/*
 * Copyright (c) 1996, 2012, Oracle and/or its affiliates. All rights reserved.
 * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
 *
 * This code is free software; you can redistribute it and/or modify it
 * under the terms of the GNU General Public License version 2 only, as
 * published by the Free Software Foundation.  Oracle designates this
 * particular file as subject to the "Classpath" exception as provided
 * by Oracle in the LICENSE file that accompanied this code.
 *
 * This code is distributed in the hope that it will be useful, but WITHOUT
 * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
 * FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
 * version 2 for more details (a copy is included in the LICENSE file that
 * accompanied this code).
 *
 * You should have received a copy of the GNU General Public License version
 * 2 along with this work; if not, write to the Free Software Foundation,
 * Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
 *
 * Please contact Oracle, 500 Oracle Parkway, Redwood Shores, CA 94065 USA
 * or visit www.oracle.com if you need additional information or have any
 * questions.
 */

package sun.tools.jar;

import java.io.*;
import java.nio.file.Path;
import java.nio.file.Files;
import java.util.*;
import java.util.zip.*;
import java.util.jar.*;
import java.util.jar.Manifest;
import java.text.MessageFormat;
import sun.misc.JarIndex;
import static sun.misc.JarIndex.INDEX_NAME;
import static java.util.jar.JarFile.MANIFEST_NAME;
import static java.nio.file.StandardCopyOption.REPLACE_EXISTING;

This class implements a simple utility for creating files in the JAR
(Java Archive) file format. The JAR format is based on the ZIP file
format, with optional meta-information stored in a MANIFEST entry.
/**
 * This class implements a simple utility for creating files in the JAR
 * (Java Archive) file format. The JAR format is based on the ZIP file
 * format, with optional meta-information stored in a MANIFEST entry.
 */
public
class Main {
    String program;
    PrintStream out, err;
    String fname, mname, ename;
    String zname = "";
    String[] files;
    String rootjar = null;

    // An entryName(path)->File map generated during "expand", it helps to
    // decide whether or not an existing entry in a jar file needs to be
    // replaced, during the "update" operation.
    Map<String, File> entryMap = new HashMap<String, File>();

    // All files need to be added/updated.
    Set<File> entries = new LinkedHashSet<File>();

    // Directories specified by "-C" operation.
    Set<String> paths = new HashSet<String>();

    /*
     * cflag: create
     * uflag: update
     * xflag: xtract
     * tflag: table
     * vflag: verbose
     * flag0: no zip compression (store only)
     * Mflag: DO NOT generate a manifest file (just ZIP)
     * iflag: generate jar index
     * pflag: preserve/don't strip leading slash and .. component from file name
     */
    boolean cflag, uflag, xflag, tflag, vflag, flag0, Mflag, iflag, pflag;

    static final String MANIFEST_DIR = "META-INF/";
    static final String VERSION = "1.0";

    private static ResourceBundle rsrc;

    
If true, maintain compatibility with JDK releases prior to 6.0 by
timestamping extracted files with the time at which they are extracted.
Default is to use the time given in the archive.
/**
     * If true, maintain compatibility with JDK releases prior to 6.0 by
     * timestamping extracted files with the time at which they are extracted.
     * Default is to use the time given in the archive.
     */
    private static final boolean useExtractionTime =
        Boolean.getBoolean("sun.tools.jar.useExtractionTime");

    
Initialize ResourceBundle
/**
     * Initialize ResourceBundle
     */
    static {
        try {
            rsrc = ResourceBundle.getBundle("sun.tools.jar.resources.jar");
        } catch (MissingResourceException e) {
            throw new Error("Fatal: Resource for jar is missing");
        }
    }

    private String getMsg(String key) {
        try {
            return (rsrc.getString(key));
        } catch (MissingResourceException e) {
            throw new Error("Error in message file");
        }
    }

    private String formatMsg(String key, String arg) {
        String msg = getMsg(key);
        String[] args = new String[1];
        args[0] = arg;
        return MessageFormat.format(msg, (Object[]) args);
    }

    private String formatMsg2(String key, String arg, String arg1) {
        String msg = getMsg(key);
        String[] args = new String[2];
        args[0] = arg;
        args[1] = arg1;
        return MessageFormat.format(msg, (Object[]) args);
    }

    public Main(PrintStream out, PrintStream err, String program) {
        this.out = out;
        this.err = err;
        this.program = program;
    }

    
Creates a new empty temporary file in the same directory as the
specified file.  A variant of File.createTempFile.
/**
     * Creates a new empty temporary file in the same directory as the
     * specified file.  A variant of File.createTempFile.
     */
    private static File createTempFileInSameDirectoryAs(File file)
        throws IOException {
        File dir = file.getParentFile();
        if (dir == null)
            dir = new File(".");
        return File.createTempFile("jartmp", null, dir);
    }

    private boolean ok;

