/*
 * Copyright (c) 1996, 2018, 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.lang.module.Configuration;
import java.lang.module.FindException;
import java.lang.module.InvalidModuleDescriptorException;
import java.lang.module.ModuleDescriptor;
import java.lang.module.ModuleDescriptor.Exports;
import java.lang.module.ModuleDescriptor.Opens;
import java.lang.module.ModuleDescriptor.Provides;
import java.lang.module.ModuleDescriptor.Version;
import java.lang.module.ModuleFinder;
import java.lang.module.ModuleReader;
import java.lang.module.ModuleReference;
import java.lang.module.ResolvedModule;
import java.net.URI;
import java.nio.ByteBuffer;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.nio.file.StandardCopyOption;
import java.text.MessageFormat;
import java.util.*;
import java.util.function.Consumer;
import java.util.jar.Attributes;
import java.util.jar.JarFile;
import java.util.jar.JarOutputStream;
import java.util.jar.Manifest;
import java.util.regex.Pattern;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import java.util.zip.CRC32;
import java.util.zip.ZipEntry;
import java.util.zip.ZipFile;
import java.util.zip.ZipInputStream;
import java.util.zip.ZipOutputStream;
import jdk.internal.module.Checks;
import jdk.internal.module.ModuleHashes;
import jdk.internal.module.ModuleHashesBuilder;
import jdk.internal.module.ModuleInfo;
import jdk.internal.module.ModuleInfoExtender;
import jdk.internal.module.ModuleResolution;
import jdk.internal.module.ModuleTarget;
import jdk.internal.util.jar.JarIndex;

import static java.nio.file.StandardCopyOption.REPLACE_EXISTING;
import static java.util.jar.JarFile.MANIFEST_NAME;
import static java.util.stream.Collectors.joining;
import static jdk.internal.util.jar.JarIndex.INDEX_NAME;

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;
    PrintWriter out, err;
    String fname, mname, ename;
    String zname = "";
    String rootjar = null;

    private static final int BASE_VERSION = 0;

    private static class Entry {
        final String name;
        final File file;
        final boolean isDir;

        Entry(File file, String name, boolean isDir) {
            this.file = file;
            this.isDir = isDir;
            this.name = name;
        }

        @Override
        public boolean equals(Object o) {
            if (this == o) return true;
            if (!(o instanceof Entry)) return false;
            return this.file.equals(((Entry)o).file);
        }

        @Override
        public int hashCode() {
            return file.hashCode();
        }
    }

    // An entryName(path)->Entry 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, Entry> entryMap = new HashMap<>();

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

    // module-info.class entries need to be added/updated.
    Map<String,byte[]> moduleInfos = new HashMap<>();

    // A paths Set for each version, where each Set contains directories
    // specified by the "-C" operation.
    Map<Integer,Set<String>> pathsMap = new HashMap<>();

    // There's also a files array per version
    Map<Integer,String[]> filesMap = new HashMap<>();

    // Do we think this is a multi-release jar?  Set to true
    // if --release option found followed by at least file
    boolean isMultiRelease;

    // The last parsed --release value, if any. Used in conjunction with
    // "-d,--describe-module" to select the operative module descriptor.
    int releaseValue = -1;

    /*
     * 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
     * nflag: Perform jar normalization at the end
     * pflag: preserve/don't strip leading slash and .. component from file name
     * dflag: print module descriptor
     */
    boolean cflag, uflag, xflag, tflag, vflag, flag0, Mflag, iflag, pflag, dflag;

    boolean suppressDeprecateMsg = false;

    /* To support additional GNU Style informational options */
    Consumer<PrintWriter> info;

    /* Modular jar related options */
    Version moduleVersion;
    Pattern modulesToHash;
    ModuleResolution moduleResolution = ModuleResolution.empty();
    ModuleFinder moduleFinder = ModuleFinder.of();

    static final String MODULE_INFO = "module-info.class";
    static final String MANIFEST_DIR = "META-INF/";
    static final String VERSIONS_DIR = MANIFEST_DIR + "versions/";
    static final String VERSION = "1.0";
    static final int VERSIONS_DIR_LENGTH = VERSIONS_DIR.length();
    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");
        }
    }

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

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

    static 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 = new PrintWriter(out, true);
        this.err = new PrintWriter(err, true);
        this.program = program;
    }

    public Main(PrintWriter out, PrintWriter 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.
     */
    @SuppressWarnings({"removal"})
    public synchronized boolean run(String args[]) {
        ok = true;
        if (!parseArgs(args)) {
            return false;
        }
        File tmpFile = null;
        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;
                if (!Mflag) {
                    if (mname != null) {
                        try (InputStream in = new FileInputStream(mname)) {
                            manifest = new Manifest(new BufferedInputStream(in));
                        }
                    } else {
                        manifest = new Manifest();
                    }
                    addVersion(manifest);
                    addCreatedBy(manifest);
                    if (isAmbiguousMainClass(manifest)) {
                        return false;
                    }
                    if (ename != null) {
                        addMainClass(manifest, ename);
                    }
                    if (isMultiRelease) {
                        addMultiRelease(manifest);
                    }
                }
                expand();
                if (!moduleInfos.isEmpty()) {
                    // All actual file entries (excl manifest and module-info.class)
                    Set<String> jentries = new HashSet<>();
                    // all packages if it's a class or resource
                    Set<String> packages = new HashSet<>();
                    entries.stream()
                           .filter(e -> !e.isDir)
                           .forEach( e -> {
                               addPackageIfNamed(packages, e.name);
                               jentries.add(e.name);
                    });
                    addExtendedModuleAttributes(moduleInfos, packages);

                    // Basic consistency checks for modular jars.
                    if (!checkModuleInfo(moduleInfos.get(MODULE_INFO), jentries))
                        return false;

