} object.
 	 * @return true if path exists
 	 * @since 3.0
 	 */
 	public boolean exists(File path) {
 		return FileUtils.exists(path);
 	}
 
 	/**
 	 * Check if path is a directory. If the OS/JRE supports symbolic links and
 	 * path is a symbolic link to a directory, this method returns false.
 	 *
 	 * @param path
 	 *            a {@link java.io.File} object.
 	 * @return true if file is a directory,
 	 * @since 3.0
 	 */
 	public boolean isDirectory(File path) {
 		return FileUtils.isDirectory(path);
 	}
 
 	/**
 	 * Examine if path represents a regular file. If the OS/JRE supports
 	 * symbolic links the test returns false if path represents a symbolic link.
 	 *
 	 * @param path
 	 *            a {@link java.io.File} object.
 	 * @return true if path represents a regular file
 	 * @since 3.0
 	 */
 	public boolean isFile(File path) {
 		return FileUtils.isFile(path);
 	}
 
 	/**
 	 * Whether path is hidden, either starts with . on unix or has the hidden
 	 * attribute in windows
 	 *
 	 * @param path
 	 *            a {@link java.io.File} object.
 	 * @return true if path is hidden, either starts with . on unix or has the
 	 *         hidden attribute in windows
 	 * @throws java.io.IOException
 	 * @since 3.0
 	 */
 	public boolean isHidden(File path) throws IOException {
 		return FileUtils.isHidden(path);
 	}
 
 	/**
 	 * Set the hidden attribute for file whose name starts with a period.
 	 *
 	 * @param path
 	 *            a {@link java.io.File} object.
 	 * @param hidden
 	 *            whether to set the file hidden
 	 * @throws java.io.IOException
 	 * @since 3.0
 	 */
 	public void setHidden(File path, boolean hidden) throws IOException {
 		FileUtils.setHidden(path, hidden);
 	}
 
 	/**
 	 * Create a symbolic link
 	 *
 	 * @param path
 	 *            a {@link java.io.File} object.
 	 * @param target
 	 *            target path of the symlink
 	 * @throws java.io.IOException
 	 * @since 3.0
 	 */
 	public void createSymLink(File path, String target) throws IOException {
 		FileUtils.createSymLink(path, target);
 	}
 
 	/**
 	 * Create a new file. See {@link java.io.File#createNewFile()}. Subclasses
 	 * of this class may take care to provide a safe implementation for this
 	 * even if {@link #supportsAtomicCreateNewFile()} is <code>false</code>
 	 *
 	 * @param path
 	 *            the file to be created
 	 * @return <code>true</code> if the file was created, <code>false</code> if
 	 *         the file already existed
 	 * @throws java.io.IOException
 	 * @since 4.5
 	 */
 	public boolean createNewFile(File path) throws IOException {
 		return path.createNewFile();
 	}
 
 	/**
 	 * See
 	 * {@link org.eclipse.jgit.util.FileUtils#relativizePath(String, String, String, boolean)}.
 	 *
 	 * @param base
 	 *            The path against which <code>other</code> should be
 	 *            relativized.
 	 * @param other
 	 *            The path that will be made relative to <code>base</code>.
 	 * @return A relative path that, when resolved against <code>base</code>,
 	 *         will yield the original <code>other</code>.
 	 * @see FileUtils#relativizePath(String, String, String, boolean)
 	 * @since 3.7
 	 */
 	public String relativize(String base, String other) {
 		return FileUtils.relativizePath(base, other, File.separator, this.isCaseSensitive());
 	}
 
 	/**
 	 * Enumerates children of a directory.
 	 *
 	 * @param directory
 	 *            to get the children of
 	 * @param fileModeStrategy
 	 *            to use to calculate the git mode of a child
 	 * @return an array of entries for the children
 	 *
 	 * @since 5.0
 	 */
 	public Entry[] list(File directory, FileModeStrategy fileModeStrategy) {
 		final File[] all = directory.listFiles();
 		if (all == null) {
 			return NO_ENTRIES;
 		}
 		final Entry[] result = new Entry[all.length];
 		for (int i = 0; i < result.length; i++) {
 			result[i] = new FileEntry(all[i], this, fileModeStrategy);
 		}
 		return result;
 	}
 