    
Starts main program with the specified arguments.
/**
     * Starts main program with the specified arguments.
     */
    public synchronized boolean run(String args[]) {
        ok = true;
        if (!parseArgs(args)) {
            return false;
        }
        try {
            if (cflag || uflag) {
                if (fname != null) {
                    // The name of the zip file as it would appear as its own
                    // zip file entry. We use this to make sure that we don't
                    // add the zip file to itself.
                    zname = fname.replace(File.separatorChar, '/');
                    if (zname.startsWith("./")) {
                        zname = zname.substring(2);
                    }
                }
            }
            if (cflag) {
                Manifest manifest = null;
                InputStream in = null;

                if (!Mflag) {
                    if (mname != null) {
                        in = new FileInputStream(mname);
                        manifest = new Manifest(new BufferedInputStream(in));
                    } else {
                        manifest = new Manifest();
                    }
                    addVersion(manifest);
                    addCreatedBy(manifest);
                    if (isAmbiguousMainClass(manifest)) {
                        if (in != null) {
                            in.close();
                        }
                        return false;
                    }
                    if (ename != null) {
                        addMainClass(manifest, ename);
                    }
                }
                expand(null, files, false);
                OutputStream out;
                if (fname != null) {
                    out = new FileOutputStream(fname);
                } else {
                    out = new FileOutputStream(FileDescriptor.out);
                    if (vflag) {
                        // Disable verbose output so that it does not appear
                        // on stdout along with file data
                        // error("Warning: -v option ignored");
                        vflag = false;
                    }
                }
                create(new BufferedOutputStream(out, 4096), manifest);
                if (in != null) {
                    in.close();
                }
                out.close();
            } else if (uflag) {
                File inputFile = null, tmpFile = null;
                FileInputStream in;
                FileOutputStream out;
                if (fname != null) {
                    inputFile = new File(fname);
                    tmpFile = createTempFileInSameDirectoryAs(inputFile);
                    in = new FileInputStream(inputFile);
                    out = new FileOutputStream(tmpFile);
                } else {
                    in = new FileInputStream(FileDescriptor.in);
                    out = new FileOutputStream(FileDescriptor.out);
                    vflag = false;
                }
                InputStream manifest = (!Mflag && (mname != null)) ?
                    (new FileInputStream(mname)) : null;
                expand(null, files, true);
                boolean updateOk = update(in, new BufferedOutputStream(out),
                                          manifest, null);
                if (ok) {
                    ok = updateOk;
                }
                in.close();
                out.close();
                if (manifest != null) {
                    manifest.close();
                }
                if (fname != null) {
                    // on Win32, we need this delete
                    inputFile.delete();
                    if (!tmpFile.renameTo(inputFile)) {
                        tmpFile.delete();
                        throw new IOException(getMsg("error.write.file"));
                    }
                    tmpFile.delete();
                }
            } else if (tflag) {
                replaceFSC(files);
                if (fname != null) {
                    list(fname, files);
                } else {
                    InputStream in = new FileInputStream(FileDescriptor.in);
                    try {
                        list(new BufferedInputStream(in), files);
                    } finally {
                        in.close();
                    }
                }
            } else if (xflag) {
                replaceFSC(files);
                if (fname != null && files != null) {
                    extract(fname, files);
                } else {
                    InputStream in = (fname == null)
                        ? new FileInputStream(FileDescriptor.in)
                        : new FileInputStream(fname);
                    try {
                        extract(new BufferedInputStream(in), files);
                    } finally {
                        in.close();
                    }
                }
            } else if (iflag) {
                genIndex(rootjar, files);
            }
        } catch (IOException e) {
            fatalError(e);
            ok = false;
        } catch (Error ee) {
            ee.printStackTrace();
            ok = false;
        } catch (Throwable t) {
            t.printStackTrace();
            ok = false;
        }
        out.flush();
        err.flush();
        return ok;
    }