                } else if (moduleVersion != null || modulesToHash != null) {
                    error(getMsg("error.module.options.without.info"));
                    return false;
                }
                if (vflag && fname == null) {
                    // Disable verbose output so that it does not appear
                    // on stdout along with file data
                    // error("Warning: -v option ignored");
                    vflag = false;
                }
                final String tmpbase = (fname == null)
                        ? "tmpjar"
                        : fname.substring(fname.indexOf(File.separatorChar) + 1);

                tmpFile = createTemporaryFile(tmpbase, ".jar");
                try (OutputStream out = new FileOutputStream(tmpFile)) {
                    create(new BufferedOutputStream(out, 4096), manifest);
                }
                validateAndClose(tmpFile);
            } else if (uflag) {
                File inputFile = null;
                if (fname != null) {
                    inputFile = new File(fname);
                    tmpFile = createTempFileInSameDirectoryAs(inputFile);
                } else {
                    vflag = false;
                    tmpFile = createTemporaryFile("tmpjar", ".jar");
                }
                expand();
                try (FileInputStream in = (fname != null) ? new FileInputStream(inputFile)
                        : new FileInputStream(FileDescriptor.in);
                     FileOutputStream out = new FileOutputStream(tmpFile);
                     InputStream manifest = (!Mflag && (mname != null)) ?
                            (new FileInputStream(mname)) : null;
                ) {
                    boolean updateOk = update(in, new BufferedOutputStream(out),
                        manifest, moduleInfos, null);
                    if (ok) {
                        ok = updateOk;
                    }
                }
                validateAndClose(tmpFile);
            } else if (tflag) {
                replaceFSC(filesMap);
                // For the "list table contents" action, access using the
                // ZipFile class is always most efficient since only a
                // "one-finger" scan through the central directory is required.
                String[] files = filesMapToFiles(filesMap);
                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(filesMap);
                // For the extract action, when extracting all the entries,
                // access using the ZipInputStream class is most efficient,
                // since only a single sequential scan through the zip file is
                // required.  When using the ZipFile class, a "two-finger" scan
                // is required, but this is likely to be more efficient when a
                // partial extract is requested.  In case the zip file has
                // "leading garbage", we fall back from the ZipInputStream
                // implementation to the ZipFile implementation, since only the
                // latter can handle it.

                String[] files = filesMapToFiles(filesMap);
                if (fname != null && files != null) {
                    extract(fname, files);
                } else {
                    InputStream in = (fname == null)
                        ? new FileInputStream(FileDescriptor.in)
                        : new FileInputStream(fname);
                    try {
                        if (!extract(new BufferedInputStream(in), files) && fname != null) {
                            extract(fname, files);
                        }
                    } finally {
                        in.close();
                    }
                }
            } else if (iflag) {
                String[] files = filesMap.get(BASE_VERSION);  // base entries only, can be null
                genIndex(rootjar, files);
            } else if (dflag) {
                boolean found;
                if (fname != null) {
                    try (ZipFile zf = new ZipFile(fname)) {
                        found = describeModule(zf);
                    }
                } else {
                    try (FileInputStream fin = new FileInputStream(FileDescriptor.in)) {
                        found = describeModuleFromStream(fin);
                    }
                }
                if (!found)
                    error(getMsg("error.module.descriptor.not.found"));
            }
        } catch (IOException e) {
            fatalError(e);
            ok = false;
        } catch (Error ee) {
            ee.printStackTrace();
            ok = false;
        } catch (Throwable t) {
            t.printStackTrace();
            ok = false;
        } finally {
            if (tmpFile != null && tmpFile.exists())
                tmpFile.delete();
        }
        out.flush();
        err.flush();
        return ok;
    }

    private void validateAndClose(File tmpfile) throws IOException {
        if (ok && isMultiRelease) {
            try (ZipFile zf = new ZipFile(tmpfile)) {
                ok = Validator.validate(this, zf);
                if (!ok) {
                    error(formatMsg("error.validator.jarfile.invalid", fname));
                }
            } catch (IOException e) {
                error(formatMsg2("error.validator.jarfile.exception", fname, e.getMessage()));
            }
        }
        Path path = tmpfile.toPath();
        try {
            if (ok) {
                if (fname != null) {
                    Files.move(path, Paths.get(fname), StandardCopyOption.REPLACE_EXISTING);
                } else {
                    Files.copy(path, new FileOutputStream(FileDescriptor.out));
                }
            }
        } finally {
            Files.deleteIfExists(path);
        }
    }

    private String[] filesMapToFiles(Map<Integer,String[]> filesMap) {
        if (filesMap.isEmpty()) return null;
        return filesMap.entrySet()
                .stream()
                .flatMap(this::filesToEntryNames)
                .toArray(String[]::new);
    }

    Stream<String> filesToEntryNames(Map.Entry<Integer,String[]> fileEntries) {
        int version = fileEntries.getKey();
        Set<String> cpaths = pathsMap.get(version);
        return Stream.of(fileEntries.getValue())
            .map(f -> toVersionedName(toEntryName(f, cpaths, false), version));
    }

    
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];