 	/**
 	 * Checks whether the given hook is defined for the given repository, then
 	 * runs it with the given arguments.
 	 * <p>
 	 * The hook's standard output and error streams will be redirected to
 	 * <code>System.out</code> and <code>System.err</code> respectively. The
 	 * hook will have no stdin.
 	 * </p>
 	 *
 	 * @param repository
 	 *            The repository for which a hook should be run.
 	 * @param hookName
 	 *            The name of the hook to be executed.
 	 * @param args
 	 *            Arguments to pass to this hook. Cannot be <code>null</code>,
 	 *            but can be an empty array.
 	 * @return The ProcessResult describing this hook's execution.
 	 * @throws org.eclipse.jgit.api.errors.JGitInternalException
 	 *             if we fail to run the hook somehow. Causes may include an
 	 *             interrupted process or I/O errors.
 	 * @since 4.0
 	 */
 	public ProcessResult runHookIfPresent(Repository repository,
 			final String hookName,
 			String[] args) throws JGitInternalException {
 		return runHookIfPresent(repository, hookName, args, System.out, System.err,
 				null);
 	}
 
 	/**
 	 * Checks whether the given hook is defined for the given repository, then
 	 * runs it with the given arguments.
 	 *
 	 * @param repository
 	 *            The repository for which a hook should be run.
 	 * @param hookName
 	 *            The name of the hook to be executed.
 	 * @param args
 	 *            Arguments to pass to this hook. Cannot be <code>null</code>,
 	 *            but can be an empty array.
 	 * @param outRedirect
 	 *            A print stream on which to redirect the hook's stdout. Can be
 	 *            <code>null</code>, in which case the hook's standard output
 	 *            will be lost.
 	 * @param errRedirect
 	 *            A print stream on which to redirect the hook's stderr. Can be
 	 *            <code>null</code>, in which case the hook's standard error
 	 *            will be lost.
 	 * @param stdinArgs
 	 *            A string to pass on to the standard input of the hook. May be
 	 *            <code>null</code>.
 	 * @return The ProcessResult describing this hook's execution.
 	 * @throws org.eclipse.jgit.api.errors.JGitInternalException
 	 *             if we fail to run the hook somehow. Causes may include an
 	 *             interrupted process or I/O errors.
 	 * @since 4.0
 	 */
 	public ProcessResult runHookIfPresent(Repository repository,
 			final String hookName,
 			String[] args, PrintStream outRedirect, PrintStream errRedirect,
 			String stdinArgs) throws JGitInternalException {
 		return new ProcessResult(Status.NOT_SUPPORTED);
 	}
 
 	/**
 	 * See
 	 * {@link #runHookIfPresent(Repository, String, String[], PrintStream, PrintStream, String)}
 	 * . Should only be called by FS supporting shell scripts execution.
 	 *
 	 * @param repository
 	 *            The repository for which a hook should be run.
 	 * @param hookName
 	 *            The name of the hook to be executed.
 	 * @param args
 	 *            Arguments to pass to this hook. Cannot be <code>null</code>,
 	 *            but can be an empty array.
 	 * @param outRedirect
 	 *            A print stream on which to redirect the hook's stdout. Can be
 	 *            <code>null</code>, in which case the hook's standard output
 	 *            will be lost.
 	 * @param errRedirect
 	 *            A print stream on which to redirect the hook's stderr. Can be
 	 *            <code>null</code>, in which case the hook's standard error
 	 *            will be lost.
 	 * @param stdinArgs
 	 *            A string to pass on to the standard input of the hook. May be
 	 *            <code>null</code>.
 	 * @return The ProcessResult describing this hook's execution.
 	 * @throws org.eclipse.jgit.api.errors.JGitInternalException
 	 *             if we fail to run the hook somehow. Causes may include an
 	 *             interrupted process or I/O errors.
 	 * @since 4.0
 	 */
 	protected ProcessResult internalRunHookIfPresent(Repository repository,
 			final String hookName, String[] args, PrintStream outRedirect,
 			PrintStream errRedirect, String stdinArgs)
 			throws JGitInternalException {
 		final File hookFile = findHook(repository, hookName);
 		if (hookFile == null)
 			return new ProcessResult(Status.NOT_PRESENT);
 