    
Parses command line arguments.
/**
     * Parses command line arguments.
     */
    boolean parseArgs(String args[]) {
        /* Preprocess and expand @file arguments */
        try {
            args = CommandLine.parse(args);
        } catch (FileNotFoundException e) {
            fatalError(formatMsg("error.cant.open", e.getMessage()));
            return false;
        } catch (IOException e) {
            fatalError(e);
            return false;
        }
        /* parse flags */
        int count = 1;
        try {
            String flags = args[0];
            if (flags.startsWith("-")) {
                flags = flags.substring(1);
            }
            for (int i = 0; i < flags.length(); i++) {
                switch (flags.charAt(i)) {
                case 'c':
                    if (xflag || tflag || uflag || iflag) {
                        usageError();
                        return false;
                    }
                    cflag = true;
                    break;
                case 'u':
                    if (cflag || xflag || tflag || iflag) {
                        usageError();
                        return false;
                    }
                    uflag = true;
                    break;
                case 'x':
                    if (cflag || uflag || tflag || iflag) {
                        usageError();
                        return false;
                    }
                    xflag = true;
                    break;
                case 't':
                    if (cflag || uflag || xflag || iflag) {
                        usageError();
                        return false;
                    }
                    tflag = true;
                    break;
                case 'M':
                    Mflag = true;
                    break;
                case 'v':
                    vflag = true;
                    break;
                case 'f':
                    fname = args[count++];
                    break;
                case 'm':
                    mname = args[count++];
                    break;
                case '0':
                    flag0 = true;
                    break;
                case 'i':
                    if (cflag || uflag || xflag || tflag) {
                        usageError();
                        return false;
                    }
                    // do not increase the counter, files will contain rootjar
                    rootjar = args[count++];
                    iflag = true;
                    break;
                case 'e':
                     ename = args[count++];
                     break;
                case 'P':
                     pflag = true;
                     break;
                default:
                    error(formatMsg("error.illegal.option",
                                String.valueOf(flags.charAt(i))));
                    usageError();
                    return false;
                }
            }
        } catch (ArrayIndexOutOfBoundsException e) {
            usageError();
            return false;
        }
        if (!cflag && !tflag && !xflag && !uflag && !iflag) {
            error(getMsg("error.bad.option"));
            usageError();
            return false;
        }
        /* parse file arguments */
        int n = args.length - count;
        if (n > 0) {
            int k = 0;
            String[] nameBuf = new String[n];
            try {
                for (int i = count; i < args.length; i++) {
                    if (args[i].equals("-C")) {
                        /* change the directory */
                        String dir = args[++i];
                        dir = (dir.endsWith(File.separator) ?
                               dir : (dir + File.separator));
                        dir = dir.replace(File.separatorChar, '/');
                        while (dir.indexOf("//") > -1) {
                            dir = dir.replace("//", "/");
                        }
                        paths.add(dir.replace(File.separatorChar, '/'));
                        nameBuf[k++] = dir + args[++i];
                    } else {
                        nameBuf[k++] = args[i];
                    }
                }
            } catch (ArrayIndexOutOfBoundsException e) {
                usageError();
                return false;
            }
            files = new String[k];
            System.arraycopy(nameBuf, 0, files, 0, k);
        } else if (cflag && (mname == null)) {
            error(getMsg("error.bad.cflag"));
            usageError();
            return false;
        } else if (uflag) {
            if ((mname != null) || (ename != null)) {
                /* just want to update the manifest */
                return true;
            } else {
                error(getMsg("error.bad.uflag"));
                usageError();
                return false;
            }
        }
        return true;
    }

    
Expands list of files to process into full list of all files that
can be found by recursively descending directories.
/**
     * Expands list of files to process into full list of all files that
     * can be found by recursively descending directories.
     */
    void expand(File dir, String[] files, boolean isUpdate) {
        if (files == null) {
            return;
        }
        for (int i = 0; i < files.length; i++) {
            File f;
            if (dir == null) {
                f = new File(files[i]);
            } else {
                f = new File(dir, files[i]);
            }
            if (f.isFile()) {
                if (entries.add(f)) {
                    if (isUpdate)
                        entryMap.put(entryName(f.getPath()), f);
                }
            } else if (f.isDirectory()) {
                if (entries.add(f)) {
                    if (isUpdate) {
                        String dirPath = f.getPath();
                        dirPath = (dirPath.endsWith(File.separator)) ? dirPath :
                            (dirPath + File.separator);
                        entryMap.put(entryName(dirPath), f);
                    }
                    expand(f, f.list(), isUpdate);
                }
            } else {
                error(formatMsg("error.nosuch.fileordir", String.valueOf(f)));
                ok = false;
            }
        }
    }

    
Creates a new JAR file.
/**
     * Creates a new JAR file.
     */
    void create(OutputStream out, Manifest manifest)
        throws IOException
    {
        ZipOutputStream zos = new JarOutputStream(out);
        if (flag0) {
            zos.setMethod(ZipOutputStream.STORED);
        }
        if (manifest != null) {
            if (vflag) {
                output(getMsg("out.added.manifest"));
            }
            ZipEntry e = new ZipEntry(MANIFEST_DIR);
            e.setTime(System.currentTimeMillis());
            e.setSize(0);
            e.setCrc(0);
            zos.putNextEntry(e);
            e = new ZipEntry(MANIFEST_NAME);
            e.setTime(System.currentTimeMillis());
            if (flag0) {
                crc32Manifest(e, manifest);
            }
            zos.putNextEntry(e);
            manifest.write(zos);
            zos.closeEntry();
        }
        for (File file: entries) {
            addFile(zos, file);
        }
        zos.close();
    }

    private char toUpperCaseASCII(char c) {
        return (c < 'a' || c > 'z') ? c : (char) (c + 'A' - 'a');
    }