            // Note: flags.length == 2 can be treated as the short version of
            // the GNU option since the there cannot be any other options,
            // excluding -C, as per the old way.
            if (flags.startsWith("--") ||
                (flags.startsWith("-") && flags.length() == 2)) {
                try {
                    count = GNUStyleOptions.parseOptions(this, args);
                } catch (GNUStyleOptions.BadArgs x) {
                    if (info == null) {
                        if (x.showUsage) {
                            usageError(x.getMessage());
                        } else {
                            error(x.getMessage());
                        }
                        return false;
                    }
                }
                if (info != null) {
                    info.accept(out);
                    return true;
                }
            } else {
                // Legacy/compatibility options
                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(getMsg("error.multiple.main.operations"));
                                return false;
                            }
                            cflag = true;
                            break;
                        case 'u':
                            if (cflag || xflag || tflag || iflag) {
                                usageError(getMsg("error.multiple.main.operations"));
                                return false;
                            }
                            uflag = true;
                            break;
                        case 'x':
                            if (cflag || uflag || tflag || iflag) {
                                usageError(getMsg("error.multiple.main.operations"));
                                return false;
                            }
                            xflag = true;
                            break;
                        case 't':
                            if (cflag || uflag || xflag || iflag) {
                                usageError(getMsg("error.multiple.main.operations"));
                                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(getMsg("error.multiple.main.operations"));
                                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:
                            usageError(formatMsg("error.illegal.option",
                                       String.valueOf(flags.charAt(i))));
                            return false;
                    }
                }
            }
        } catch (ArrayIndexOutOfBoundsException e) {
            usageError(getMsg("main.usage.summary"));
            return false;
        }
        if (!cflag && !tflag && !xflag && !uflag && !iflag && !dflag) {
            usageError(getMsg("error.bad.option"));
            return false;
        }

        /* parse file arguments */
        int n = args.length - count;
        if (n > 0) {
            int version = BASE_VERSION;
            int k = 0;
            String[] nameBuf = new String[n];
            pathsMap.put(version, new HashSet<>());
            try {
                for (int i = count; i < args.length; i++) {
                    if (args[i].equals("-C")) {
                        if (dflag) {
                            // "--describe-module/-d" does not require file argument(s),
                            // but does accept --release
                            usageError(getMsg("error.bad.dflag"));
                            return false;
                        }
                        /* change the directory */
                        String dir = args[++i];
                        dir = (dir.endsWith(File.separator) ?
                               dir : (dir + File.separator));
                        dir = dir.replace(File.separatorChar, '/');

                        boolean hasUNC = (File.separatorChar == '\\'&&  dir.startsWith("//"));
                        while (dir.indexOf("//") > -1) {
                            dir = dir.replace("//", "/");
                        }
                        if (hasUNC) { // Restore Windows UNC path.
                            dir = "/" + dir;
                        }
                        pathsMap.get(version).add(dir);
                        nameBuf[k++] = dir + args[++i];
                    } else if (args[i].startsWith("--release")) {
                        int v = BASE_VERSION;
                        try {
                            v = Integer.valueOf(args[++i]);
                        } catch (NumberFormatException x) {
                            error(formatMsg("error.release.value.notnumber", args[i]));
                            // this will fall into the next error, thus returning false
                        }
                        if (v < 9) {
                            usageError(formatMsg("error.release.value.toosmall", String.valueOf(v)));
                            return false;
                        }
                        // associate the files, if any, with the previous version number
                        if (k > 0) {
                            String[] files = new String[k];
                            System.arraycopy(nameBuf, 0, files, 0, k);
                            filesMap.put(version, files);
                            isMultiRelease = version > BASE_VERSION;
                        }
                        // reset the counters and start with the new version number
                        k = 0;
                        nameBuf = new String[n];
                        version = v;
                        releaseValue = version;
                        pathsMap.put(version, new HashSet<>());
                    } else {
                        if (dflag) {
                            // "--describe-module/-d" does not require file argument(s),
                            // but does accept --release
                            usageError(getMsg("error.bad.dflag"));
                            return false;
                        }
                        nameBuf[k++] = args[i];
                    }
                }
            } catch (ArrayIndexOutOfBoundsException e) {
                usageError(getMsg("error.bad.file.arg"));
                return false;
            }
            // associate remaining files, if any, with a version
            if (k > 0) {
                String[] files = new String[k];
                System.arraycopy(nameBuf, 0, files, 0, k);
                filesMap.put(version, files);
                isMultiRelease = version > BASE_VERSION;
            }
        } else if (cflag && (mname == null)) {
            usageError(getMsg("error.bad.cflag"));
            return false;
        } else if (uflag) {
            if ((mname != null) || (ename != null) || moduleVersion != null) {
                /* just want to update the manifest */
                return true;
            } else {
                usageError(getMsg("error.bad.uflag"));
                return false;
            }
        }
        return true;
    }

    /*
     * Add the package of the given resource name if it's a .class
     * or a resource in a named package.
     */
    void addPackageIfNamed(Set<String> packages, String name) {
        if (name.startsWith(VERSIONS_DIR)) {
            // trim the version dir prefix
            int i0 = VERSIONS_DIR_LENGTH;
            int i = name.indexOf('/', i0);
            if (i <= 0) {
                warn(formatMsg("warn.release.unexpected.versioned.entry", name));
                return;
            }
            while (i0 < i) {
                char c = name.charAt(i0);
                if (c < '0' || c > '9') {
                    warn(formatMsg("warn.release.unexpected.versioned.entry", name));
                    return;
                }
                i0++;
            }
            name = name.substring(i + 1, name.length());
        }
        String pn = toPackageName(name);
        // add if this is a class or resource in a package
        if (Checks.isPackageName(pn)) {
            packages.add(pn);
        }
    }

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

    private static String toVersionedName(String name, int version) {
        return version > BASE_VERSION
                ? VERSIONS_DIR + version + "/" + name : name;
    }

    private static String toPackageName(String path) {
        int index = path.lastIndexOf('/');
        if (index != -1) {
            return path.substring(0, index).replace('/', '.');
        } else {
            return "";
        }
    }

    private void expand() throws IOException {
        for (int version : filesMap.keySet()) {
            String[] files = filesMap.get(version);
            expand(null, files, pathsMap.get(version), version);
        }
    }