 		final String hookPath = hookFile.getAbsolutePath();
 		final File runDirectory;
 		if (repository.isBare())
 			runDirectory = repository.getDirectory();
 		else
 			runDirectory = repository.getWorkTree();
 		final String cmd = relativize(runDirectory.getAbsolutePath(),
 				hookPath);
 		ProcessBuilder hookProcess = runInShell(cmd, args);
 		hookProcess.directory(runDirectory);
 		try {
 			return new ProcessResult(runProcess(hookProcess, outRedirect,
 					errRedirect, stdinArgs), Status.OK);
 		} catch (IOException e) {
 			throw new JGitInternalException(MessageFormat.format(
 					JGitText.get().exceptionCaughtDuringExecutionOfHook,
 					hookName), e);
 		} catch (InterruptedException e) {
 			throw new JGitInternalException(MessageFormat.format(
 					JGitText.get().exceptionHookExecutionInterrupted,
 							hookName), e);
 		}
 	}
 
 
 	/**
 	 * Tries to find a hook matching the given one in the given repository.
 	 *
 	 * @param repository
 	 *            The repository within which to find a hook.
 	 * @param hookName
 	 *            The name of the hook we're trying to find.
 	 * @return The {@link java.io.File} containing this particular hook if it
 	 *         exists in the given repository, <code>null</code> otherwise.
 	 * @since 4.0
 	 */
 	public File findHook(Repository repository, String hookName) {
 		File gitDir = repository.getDirectory();
 		if (gitDir == null)
 			return null;
 		final File hookFile = new File(new File(gitDir,
 				Constants.HOOKS), hookName);
 		return hookFile.isFile() ? hookFile : null;
 	}
 
 	/**
 	 * Runs the given process until termination, clearing its stdout and stderr
 	 * streams on-the-fly.
 	 *
 	 * @param processBuilder
 	 *            The process builder configured for this process.
 	 * @param outRedirect
 	 *            A OutputStream on which to redirect the processes stdout. Can
 	 *            be <code>null</code>, in which case the processes standard
 	 *            output will be lost.
 	 * @param errRedirect
 	 *            A OutputStream on which to redirect the processes stderr. Can
 	 *            be <code>null</code>, in which case the processes standard
 	 *            error will be lost.
 	 * @param stdinArgs
 	 *            A string to pass on to the standard input of the hook. Can be
 	 *            <code>null</code>.
 	 * @return the exit value of this process.
 	 * @throws java.io.IOException
 	 *             if an I/O error occurs while executing this process.
 	 * @throws java.lang.InterruptedException
 	 *             if the current thread is interrupted while waiting for the
 	 *             process to end.
 	 * @since 4.2
 	 */
 	public int runProcess(ProcessBuilder processBuilder,
 			OutputStream outRedirect, OutputStream errRedirect, String stdinArgs)
 			throws IOException, InterruptedException {
 		InputStream in = (stdinArgs == null) ? null : new ByteArrayInputStream(
 				stdinArgs.getBytes(Constants.CHARACTER_ENCODING));
 		return runProcess(processBuilder, outRedirect, errRedirect, in);
 	}
 