    
Compares two strings for equality, ignoring case.  The second
argument must contain only upper-case ASCII characters.
We don't want case comparison to be locale-dependent (else we
have the notorious "turkish i bug").
/**
     * Compares two strings for equality, ignoring case.  The second
     * argument must contain only upper-case ASCII characters.
     * We don't want case comparison to be locale-dependent (else we
     * have the notorious "turkish i bug").
     */
    private boolean equalsIgnoreCase(String s, String upper) {
        assert upper.toUpperCase(java.util.Locale.ENGLISH).equals(upper);
        int len;
        if ((len = s.length()) != upper.length())
            return false;
        for (int i = 0; i < len; i++) {
            char c1 = s.charAt(i);
            char c2 = upper.charAt(i);
            if (c1 != c2 && toUpperCaseASCII(c1) != c2)
                return false;
        }
        return true;
    }

    
Updates an existing jar file.
/**
     * Updates an existing jar file.
     */
    boolean update(InputStream in, OutputStream out,
                   InputStream newManifest,
                   JarIndex jarIndex) throws IOException
    {
        ZipInputStream zis = new ZipInputStream(in);
        ZipOutputStream zos = new JarOutputStream(out);
        ZipEntry e = null;
        boolean foundManifest = false;
        boolean updateOk = true;

        if (jarIndex != null) {
            addIndex(jarIndex, zos);
        }

        // put the old entries first, replace if necessary
        while ((e = zis.getNextEntry()) != null) {
            String name = e.getName();

            boolean isManifestEntry = equalsIgnoreCase(name, MANIFEST_NAME);

            if ((jarIndex != null && equalsIgnoreCase(name, INDEX_NAME))
                || (Mflag && isManifestEntry)) {
                continue;
            } else if (isManifestEntry && ((newManifest != null) ||
                        (ename != null))) {
                foundManifest = true;
                if (newManifest != null) {
                    // Don't read from the newManifest InputStream, as we
                    // might need it below, and we can't re-read the same data
                    // twice.
                    FileInputStream fis = new FileInputStream(mname);
                    boolean ambiguous = isAmbiguousMainClass(new Manifest(fis));
                    fis.close();
                    if (ambiguous) {
                        return false;
                    }
                }

                // Update the manifest.
                Manifest old = new Manifest(zis);
                if (newManifest != null) {
                    old.read(newManifest);
                }
                updateManifest(old, zos);
            } else {
                if (!entryMap.containsKey(name)) { // copy the old stuff
                    // do our own compression
                    ZipEntry e2 = new ZipEntry(name);
                    e2.setMethod(e.getMethod());
                    e2.setTime(e.getTime());
                    e2.setComment(e.getComment());
                    e2.setExtra(e.getExtra());
                    if (e.getMethod() == ZipEntry.STORED) {
                        e2.setSize(e.getSize());
                        e2.setCrc(e.getCrc());
                    }
                    zos.putNextEntry(e2);
                    copy(zis, zos);
                } else { // replace with the new files
                    File f = entryMap.get(name);
                    addFile(zos, f);
                    entryMap.remove(name);
                    entries.remove(f);
                }
            }
        }

        // add the remaining new files
        for (File f: entries) {
            addFile(zos, f);
        }
        if (!foundManifest) {
            if (newManifest != null) {
                Manifest m = new Manifest(newManifest);
                updateOk = !isAmbiguousMainClass(m);
                if (updateOk) {
                    updateManifest(m, zos);
                }
            } else if (ename != null) {
                updateManifest(new Manifest(), zos);
            }
        }
        zis.close();
        zos.close();
        return updateOk;
    }

    private void addIndex(JarIndex index, ZipOutputStream zos)
        throws IOException
    {
        ZipEntry e = new ZipEntry(INDEX_NAME);
        e.setTime(System.currentTimeMillis());
        if (flag0) {
            CRC32OutputStream os = new CRC32OutputStream();
            index.write(os);
            os.updateEntry(e);
        }
        zos.putNextEntry(e);
        index.write(zos);
        zos.closeEntry();
    }

    private void updateManifest(Manifest m, ZipOutputStream zos)
        throws IOException
    {
        addVersion(m);
        addCreatedBy(m);
        if (ename != null) {
            addMainClass(m, ename);
        }
        ZipEntry e = new ZipEntry(MANIFEST_NAME);
        e.setTime(System.currentTimeMillis());
        if (flag0) {
            crc32Manifest(e, m);
        }
        zos.putNextEntry(e);
        m.write(zos);
        if (vflag) {
            output(getMsg("out.update.manifest"));
        }
    }

    private static final boolean isWinDriveLetter(char c) {
        return ((c >= 'a') && (c <= 'z')) || ((c >= 'A') && (c <= 'Z'));
    }