    
Expands list of files to process into full list of all files that
can be found by recursively descending directories.
Params:
dir –    parent directory
files –  list of files to expand
cpaths – set of directories specified by -C option for the files
Throws:
IOException – if an I/O error occurs/**
     * Expands list of files to process into full list of all files that
     * can be found by recursively descending directories.
     *
     * @param dir    parent directory
     * @param files  list of files to expand
     * @param cpaths set of directories specified by -C option for the files
     * @throws IOException if an I/O error occurs
     */
    private void expand(File dir, String[] files, Set<String> cpaths, int version)
        throws IOException
    {
        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]);

            boolean isDir = f.isDirectory();
            String name = toEntryName(f.getPath(), cpaths, isDir);

            if (version != BASE_VERSION) {
                if (name.startsWith(VERSIONS_DIR)) {
                    // the entry starts with VERSIONS_DIR and version != BASE_VERSION,
                    // which means the "[dirs|files]" in --release v [dirs|files]
                    // includes VERSIONS_DIR-ed entries --> warning and skip (?)
                    error(formatMsg2("error.release.unexpected.versioned.entry",
                                     name, String.valueOf(version)));
                    ok = false;
                    return;
                }
                name = toVersionedName(name, version);
            }

            if (f.isFile()) {
                Entry e = new Entry(f, name, false);
                if (isModuleInfoEntry(name)) {
                    moduleInfos.putIfAbsent(name, Files.readAllBytes(f.toPath()));
                    if (uflag)
                        entryMap.put(name, e);
                } else if (entries.add(e)) {
                    if (uflag)
                        entryMap.put(name, e);
                }
            } else if (isDir) {
                Entry e = new Entry(f, name, true);
                if (entries.add(e)) {
                    // utilize entryMap for the duplicate dir check even in
                    // case of cflag == true.
                    // dir name confilict/duplicate could happen with -C option.
                    // just remove the last "e" from the "entries" (zos will fail
                    // with "duplicated" entries), but continue expanding the
                    // sub tree
                    if (entryMap.containsKey(name)) {
                        entries.remove(e);
                    } else {
                        entryMap.put(name, e);
                    }
                    expand(f, f.list(), cpaths, version);
                }
            } 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
    {
        try (ZipOutputStream zos = new JarOutputStream(out)) {
            if (flag0) {
                zos.setMethod(ZipOutputStream.STORED);
            }
            // TODO: check module-info attributes against manifest ??
            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();
            }
            updateModuleInfo(moduleInfos, zos);
            for (Entry entry : entries) {
                addFile(zos, entry);
            }
        }
    }

    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,
                   Map<String,byte[]> moduleInfos,
                   JarIndex jarIndex) throws IOException
    {
        ZipInputStream zis = new ZipInputStream(in);
        ZipOutputStream zos = new JarOutputStream(out);
        ZipEntry e = null;
        boolean foundManifest = false;
        boolean updateOk = true;

        // All actual entries added/updated/existing, in the jar file (excl manifest
        // and module-info.class ).
        Set<String> jentries = new HashSet<>();

        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);
            boolean isModuleInfoEntry = isModuleInfoEntry(name);

            if ((jarIndex != null && equalsIgnoreCase(name, INDEX_NAME))
                || (Mflag && isManifestEntry)) {
                continue;
            } else if (isManifestEntry && ((newManifest != null) ||
                        (ename != null) || isMultiRelease)) {
                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.
                    try (FileInputStream fis = new FileInputStream(mname)) {
                        if (isAmbiguousMainClass(new Manifest(fis))) {
                            return false;
                        }
                    }
                }
                // Update the manifest.
                Manifest old = new Manifest(zis);
                if (newManifest != null) {
                    old.read(newManifest);
                }
                if (!updateManifest(old, zos)) {
                    return false;
                }
            } else if (moduleInfos != null && isModuleInfoEntry) {
                moduleInfos.putIfAbsent(name, zis.readAllBytes());
            } else {
                boolean isDir = e.isDirectory();
                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
                    Entry ent = entryMap.get(name);
                    addFile(zos, ent);
                    entryMap.remove(name);
                    entries.remove(ent);
                    isDir = ent.isDir;
                }
                if (!isDir) {
                    jentries.add(name);
                }
            }
        }

        // add the remaining new files
        for (Entry entry : entries) {
            addFile(zos, entry);
            if (!entry.isDir) {
                jentries.add(entry.name);
            }
        }
        if (!foundManifest) {
            if (newManifest != null) {
                Manifest m = new Manifest(newManifest);
                updateOk = !isAmbiguousMainClass(m);
                if (updateOk) {
                    if (!updateManifest(m, zos)) {
                        updateOk = false;
                    }
                }
            } else if (ename != null) {
                if (!updateManifest(new Manifest(), zos)) {
                    updateOk = false;
                }
            }
        }
        if (updateOk) {
            if (moduleInfos != null && !moduleInfos.isEmpty()) {
                Set<String> pkgs = new HashSet<>();
                jentries.forEach( je -> addPackageIfNamed(pkgs, je));
                addExtendedModuleAttributes(moduleInfos, pkgs);
                updateOk = checkModuleInfo(moduleInfos.get(MODULE_INFO), jentries);
                updateModuleInfo(moduleInfos, zos);
                // TODO: check manifest main classes, etc
            } else if (moduleVersion != null || modulesToHash != null) {
                error(getMsg("error.module.options.without.info"));
                updateOk = false;
            }
        }
        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 updateModuleInfo(Map<String,byte[]> moduleInfos, ZipOutputStream zos)
        throws IOException
    {
        String fmt = uflag ? "out.update.module-info": "out.added.module-info";
        for (Map.Entry<String,byte[]> mi : moduleInfos.entrySet()) {
            String name = mi.getKey();
            byte[] bytes = mi.getValue();
            ZipEntry e = new ZipEntry(name);
            e.setTime(System.currentTimeMillis());
            if (flag0) {
                crc32ModuleInfo(e, bytes);
            }
            zos.putNextEntry(e);
            zos.write(bytes);
            zos.closeEntry();
            if (vflag) {
                output(formatMsg(fmt, name));
            }
        }
    }

    private boolean updateManifest(Manifest m, ZipOutputStream zos)
        throws IOException
    {
        addVersion(m);
        addCreatedBy(m);
        if (ename != null) {
            addMainClass(m, ename);
        }
        if (isMultiRelease) {
            addMultiRelease(m);
        }
        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"));
        }
        return true;
    }