 	/**
 	 * Runs the given process until termination, clearing its stdout and stderr
 	 * streams on-the-fly.
 	 *
 	 * @param processBuilder
 	 *            The process builder configured for this process.
 	 * @param outRedirect
 	 *            An OutputStream on which to redirect the processes stdout. Can
 	 *            be <code>null</code>, in which case the processes standard
 	 *            output will be lost.
 	 * @param errRedirect
 	 *            An OutputStream on which to redirect the processes stderr. Can
 	 *            be <code>null</code>, in which case the processes standard
 	 *            error will be lost.
 	 * @param inRedirect
 	 *            An InputStream from which to redirect the processes stdin. Can
 	 *            be <code>null</code>, in which case the process doesn't get
 	 *            any data over stdin. It is assumed that the whole InputStream
 	 *            will be consumed by the process. The method will close the
 	 *            inputstream after all bytes are read.
 	 * @return the return code of this process.
 	 * @throws java.io.IOException
 	 *             if an I/O error occurs while executing this process.
 	 * @throws java.lang.InterruptedException
 	 *             if the current thread is interrupted while waiting for the
 	 *             process to end.
 	 * @since 4.2
 	 */
 	public int runProcess(ProcessBuilder processBuilder,
 			OutputStream outRedirect, OutputStream errRedirect,
 			InputStream inRedirect) throws IOException,
 			InterruptedException {
 		final ExecutorService executor = Executors.newFixedThreadPool(2);
 		Process process = null;
 		// We'll record the first I/O exception that occurs, but keep on trying
 		// to dispose of our open streams and file handles
 		IOException ioException = null;
 		try {
 			process = processBuilder.start();
 			executor.execute(
 					new StreamGobbler(process.getErrorStream(), errRedirect));
 			executor.execute(
 					new StreamGobbler(process.getInputStream(), outRedirect));
 			@SuppressWarnings("resource") // Closed in the finally block
 			OutputStream outputStream = process.getOutputStream();
 			try {
 				if (inRedirect != null) {
 					new StreamGobbler(inRedirect, outputStream).copy();
 				}
 			} finally {
 				try {
 					outputStream.close();
 				} catch (IOException e) {
 					// When the process exits before consuming the input, the OutputStream
 					// is replaced with the null output stream. This null output stream
 					// throws IOException for all write calls. When StreamGobbler fails to
 					// flush the buffer because of this, this close call tries to flush it
 					// again. This causes another IOException. Since we ignore the
 					// IOException in StreamGobbler, we also ignore the exception here.
 				}
 			}
 			return process.waitFor();
 		} catch (IOException e) {
 			ioException = e;
 		} finally {
 			shutdownAndAwaitTermination(executor);
 			if (process != null) {
 				try {
 					process.waitFor();
 				} catch (InterruptedException e) {
 					// Thrown by the outer try.
 					// Swallow this one to carry on our cleanup, and clear the
 					// interrupted flag (processes throw the exception without
 					// clearing the flag).
 					Thread.interrupted();
 				}
 				// A process doesn't clean its own resources even when destroyed
 				// Explicitly try and close all three streams, preserving the
 				// outer I/O exception if any.
 				if (inRedirect != null) {
 					inRedirect.close();
 				}
 				try {
 					process.getErrorStream().close();
 				} catch (IOException e) {
 					ioException = ioException != null ? ioException : e;
 				}
 				try {
 					process.getInputStream().close();
 				} catch (IOException e) {
 					ioException = ioException != null ? ioException : e;
 				}
 				try {
 					process.getOutputStream().close();
 				} catch (IOException e) {
 					ioException = ioException != null ? ioException : e;
 				}
 				process.destroy();
 			}
 		}
 		// We can only be here if the outer try threw an IOException.
 		throw ioException;
 	}
 