    private String safeName(String name) {
        if (!pflag) {
            int len = name.length();
            int i = name.lastIndexOf("../");
            if (i == -1) {
                i = 0;
            } else {
                i += 3; // strip any dot-dot components
            }
            if (File.separatorChar == '\\') {
                // the spec requests no drive letter. skip if
                // the entry name has one.
                while (i < len) {
                    int off = i;
                    if (i + 1 < len &&
                        name.charAt(i + 1) == ':' &&
                        isWinDriveLetter(name.charAt(i))) {
                        i += 2;
                    }
                    while (i < len && name.charAt(i) == '/') {
                        i++;
                    }
                    if (i == off) {
                        break;
                    }
                }
            } else {
                while (i < len && name.charAt(i) == '/') {
                    i++;
                }
            }
            if (i != 0) {
                name = name.substring(i);
            }
        }
        return name;
    }

    private String entryName(String name) {
        name = name.replace(File.separatorChar, '/');
        String matchPath = "";
        for (String path : paths) {
            if (name.startsWith(path)
                && (path.length() > matchPath.length())) {
                matchPath = path;
            }
        }
        name = name.substring(matchPath.length());
        name = safeName(name);
        // the old implementaton doesn't remove
        // "./" if it was led by "/" (?)
        if (name.startsWith("./")) {
            name = name.substring(2);
        }
        return name;
    }

    private void addVersion(Manifest m) {
        Attributes global = m.getMainAttributes();
        if (global.getValue(Attributes.Name.MANIFEST_VERSION) == null) {
            global.put(Attributes.Name.MANIFEST_VERSION, VERSION);
        }
    }

    private void addCreatedBy(Manifest m) {
        Attributes global = m.getMainAttributes();
        if (global.getValue(new Attributes.Name("Created-By")) == null) {
            String javaVendor = System.getProperty("java.vendor");
            String jdkVersion = System.getProperty("java.version");
            global.put(new Attributes.Name("Created-By"), jdkVersion + " (" +
                        javaVendor + ")");
        }
    }

    private void addMainClass(Manifest m, String mainApp) {
        Attributes global = m.getMainAttributes();

        // overrides any existing Main-Class attribute
        global.put(Attributes.Name.MAIN_CLASS, mainApp);
    }

    private boolean isAmbiguousMainClass(Manifest m) {
        if (ename != null) {
            Attributes global = m.getMainAttributes();
            if ((global.get(Attributes.Name.MAIN_CLASS) != null)) {
                error(getMsg("error.bad.eflag"));
                usageError();
                return true;
            }
        }
        return false;
    }

    
Adds a new file entry to the ZIP output stream.
/**
     * Adds a new file entry to the ZIP output stream.
     */
    void addFile(ZipOutputStream zos, File file) throws IOException {
        String name = file.getPath();
        boolean isDir = file.isDirectory();
        if (isDir) {
            name = name.endsWith(File.separator) ? name :
                (name + File.separator);
        }
        name = entryName(name);

        if (name.equals("") || name.equals(".") || name.equals(zname)) {
            return;
        } else if ((name.equals(MANIFEST_DIR) || name.equals(MANIFEST_NAME))
                   && !Mflag) {
            if (vflag) {
                output(formatMsg("out.ignore.entry", name));
            }
            return;
        }

        long size = isDir ? 0 : file.length();

        if (vflag) {
            out.print(formatMsg("out.adding", name));
        }
        ZipEntry e = new ZipEntry(name);
        e.setTime(file.lastModified());
        if (size == 0) {
            e.setMethod(ZipEntry.STORED);
            e.setSize(0);
            e.setCrc(0);
        } else if (flag0) {
            crc32File(e, file);
        }
        zos.putNextEntry(e);
        if (!isDir) {
            copy(file, zos);
        }
        zos.closeEntry();
        /* report how much compression occurred. */
        if (vflag) {
            size = e.getSize();
            long csize = e.getCompressedSize();
            out.print(formatMsg2("out.size", String.valueOf(size),
                        String.valueOf(csize)));
            if (e.getMethod() == ZipEntry.DEFLATED) {
                long ratio = 0;
                if (size != 0) {
                    ratio = ((size - csize) * 100) / size;
                }
                output(formatMsg("out.deflated", String.valueOf(ratio)));
            } else {
                output(getMsg("out.stored"));
            }
        }
    }

    
A buffer for use only by copy(InputStream, OutputStream).
Not as clean as allocating a new buffer as needed by copy,
but significantly more efficient.
/**
     * A buffer for use only by copy(InputStream, OutputStream).
     * Not as clean as allocating a new buffer as needed by copy,
     * but significantly more efficient.
     */
    private byte[] copyBuf = new byte[8192];