    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 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 void addMultiRelease(Manifest m) {
        Attributes global = m.getMainAttributes();
        global.put(Attributes.Name.MULTI_RELEASE, "true");
    }

    private boolean isAmbiguousMainClass(Manifest m) {
        if (ename != null) {
            Attributes global = m.getMainAttributes();
            if ((global.get(Attributes.Name.MAIN_CLASS) != null)) {
                usageError(getMsg("error.bad.eflag"));
                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, Entry entry) throws IOException {

        File file = entry.file;
        String name = entry.name;
        boolean isDir = entry.isDir;

        if (name.isEmpty() || 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;
        } else if (name.equals(MODULE_INFO)) {
            throw new Error("Unexpected module info: " + name);
        }

        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 {
        try (InputStream in = new FileInputStream(from)) {
            copy(in, to);
        }
    }

    
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 {
        try (OutputStream out = new FileOutputStream(to)) {
            copy(from, out);
        }
    }

    
Computes the crc32 of a module-info.class.  This is necessary when the
ZipOutputStream is in STORED mode.
/**
     * Computes the crc32 of a module-info.class.  This is necessary when the
     * ZipOutputStream is in STORED mode.
     */
    private void crc32ModuleInfo(ZipEntry e, byte[] bytes) throws IOException {
        CRC32OutputStream os = new CRC32OutputStream();
        ByteArrayInputStream in = new ByteArrayInputStream(bytes);
        in.transferTo(os);
        os.updateEntry(e);
    }

    
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(Map<Integer, String []> filesMap) {
        filesMap.keySet().forEach(version -> {
            String[] files = filesMap.get(version);
            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.
Returns:
whether entries were found and successfully extracted
(indicating this was a zip file without "leading garbage")/**
     * Extracts specified entries from JAR file.
     *
     * @return whether entries were found and successfully extracted
     * (indicating this was a zip file without "leading garbage")
     */
    boolean 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.
        boolean entriesFound = false;
        Set<ZipEntry> dirs = newDirSet();
        while ((e = zis.getNextEntry()) != null) {
            entriesFound = true;
            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);

        return entriesFound;
    }

    
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, 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(String s) {
        err.println(s);
        err.println(getMsg("main.usage.summary.try"));
    }

    
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
     */
    void error(String s) {
        err.println(s);
    }

    
Print a warning message
/**
     * Print a warning message
     */
    void warn(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());
        }
    }

    
Attempt to create temporary file in the system-provided temporary folder, if failed attempts
to create it in the same folder as the file in parameter (if any)
/**
     * Attempt to create temporary file in the system-provided temporary folder, if failed attempts
     * to create it in the same folder as the file in parameter (if any)
     */
    private File createTemporaryFile(String tmpbase, String suffix) {
        File tmpfile = null;

        try {
            tmpfile = File.createTempFile(tmpbase, suffix);
        } catch (IOException | SecurityException e) {
            // Unable to create file due to permission violation or security exception
        }
        if (tmpfile == null) {
            // Were unable to create temporary file, fall back to temporary file in the same folder
            if (fname != null) {
                try {
                    File tmpfolder = new File(fname).getAbsoluteFile().getParentFile();
                    tmpfile = File.createTempFile(fname, ".tmp" + suffix, tmpfolder);
                } catch (IOException ioe) {
                    // Last option failed - fall gracefully
                    fatalError(ioe);
                }
            } else {
                // No options left - we can not compress to stdout without access to the temporary folder
                fatalError(new IOException(getMsg("error.create.tempfile")));
            }
        }
        return tmpfile;
    }

    // Modular jar support

    
Associates a module descriptor's zip entry name along with its
bytes and an optional URI. Used when describing modules.
/**
     * Associates a module descriptor's zip entry name along with its
     * bytes and an optional URI. Used when describing modules.
     */
    interface ModuleInfoEntry {
       String name();
       Optional<String> uriString();
       InputStream bytes() throws IOException;
    }

    static class ZipFileModuleInfoEntry implements ModuleInfoEntry {
        private final ZipFile zipFile;
        private final ZipEntry entry;
        ZipFileModuleInfoEntry(ZipFile zipFile, ZipEntry entry) {
            this.zipFile = zipFile;
            this.entry = entry;
        }
        @Override public String name() { return entry.getName(); }
        @Override public InputStream bytes() throws IOException {
            return zipFile.getInputStream(entry);
        }
        
Returns an optional containing the effective URI. /** Returns an optional containing the effective URI. */
        @Override public Optional<String> uriString() {
            String uri = (Paths.get(zipFile.getName())).toUri().toString();
            uri = "jar:" + uri + "/!" + entry.getName();
            return Optional.of(uri);
        }
    }

    static class StreamedModuleInfoEntry implements ModuleInfoEntry {
        private final String name;
        private final byte[] bytes;
        StreamedModuleInfoEntry(String name, byte[] bytes) {
            this.name = name;
            this.bytes = bytes;
        }
        @Override public String name() { return name; }
        @Override public InputStream bytes() throws IOException {
            return new ByteArrayInputStream(bytes);
        }
        