 	/**
 	 * Shuts down an {@link ExecutorService} in two phases, first by calling
 	 * {@link ExecutorService#shutdown() shutdown} to reject incoming tasks, and
 	 * then calling {@link ExecutorService#shutdownNow() shutdownNow}, if
 	 * necessary, to cancel any lingering tasks. Returns true if the pool has
 	 * been properly shutdown, false otherwise.
 	 * <p>
 	 *
 	 * @param pool
 	 *            the pool to shutdown
 	 * @return <code>true</code> if the pool has been properly shutdown,
 	 *         <code>false</code> otherwise.
 	 */
 	private static boolean shutdownAndAwaitTermination(ExecutorService pool) {
 		boolean hasShutdown = true;
 		pool.shutdown(); // Disable new tasks from being submitted
 		try {
 			// Wait a while for existing tasks to terminate
 			if (!pool.awaitTermination(60, TimeUnit.SECONDS)) {
 				pool.shutdownNow(); // Cancel currently executing tasks
 				// Wait a while for tasks to respond to being canceled
 				if (!pool.awaitTermination(60, TimeUnit.SECONDS))
 					hasShutdown = false;
 			}
 		} catch (InterruptedException ie) {
 			// (Re-)Cancel if current thread also interrupted
 			pool.shutdownNow();
 			// Preserve interrupt status
 			Thread.currentThread().interrupt();
 			hasShutdown = false;
 		}
 		return hasShutdown;
 	}
 
 	/**
 	 * Initialize a ProcessBuilder to run a command using the system shell.
 	 *
 	 * @param cmd
 	 *            command to execute. This string should originate from the
 	 *            end-user, and thus is platform specific.
 	 * @param args
 	 *            arguments to pass to command. These should be protected from
 	 *            shell evaluation.
 	 * @return a partially completed process builder. Caller should finish
 	 *         populating directory, environment, and then start the process.
 	 */
 	public abstract ProcessBuilder runInShell(String cmd, String[] args);
 
 	/**
 	 * Execute a command defined by a {@link java.lang.ProcessBuilder}.
 	 *
 	 * @param pb
 	 *            The command to be executed
 	 * @param in
 	 *            The standard input stream passed to the process
 	 * @return The result of the executed command
 	 * @throws java.lang.InterruptedException
 	 * @throws java.io.IOException
 	 * @since 4.2
 	 */
 	public ExecutionResult execute(ProcessBuilder pb, InputStream in)
 			throws IOException, InterruptedException {
 		try (TemporaryBuffer stdout = new TemporaryBuffer.LocalFile(null);
 				TemporaryBuffer stderr = new TemporaryBuffer.Heap(1024,
 						1024 * 1024)) {
 			int rc = runProcess(pb, stdout, stderr, in);
 			return new ExecutionResult(stdout, stderr, rc);
 		}
 	}
 
 	private static class Holder<V> {
 		final V value;
 
 		Holder(V value) {
 			this.value = value;
 		}
 	}
 
 	/**
 	 * File attributes we typically care for.
 	 *
 	 * @since 3.3
 	 */
 	public static class Attributes {
 
 		/**
 		 * @return true if this are the attributes of a directory
 		 */
 		public boolean isDirectory() {
 			return isDirectory;
 		}
 
 		/**
 		 * @return true if this are the attributes of an executable file
 		 */
 		public boolean isExecutable() {
 			return isExecutable;
 		}
 
 		/**
 		 * @return true if this are the attributes of a symbolic link
 		 */
 		public boolean isSymbolicLink() {
 			return isSymbolicLink;
 		}
 
 		/**
 		 * @return true if this are the attributes of a regular file
 		 */
 		public boolean isRegularFile() {
 			return isRegularFile;
 		}
 
 		/**
 		 * @return the time when the file was created
 		 */
 		public long getCreationTime() {
 			return creationTime;
 		}
 
 		/**
 		 * @return the time (milliseconds since 1970-01-01) when this object was
 		 *         last modified
 		 */
 		public long getLastModifiedTime() {
 			return lastModifiedTime;
 		}
 
 		private final boolean isDirectory;
 
 		private final boolean isSymbolicLink;
 
 		private final boolean isRegularFile;
 
 		private final long creationTime;
 
 		private final long lastModifiedTime;
 
 		private final boolean isExecutable;
 
 		private final File file;
 
 		private final boolean exists;
 
 		/**
 		 * file length
 		 */
 		protected long length = -1;
 
 		final FS fs;
 