    
Copies all bytes from the input stream to the output stream.
Does not close or flush either stream.
Params:
from – the input stream to read from
to – the output stream to write to
Throws:
IOException – if an I/O error occurs/**
     * Copies all bytes from the input stream to the output stream.
     * Does not close or flush either stream.
     *
     * @param from the input stream to read from
     * @param to the output stream to write to
     * @throws IOException if an I/O error occurs
     */
    private void copy(InputStream from, OutputStream to) throws IOException {
        int n;
        while ((n = from.read(copyBuf)) != -1)
            to.write(copyBuf, 0, n);
    }

    
Copies all bytes from the input file to the output stream.
Does not close or flush the output stream.
Params:
from – the input file to read from
to – the output stream to write to
Throws:
IOException – if an I/O error occurs/**
     * Copies all bytes from the input file to the output stream.
     * Does not close or flush the output stream.
     *
     * @param from the input file to read from
     * @param to the output stream to write to
     * @throws IOException if an I/O error occurs
     */
    private void copy(File from, OutputStream to) throws IOException {
        InputStream in = new FileInputStream(from);
        try {
            copy(in, to);
        } finally {
            in.close();
        }
    }

    
Copies all bytes from the input stream to the output file.
Does not close the input stream.
Params:
from – the input stream to read from
to – the output file to write to
Throws:
IOException – if an I/O error occurs/**
     * Copies all bytes from the input stream to the output file.
     * Does not close the input stream.
     *
     * @param from the input stream to read from
     * @param to the output file to write to
     * @throws IOException if an I/O error occurs
     */
    private void copy(InputStream from, File to) throws IOException {
        OutputStream out = new FileOutputStream(to);
        try {
            copy(from, out);
        } finally {
            out.close();
        }
    }

    
Computes the crc32 of a Manifest.  This is necessary when the
ZipOutputStream is in STORED mode.
/**
     * Computes the crc32 of a Manifest.  This is necessary when the
     * ZipOutputStream is in STORED mode.
     */
    private void crc32Manifest(ZipEntry e, Manifest m) throws IOException {
        CRC32OutputStream os = new CRC32OutputStream();
        m.write(os);
        os.updateEntry(e);
    }

    
Computes the crc32 of a File.  This is necessary when the
ZipOutputStream is in STORED mode.
/**
     * Computes the crc32 of a File.  This is necessary when the
     * ZipOutputStream is in STORED mode.
     */
    private void crc32File(ZipEntry e, File f) throws IOException {
        CRC32OutputStream os = new CRC32OutputStream();
        copy(f, os);
        if (os.n != f.length()) {
            throw new JarException(formatMsg(
                        "error.incorrect.length", f.getPath()));
        }
        os.updateEntry(e);
    }

    void replaceFSC(String files[]) {
        if (files != null) {
            for (int i = 0; i < files.length; i++) {
                files[i] = files[i].replace(File.separatorChar, '/');
            }
        }
    }

    @SuppressWarnings("serial")
    Set<ZipEntry> newDirSet() {
        return new HashSet<ZipEntry>() {
            public boolean add(ZipEntry e) {
                return ((e == null || useExtractionTime) ? false : super.add(e));
            }};
    }

    void updateLastModifiedTime(Set<ZipEntry> zes) throws IOException {
        for (ZipEntry ze : zes) {
            long lastModified = ze.getTime();
            if (lastModified != -1) {
                String name = safeName(ze.getName().replace(File.separatorChar, '/'));
                if (name.length() != 0) {
                    File f = new File(name.replace('/', File.separatorChar));
                    f.setLastModified(lastModified);
                }
            }
        }
    }

    
Extracts specified entries from JAR file.
/**
     * Extracts specified entries from JAR file.
     */
    void extract(InputStream in, String files[]) throws IOException {
        ZipInputStream zis = new ZipInputStream(in);
        ZipEntry e;
        // Set of all directory entries specified in archive.  Disallows
        // null entries.  Disallows all entries if using pre-6.0 behavior.
        Set<ZipEntry> dirs = newDirSet();
        while ((e = zis.getNextEntry()) != null) {
            if (files == null) {
                dirs.add(extractFile(zis, e));
            } else {
                String name = e.getName();
                for (String file : files) {
                    if (name.startsWith(file)) {
                        dirs.add(extractFile(zis, e));
                        break;
                    }
                }
            }
        }

        // Update timestamps of directories specified in archive with their
        // timestamps as given in the archive.  We do this after extraction,
        // instead of during, because creating a file in a directory changes
        // that directory's timestamp.
        updateLastModifiedTime(dirs);
    }