Returns an empty optional. /** Returns an empty optional. */
        @Override public Optional<String> uriString() {
            return Optional.empty();  // no URI can be derived
        }
    }

    
Describes a module from a given zip file. /** Describes a module from a given zip file. */
    private boolean describeModule(ZipFile zipFile) throws IOException {
        ZipFileModuleInfoEntry[] infos = zipFile.stream()
                .filter(e -> isModuleInfoEntry(e.getName()))
                .sorted(ENTRY_COMPARATOR)
                .map(e -> new ZipFileModuleInfoEntry(zipFile, e))
                .toArray(ZipFileModuleInfoEntry[]::new);

        if (infos.length == 0) {
            // No module descriptor found, derive and describe the automatic module
            String fn = zipFile.getName();
            ModuleFinder mf = ModuleFinder.of(Paths.get(fn));
            try {
                Set<ModuleReference> mref = mf.findAll();
                if (mref.isEmpty()) {
                    output(formatMsg("error.unable.derive.automodule", fn));
                    return true;
                }
                ModuleDescriptor md = mref.iterator().next().descriptor();
                output(getMsg("out.automodule") + "\n");
                describeModule(md, null, null, "");
            } catch (FindException e) {
                String msg = formatMsg("error.unable.derive.automodule", fn);
                Throwable t = e.getCause();
                if (t != null)
                    msg = msg + "\n" + t.getMessage();
                output(msg);
            }
        } else {
            return describeModuleFromEntries(infos);
        }
        return true;
    }

    private boolean describeModuleFromStream(FileInputStream fis)
        throws IOException
    {
        List<ModuleInfoEntry> infos = new LinkedList<>();

        try (BufferedInputStream bis = new BufferedInputStream(fis);
             ZipInputStream zis = new ZipInputStream(bis)) {
            ZipEntry e;
            while ((e = zis.getNextEntry()) != null) {
                String ename = e.getName();
                if (isModuleInfoEntry(ename)) {
                    infos.add(new StreamedModuleInfoEntry(ename, zis.readAllBytes()));
                }
            }
        }

        if (infos.size() == 0)
            return false;

        ModuleInfoEntry[] sorted = infos.stream()
                .sorted(Comparator.comparing(ModuleInfoEntry::name, ENTRYNAME_COMPARATOR))
                .toArray(ModuleInfoEntry[]::new);

        return describeModuleFromEntries(sorted);
    }

    private boolean lessThanEqualReleaseValue(ModuleInfoEntry entry) {
        return intVersionFromEntry(entry) <= releaseValue ? true : false;
    }

    private static String versionFromEntryName(String name) {
        String s = name.substring(VERSIONS_DIR_LENGTH);
        return s.substring(0, s.indexOf("/"));
    }

    private static int intVersionFromEntry(ModuleInfoEntry entry) {
        String name = entry.name();
        if (!name.startsWith(VERSIONS_DIR))
            return BASE_VERSION;

        String s = name.substring(VERSIONS_DIR_LENGTH);
        s = s.substring(0, s.indexOf('/'));
        return Integer.valueOf(s);
    }

    
Describes a single module descriptor, determined by the specified
--release, if any, from the given ordered entries.
The given infos must be ordered as per ENTRY_COMPARATOR.
/**
     * Describes a single module descriptor, determined by the specified
     * --release, if any, from the given ordered entries.
     * The given infos must be ordered as per ENTRY_COMPARATOR.
     */
    private boolean describeModuleFromEntries(ModuleInfoEntry[] infos)
        throws IOException
    {
        assert infos.length > 0;

        // Informative: output all non-root descriptors, if any
        String releases = Arrays.stream(infos)
                .filter(e -> !e.name().equals(MODULE_INFO))
                .map(ModuleInfoEntry::name)
                .map(Main::versionFromEntryName)
                .collect(joining(" "));
        if (!releases.isEmpty())
            output("releases: " + releases + "\n");

        // Describe the operative descriptor for the specified --release, if any
        if (releaseValue != -1) {
            ModuleInfoEntry entry = null;
            int i = 0;
            while (i < infos.length && lessThanEqualReleaseValue(infos[i])) {
                entry = infos[i];
                i++;
            }

            if (entry == null) {
                output(formatMsg("error.no.operative.descriptor",
                                 String.valueOf(releaseValue)));
                return false;
            }

            String uriString = entry.uriString().orElse("");
            try (InputStream is = entry.bytes()) {
                describeModule(is, uriString);
            }
        } else {
            // no specific --release specified, output the root, if any
            if (infos[0].name().equals(MODULE_INFO)) {
                String uriString = infos[0].uriString().orElse("");
                try (InputStream is = infos[0].bytes()) {
                    describeModule(is, uriString);
                }
            } else {
                // no root, output message to specify --release
                output(getMsg("error.no.root.descriptor"));
            }
        }
        return true;
    }

    static <T> String toLowerCaseString(Collection<T> set) {
        if (set.isEmpty()) { return ""; }
        return " " + set.stream().map(e -> e.toString().toLowerCase(Locale.ROOT))
                  .sorted().collect(joining(" "));
    }

    static <T> String toString(Collection<T> set) {
        if (set.isEmpty()) { return ""; }
        return " " + set.stream().map(e -> e.toString()).sorted().collect(joining(" "));
    }

    private void describeModule(InputStream entryInputStream, String uriString)
        throws IOException
    {
        ModuleInfo.Attributes attrs = ModuleInfo.read(entryInputStream, null);
        ModuleDescriptor md = attrs.descriptor();
        ModuleTarget target = attrs.target();
        ModuleHashes hashes = attrs.recordedHashes();

        describeModule(md, target, hashes, uriString);
    }

    private void describeModule(ModuleDescriptor md,
                                ModuleTarget target,
                                ModuleHashes hashes,
                                String uriString)
        throws IOException
    {
        StringBuilder sb = new StringBuilder();

        sb.append(md.toNameAndVersion());

        if (!uriString.isEmpty())
            sb.append(" ").append(uriString);
        if (md.isOpen())
            sb.append(" open");
        if (md.isAutomatic())
            sb.append(" automatic");
        sb.append("\n");