 		Attributes(FS fs, File file, boolean exists, boolean isDirectory,
 				boolean isExecutable, boolean isSymbolicLink,
 				boolean isRegularFile, long creationTime,
 				long lastModifiedTime, long length) {
 			this.fs = fs;
 			this.file = file;
 			this.exists = exists;
 			this.isDirectory = isDirectory;
 			this.isExecutable = isExecutable;
 			this.isSymbolicLink = isSymbolicLink;
 			this.isRegularFile = isRegularFile;
 			this.creationTime = creationTime;
 			this.lastModifiedTime = lastModifiedTime;
 			this.length = length;
 		}
 
 		/**
 		 * Constructor when there are issues with reading. All attributes except
 		 * given will be set to the default values.
 		 *
 		 * @param fs
 		 * @param path
 		 */
 		public Attributes(File path, FS fs) {
 			this(fs, path, false, false, false, false, false, 0L, 0L, 0L);
 		}
 
 		/**
 		 * @return length of this file object
 		 */
 		public long getLength() {
 			if (length == -1)
 				return length = file.length();
 			return length;
 		}
 
 		/**
 		 * @return the filename
 		 */
 		public String getName() {
 			return file.getName();
 		}
 
 		/**
 		 * @return the file the attributes apply to
 		 */
 		public File getFile() {
 			return file;
 		}
 
 		boolean exists() {
 			return exists;
 		}
 	}
 
 	/**
 	 * Get the file attributes we care for.
 	 *
 	 * @param path
 	 *            a {@link java.io.File} object.
 	 * @return the file attributes we care for.
 	 * @since 3.3
 	 */
 	public Attributes getAttributes(File path) {
 		boolean isDirectory = isDirectory(path);
 		boolean isFile = !isDirectory && path.isFile();
 		assert path.exists() == isDirectory || isFile;
 		boolean exists = isDirectory || isFile;
 		boolean canExecute = exists && !isDirectory && canExecute(path);
 		boolean isSymlink = false;
 		long lastModified = exists ? path.lastModified() : 0L;
 		long createTime = 0L;
 		return new Attributes(this, path, exists, isDirectory, canExecute,
 				isSymlink, isFile, createTime, lastModified, -1);
 	}
 
 	/**
 	 * Normalize the unicode path to composed form.
 	 *
 	 * @param file
 	 *            a {@link java.io.File} object.
 	 * @return NFC-format File
 	 * @since 3.3
 	 */
 	public File normalize(File file) {
 		return file;
 	}
 
 	/**
 	 * Normalize the unicode path to composed form.
 	 *
 	 * @param name
 	 *            path name
 	 * @return NFC-format string
 	 * @since 3.3
 	 */
 	public String normalize(String name) {
 		return name;
 	}
 
 	/**
 	 * This runnable will consume an input stream's content into an output
 	 * stream as soon as it gets available.
 	 * <p>
 	 * Typically used to empty processes' standard output and error, preventing
 	 * them to choke.
 	 * </p>
 	 * <p>
 	 * <b>Note</b> that a {@link StreamGobbler} will never close either of its
 	 * streams.
 	 * </p>
 	 */
 	private static class StreamGobbler implements Runnable {
 		private InputStream in;
 
 		private OutputStream out;
 
 		public StreamGobbler(InputStream stream, OutputStream output) {
 			this.in = stream;
 			this.out = output;
 		}
 
 		@Override
 		public void run() {
 			try {
 				copy();
 			} catch (IOException e) {
 				// Do nothing on read failure; leave streams open.
 			}
 		}
 
 		void copy() throws IOException {
 			boolean writeFailure = false;
 			byte buffer[] = new byte[4096];
 			int readBytes;
 			while ((readBytes = in.read(buffer)) != -1) {
 				// Do not try to write again after a failure, but keep
 				// reading as long as possible to prevent the input stream
 				// from choking.
 				if (!writeFailure && out != null) {
 					try {
 						out.write(buffer, 0, readBytes);
 						out.flush();
 					} catch (IOException e) {
 						writeFailure = true;
 					}
 				}
 			}
 		}
 	}
 }