    
Extracts specified entries from JAR file, via ZipFile.
/**
     * Extracts specified entries from JAR file, via ZipFile.
     */
    void extract(String fname, String files[]) throws IOException {
        ZipFile zf = new ZipFile(fname);
        Set<ZipEntry> dirs = newDirSet();
        Enumeration<? extends ZipEntry> zes = zf.entries();
        while (zes.hasMoreElements()) {
            ZipEntry e = zes.nextElement();
            if (files == null) {
                dirs.add(extractFile(zf.getInputStream(e), e));
            } else {
                String name = e.getName();
                for (String file : files) {
                    if (name.startsWith(file)) {
                        dirs.add(extractFile(zf.getInputStream(e), e));
                        break;
                    }
                }
            }
        }
        zf.close();
        updateLastModifiedTime(dirs);
    }

    
Extracts next entry from JAR file, creating directories as needed.  If
the entry is for a directory which doesn't exist prior to this
invocation, returns that entry, otherwise returns null.
/**
     * Extracts next entry from JAR file, creating directories as needed.  If
     * the entry is for a directory which doesn't exist prior to this
     * invocation, returns that entry, otherwise returns null.
     */
    ZipEntry extractFile(InputStream is, ZipEntry e) throws IOException {
        ZipEntry rc = null;
        // The spec requres all slashes MUST be forward '/', it is possible
        // an offending zip/jar entry may uses the backwards slash in its
        // name. It might cause problem on Windows platform as it skips
        // our "safe" check for leading slahs and dot-dot. So replace them
        // with '/'.
        String name = safeName(e.getName().replace(File.separatorChar, '/'));
        if (name.length() == 0) {
            return rc;    // leading '/' or 'dot-dot' only path
        }
        File f = new File(name.replace('/', File.separatorChar));
        if (e.isDirectory()) {
            if (f.exists()) {
                if (!f.isDirectory()) {
                    throw new IOException(formatMsg("error.create.dir",
                        f.getPath()));
                }
            } else {
                if (!f.mkdirs()) {
                    throw new IOException(formatMsg("error.create.dir",
                        f.getPath()));
                } else {
                    rc = e;
                }
            }

            if (vflag) {
                output(formatMsg("out.create", name));
            }
        } else {
            if (f.getParent() != null) {
                File d = new File(f.getParent());
                if (!d.exists() && !d.mkdirs() || !d.isDirectory()) {
                    throw new IOException(formatMsg(
                        "error.create.dir", d.getPath()));
                }
            }
            try {
                copy(is, f);
            } finally {
                if (is instanceof ZipInputStream)
                    ((ZipInputStream)is).closeEntry();
                else
                    is.close();
            }
            if (vflag) {
                if (e.getMethod() == ZipEntry.DEFLATED) {
                    output(formatMsg("out.inflated", name));
                } else {
                    output(formatMsg("out.extracted", name));
                }
            }
        }
        if (!useExtractionTime) {
            long lastModified = e.getTime();
            if (lastModified != -1) {
                f.setLastModified(lastModified);
            }
        }
        return rc;
    }

    
Lists contents of JAR file.
/**
     * Lists contents of JAR file.
     */
    void list(InputStream in, String files[]) throws IOException {
        ZipInputStream zis = new ZipInputStream(in);
        ZipEntry e;
        while ((e = zis.getNextEntry()) != null) {
            /*
             * In the case of a compressed (deflated) entry, the entry size
             * is stored immediately following the entry data and cannot be
             * determined until the entry is fully read. Therefore, we close
             * the entry first before printing out its attributes.
             */
            zis.closeEntry();
            printEntry(e, files);
        }
    }

    
Lists contents of JAR file, via ZipFile.
/**
     * Lists contents of JAR file, via ZipFile.
     */
    void list(String fname, String files[]) throws IOException {
        ZipFile zf = new ZipFile(fname);
        Enumeration<? extends ZipEntry> zes = zf.entries();
        while (zes.hasMoreElements()) {
            printEntry(zes.nextElement(), files);
        }
        zf.close();
    }

    
Outputs the class index table to the INDEX.LIST file of the
root jar file.
/**
     * Outputs the class index table to the INDEX.LIST file of the
     * root jar file.
     */
    void dumpIndex(String rootjar, JarIndex index) throws IOException {
        File jarFile = new File(rootjar);
        Path jarPath = jarFile.toPath();
        Path tmpPath = createTempFileInSameDirectoryAs(jarFile).toPath();
        try {
            if (update(Files.newInputStream(jarPath),
                       Files.newOutputStream(tmpPath),
                       null, index)) {
                try {
                    Files.move(tmpPath, jarPath, REPLACE_EXISTING);
                } catch (IOException e) {
                    throw new IOException(getMsg("error.write.file"), e);
                }
            }
        } finally {
            Files.deleteIfExists(tmpPath);
        }
    }

    private HashSet<String> jarPaths = new HashSet<String>();

    
Generates the transitive closure of the Class-Path attribute for
the specified jar file.
/**
     * Generates the transitive closure of the Class-Path attribute for
     * the specified jar file.
     */
    List<String> getJarPath(String jar) throws IOException {
        List<String> files = new ArrayList<String>();
        files.add(jar);
        jarPaths.add(jar);