        // unqualified exports (sorted by package)
        md.exports().stream()
                .sorted(Comparator.comparing(Exports::source))
                .filter(e -> !e.isQualified())
                .forEach(e -> sb.append("exports ").append(e.source())
                                .append(toLowerCaseString(e.modifiers()))
                                .append("\n"));

        // dependences
        md.requires().stream().sorted()
                .forEach(r -> sb.append("requires ").append(r.name())
                                .append(toLowerCaseString(r.modifiers()))
                                .append("\n"));

        // service use and provides
        md.uses().stream().sorted()
                .forEach(s -> sb.append("uses ").append(s).append("\n"));

        md.provides().stream()
                .sorted(Comparator.comparing(Provides::service))
                .forEach(p -> sb.append("provides ").append(p.service())
                                .append(" with")
                                .append(toString(p.providers()))
                                .append("\n"));

        // qualified exports
        md.exports().stream()
                .sorted(Comparator.comparing(Exports::source))
                .filter(Exports::isQualified)
                .forEach(e -> sb.append("qualified exports ").append(e.source())
                                .append(" to").append(toLowerCaseString(e.targets()))
                                .append("\n"));

        // open packages
        md.opens().stream()
                .sorted(Comparator.comparing(Opens::source))
                .filter(o -> !o.isQualified())
                .forEach(o -> sb.append("opens ").append(o.source())
                                 .append(toLowerCaseString(o.modifiers()))
                                 .append("\n"));

        md.opens().stream()
                .sorted(Comparator.comparing(Opens::source))
                .filter(Opens::isQualified)
                .forEach(o -> sb.append("qualified opens ").append(o.source())
                                 .append(toLowerCaseString(o.modifiers()))
                                 .append(" to").append(toLowerCaseString(o.targets()))
                                 .append("\n"));

        // non-exported/non-open packages
        Set<String> concealed = new TreeSet<>(md.packages());
        md.exports().stream().map(Exports::source).forEach(concealed::remove);
        md.opens().stream().map(Opens::source).forEach(concealed::remove);
        concealed.forEach(p -> sb.append("contains ").append(p).append("\n"));

        md.mainClass().ifPresent(v -> sb.append("main-class ").append(v).append("\n"));

        if (target != null) {
            String targetPlatform = target.targetPlatform();
            if (!targetPlatform.isEmpty())
                sb.append("platform ").append(targetPlatform).append("\n");
       }

       if (hashes != null) {
           hashes.names().stream().sorted().forEach(
                   mod -> sb.append("hashes ").append(mod).append(" ")
                            .append(hashes.algorithm()).append(" ")
                            .append(toHex(hashes.hashFor(mod)))
                            .append("\n"));
        }

        output(sb.toString());
    }

    private static String toHex(byte[] ba) {
        StringBuilder sb = new StringBuilder(ba.length << 1);
        for (byte b: ba) {
            sb.append(String.format("%02x", b & 0xff));
        }
        return sb.toString();
    }

    static String toBinaryName(String classname) {
        return (classname.replace('.', '/')) + ".class";
    }

    private boolean checkModuleInfo(byte[] moduleInfoBytes, Set<String> entries)
        throws IOException
    {
        boolean ok = true;
        if (moduleInfoBytes != null) {  // no root module-info.class if null
            try {
                // ModuleDescriptor.read() checks open/exported pkgs vs packages
                ModuleDescriptor md = ModuleDescriptor.read(ByteBuffer.wrap(moduleInfoBytes));
                // A module must have the implementation class of the services it 'provides'.
                if (md.provides().stream().map(Provides::providers).flatMap(List::stream)
                      .filter(p -> !entries.contains(toBinaryName(p)))
                      .peek(p -> fatalError(formatMsg("error.missing.provider", p)))
                      .count() != 0) {
                    ok = false;
                }
            } catch (InvalidModuleDescriptorException x) {
                fatalError(x.getMessage());
                ok = false;
            }
        }
        return ok;
    }

    
Adds extended modules attributes to the given module-info's.  The given
Map values are updated in-place. Returns false if an error occurs.
/**
     * Adds extended modules attributes to the given module-info's.  The given
     * Map values are updated in-place. Returns false if an error occurs.
     */
    private void addExtendedModuleAttributes(Map<String,byte[]> moduleInfos,
                                                Set<String> packages)
        throws IOException
    {
        for (Map.Entry<String,byte[]> e: moduleInfos.entrySet()) {
            ModuleDescriptor md = ModuleDescriptor.read(ByteBuffer.wrap(e.getValue()));
            e.setValue(extendedInfoBytes(md, e.getValue(), packages));
        }
    }

    static boolean isModuleInfoEntry(String name) {
        // root or versioned module-info.class
        if (name.endsWith(MODULE_INFO)) {
            int end = name.length() - MODULE_INFO.length();
            if (end == 0)
                return true;
            if (name.startsWith(VERSIONS_DIR)) {
                int off = VERSIONS_DIR_LENGTH;
                if (off == end)      // meta-inf/versions/module-info.class
                    return false;
                while (off < end - 1) {
                    char c = name.charAt(off++);
                    if (c < '0' || c > '9')
                        return false;
                }
                return name.charAt(off) == '/';
            }
        }
        return false;
    }