        // take out the current path
        String path = jar.substring(0, Math.max(0, jar.lastIndexOf('/') + 1));

        // class path attribute will give us jar file name with
        // '/' as separators, so we need to change them to the
        // appropriate one before we open the jar file.
        JarFile rf = new JarFile(jar.replace('/', File.separatorChar));

        if (rf != null) {
            Manifest man = rf.getManifest();
            if (man != null) {
                Attributes attr = man.getMainAttributes();
                if (attr != null) {
                    String value = attr.getValue(Attributes.Name.CLASS_PATH);
                    if (value != null) {
                        StringTokenizer st = new StringTokenizer(value);
                        while (st.hasMoreTokens()) {
                            String ajar = st.nextToken();
                            if (!ajar.endsWith("/")) {  // it is a jar file
                                ajar = path.concat(ajar);
                                /* check on cyclic dependency */
                                if (! jarPaths.contains(ajar)) {
                                    files.addAll(getJarPath(ajar));
                                }
                            }
                        }
                    }
                }
            }
        }
        rf.close();
        return files;
    }

    
Generates class index file for the specified root jar file.
/**
     * Generates class index file for the specified root jar file.
     */
    void genIndex(String rootjar, String[] files) throws IOException {
        List<String> jars = getJarPath(rootjar);
        int njars = jars.size();
        String[] jarfiles;

        if (njars == 1 && files != null) {
            // no class-path attribute defined in rootjar, will
            // use command line specified list of jars
            for (int i = 0; i < files.length; i++) {
                jars.addAll(getJarPath(files[i]));
            }
            njars = jars.size();
        }
        jarfiles = jars.toArray(new String[njars]);
        JarIndex index = new JarIndex(jarfiles);
        dumpIndex(rootjar, index);
    }

    
Prints entry information, if requested.
/**
     * Prints entry information, if requested.
     */
    void printEntry(ZipEntry e, String[] files) throws IOException {
        if (files == null) {
            printEntry(e);
        } else {
            String name = e.getName();
            for (String file : files) {
                if (name.startsWith(file)) {
                    printEntry(e);
                    return;
                }
            }
        }
    }

    
Prints entry information.
/**
     * Prints entry information.
     */
    void printEntry(ZipEntry e) throws IOException {
        if (vflag) {
            StringBuilder sb = new StringBuilder();
            String s = Long.toString(e.getSize());
            for (int i = 6 - s.length(); i > 0; --i) {
                sb.append(' ');
            }
            sb.append(s).append(' ').append(new Date(e.getTime()).toString());
            sb.append(' ').append(e.getName());
            output(sb.toString());
        } else {
            output(e.getName());
        }
    }

    
Prints usage message.
/**
     * Prints usage message.
     */
    void usageError() {
        error(getMsg("usage"));
    }

    
A fatal exception has been caught.  No recovery possible
/**
     * A fatal exception has been caught.  No recovery possible
     */
    void fatalError(Exception e) {
        e.printStackTrace();
    }

    
A fatal condition has been detected; message is "s".
No recovery possible
/**
     * A fatal condition has been detected; message is "s".
     * No recovery possible
     */
    void fatalError(String s) {
        error(program + ": " + s);
    }

    
Print an output message; like verbose output and the like
/**
     * Print an output message; like verbose output and the like
     */
    protected void output(String s) {
        out.println(s);
    }

    
Print an error message; like something is broken
/**
     * Print an error message; like something is broken
     */
    protected void error(String s) {
        err.println(s);
    }

    
Main routine to start program.
/**
     * Main routine to start program.
     */
    public static void main(String args[]) {
        Main jartool = new Main(System.out, System.err, "jar");
        System.exit(jartool.run(args) ? 0 : 1);
    }

    
An OutputStream that doesn't send its output anywhere, (but could).
It's here to find the CRC32 of an input file, necessary for STORED
mode in ZIP.
/**
     * An OutputStream that doesn't send its output anywhere, (but could).
     * It's here to find the CRC32 of an input file, necessary for STORED
     * mode in ZIP.
     */
    private static class CRC32OutputStream extends java.io.OutputStream {
        final CRC32 crc = new CRC32();
        long n = 0;

        CRC32OutputStream() {}

        public void write(int r) throws IOException {
            crc.update(r);
            n++;
        }

        public void write(byte[] b, int off, int len) throws IOException {
            crc.update(b, off, len);
            n += len;
        }

        
Updates a ZipEntry which describes the data read by this
output stream, in STORED mode.
/**
         * Updates a ZipEntry which describes the data read by this
         * output stream, in STORED mode.
         */
        public void updateEntry(ZipEntry e) {
            e.setMethod(ZipEntry.STORED);
            e.setSize(n);
            e.setCrc(crc.getValue());
        }
    }
}