    
Returns a byte array containing the given module-info.class plus any
extended attributes.
If --module-version, --main-class, or other options were provided
then the corresponding class file attributes are added to the
module-info here.
/**
     * Returns a byte array containing the given module-info.class plus any
     * extended attributes.
     *
     * If --module-version, --main-class, or other options were provided
     * then the corresponding class file attributes are added to the
     * module-info here.
     */
    private byte[] extendedInfoBytes(ModuleDescriptor md,
                                     byte[] miBytes,
                                     Set<String> packages)
        throws IOException
    {
        ByteArrayOutputStream baos = new ByteArrayOutputStream();
        InputStream is = new ByteArrayInputStream(miBytes);
        ModuleInfoExtender extender = ModuleInfoExtender.newExtender(is);

        // Add (or replace) the Packages attribute
        extender.packages(packages);

        // --main-class
        if (ename != null)
            extender.mainClass(ename);

        // --module-version
        if (moduleVersion != null)
            extender.version(moduleVersion);

        // --hash-modules
        if (modulesToHash != null) {
            String mn = md.name();
            Hasher hasher = new Hasher(md, fname);
            ModuleHashes moduleHashes = hasher.computeHashes(mn);
            if (moduleHashes != null) {
                extender.hashes(moduleHashes);
            } else {
                warn("warning: no module is recorded in hash in " + mn);
            }
        }

        if (moduleResolution.value() != 0) {
            extender.moduleResolution(moduleResolution);
        }

        extender.write(baos);
        return baos.toByteArray();
    }

    
Compute and record hashes
/**
     * Compute and record hashes
     */
    private class Hasher {
        final ModuleHashesBuilder hashesBuilder;
        final ModuleFinder finder;
        final Set<String> modules;
        Hasher(ModuleDescriptor descriptor, String fname) throws IOException {
            // Create a module finder that finds the modular JAR
            // being created/updated
            URI uri = Paths.get(fname).toUri();
            ModuleReference mref = new ModuleReference(descriptor, uri) {
                @Override
                public ModuleReader open() {
                    throw new UnsupportedOperationException("should not reach here");
                }
            };

            // Compose a module finder with the module path and
            // the modular JAR being created or updated
            this.finder = ModuleFinder.compose(moduleFinder,
                new ModuleFinder() {
                    @Override
                    public Optional<ModuleReference> find(String name) {
                        if (descriptor.name().equals(name))
                            return Optional.of(mref);
                        else
                            return Optional.empty();
                    }

                    @Override
                    public Set<ModuleReference> findAll() {
                        return Collections.singleton(mref);
                    }
                });

            // Determine the modules that matches the pattern {@code modulesToHash}
            Set<String> roots = finder.findAll().stream()
                .map(ref -> ref.descriptor().name())
                .filter(mn -> modulesToHash.matcher(mn).find())
                .collect(Collectors.toSet());

            // use system module path unless it creates a modular JAR for
            // a module that is present in the system image e.g. upgradeable
            // module
            ModuleFinder system;
            String name = descriptor.name();
            if (name != null && ModuleFinder.ofSystem().find(name).isPresent()) {
                system = ModuleFinder.of();
            } else {
                system = ModuleFinder.ofSystem();
            }
            // get a resolved module graph
            Configuration config =
                Configuration.empty().resolve(system, finder, roots);

            // filter modules resolved from the system module finder
            this.modules = config.modules().stream()
                .map(ResolvedModule::name)
                .filter(mn -> roots.contains(mn) && !system.find(mn).isPresent())
                .collect(Collectors.toSet());

            this.hashesBuilder = new ModuleHashesBuilder(config, modules);
        }

        
Compute hashes of the specified module.
It records the hashing modules that depend upon the specified
module directly or indirectly.
/**
         * Compute hashes of the specified module.
         *
         * It records the hashing modules that depend upon the specified
         * module directly or indirectly.
         */
        ModuleHashes computeHashes(String name) {
            if (hashesBuilder == null)
                return null;

            return hashesBuilder.computeHashes(Set.of(name)).get(name);
        }
    }

    // sort base entries before versioned entries, and sort entry classes with
    // nested classes so that the outter class appears before the associated
    // nested class
    static Comparator<String> ENTRYNAME_COMPARATOR = (s1, s2) ->  {

        if (s1.equals(s2)) return 0;
        boolean b1 = s1.startsWith(VERSIONS_DIR);
        boolean b2 = s2.startsWith(VERSIONS_DIR);
        if (b1 && !b2) return 1;
        if (!b1 && b2) return -1;
        int n = 0; // starting char for String compare
        if (b1 && b2) {
            // normally strings would be sorted so "10" goes before "9", but
            // version number strings need to be sorted numerically
            n = VERSIONS_DIR.length();   // skip the common prefix
            int i1 = s1.indexOf('/', n);
            int i2 = s2.indexOf('/', n);
            if (i1 == -1) throw new Validator.InvalidJarException(s1);
            if (i2 == -1) throw new Validator.InvalidJarException(s2);
            // shorter version numbers go first
            if (i1 != i2) return i1 - i2;
            // otherwise, handle equal length numbers below
        }
        int l1 = s1.length();
        int l2 = s2.length();
        int lim = Math.min(l1, l2);
        for (int k = n; k < lim; k++) {
            char c1 = s1.charAt(k);
            char c2 = s2.charAt(k);
            if (c1 != c2) {
                // change natural ordering so '.' comes before '$'
                // i.e. outer classes come before nested classes
                if (c1 == '$' && c2 == '.') return 1;
                if (c1 == '.' && c2 == '$') return -1;
                return c1 - c2;
            }
        }
        return l1 - l2;
    };

    static Comparator<ZipEntry> ENTRY_COMPARATOR =
        Comparator.comparing(ZipEntry::getName, ENTRYNAME_COMPARATOR);

}