/**
 JavaX runner version 12 as embeddable class (non-public)

 Changes to v11:
 -Ported to Windows

 */

class x12 {
  static final String version = "JavaX 12";

  static boolean verbose = false, translate = false, list = false, virtualizeTranslators = true;
  static boolean preferCached = false;
  static List<String> mainTranslators = new ArrayList<String>();
  private static Map<Long, String> memSnippetCache = new HashMap<Long, String>();
  private static int processesStarted;

  public static void main(String[] args) throws Exception {
    File ioBaseDir = new File("."), inputDir = null, outputDir = null;
    String src = ".";
    for (int i = 0; i < args.length; i++) {
      String arg = args[i];
      if (arg.equals("-v") || arg.equals("-verbose"))
        verbose = true;
      else if (arg.equals("-finderror"))
        verbose = true;
      else if (arg.equals("-offline") || arg.equalsIgnoreCase("-prefercached"))
        preferCached = true;
      else if (arg.equals("-novirt"))
        virtualizeTranslators = false;
      else if (arg.equals("translate"))
        translate = true;
      else if (arg.equals("list"))
        list = true;
      else if (arg.equals("run")) {
        // it's the default command anyway
      } else if (arg.startsWith("input="))
        inputDir = new File(arg.substring(6));
      else if (arg.startsWith("output="))
        outputDir = new File(arg.substring(7));
      else if (arg.equals("with"))
        mainTranslators.add(args[++i]);
      else
        src = arg;
    }

    if (virtualizeTranslators && !preferCached)
      initDiskSnippetCache(TempDirMaker_make());

    if (inputDir != null) {
      ioBaseDir = TempDirMaker_make();
      System.out.println("Taking input from: " + inputDir.getAbsolutePath());
      System.out.println("Output is in: " + new File(ioBaseDir, "output").getAbsolutePath());
      copyInput(inputDir, new File(ioBaseDir, "input"));
    }

    javax4(src, ioBaseDir, translate, list);

    if (outputDir != null) {
      copyInput(new File(ioBaseDir, "output"), outputDir);
      System.out.println("Output copied to: " + outputDir.getAbsolutePath());
    }

    if (verbose)
      System.out.println("Processes started: " + processesStarted);
  }

  public static void javax4(String src, File ioDir, boolean translate, boolean list) throws Exception {
    File srcDir;
    if (isSnippetID(src))
      srcDir = loadSnippetAsMainJava(src);
    else {
      srcDir = new File(src);
      if (!new File(srcDir, "main.java").exists()) {
        System.out.println("This is " + version  + ".\n" +
          "No main.java found, exiting");
        return;
      }
    }

    // translate

    List<File> libraries = new ArrayList<File>();
    File X = srcDir;
    X = applyTranslators(X, mainTranslators, libraries);
    X = defaultTranslate(X, libraries);

    // list or run

    if (translate)
      System.out.println("Program translated to: " + X.getAbsolutePath());
    else if (list)
      System.out.println(loadTextFile(new File(X, "main.java").getPath(), null));
    else
      javax2(X, ioDir, false, false, libraries);
  }

  private static File defaultTranslate(File x, List<File> libraries_out) throws Exception {
    x = luaPrintToJavaPrint(x);
    x = autoTranslate(x, libraries_out);
    return x;
  }

  private static File autoTranslate(File x, List<File> libraries_out) throws Exception {
    String main = loadTextFile(new File(x, "main.java").getPath(), null);
    List<String> lines = toLines(main);
    List<String> translators = findTranslators(lines);
    if (translators.isEmpty())
      return x;

    main = fromLines(lines);
    File newDir = TempDirMaker_make();
    saveTextFile(new File(newDir, "main.java").getPath(), main);
    return applyTranslators(newDir, translators, libraries_out);
  }

  private static List<String> findTranslators(List<String> lines) {
    List<String> translators = new ArrayList<String>();
    Pattern pattern = Pattern.compile("^!([0-9# \t]+)");
    for (ListIterator<String> iterator = lines.listIterator(); iterator.hasNext(); ) {
      String line = iterator.next();
      line = line.trim();
      Matcher matcher = pattern.matcher(line);
      if (matcher.find()) {
        translators.addAll(Arrays.asList(matcher.group(1).split("[ \t]+")));
        iterator.remove();
      }
    }
    return translators;
  }

  public static List<String> toLines(String s) {
    List<String> lines = new ArrayList<String>();
    int start = 0;
    while (true) {
      int i = toLines_nextLineBreak(s, start);
      if (i < 0) {
        if (s.length() > start) lines.add(s.substring(start));
        break;
      }

      lines.add(s.substring(start, i));
      if (s.charAt(i) == '\r' && i+1 < s.length() && s.charAt(i+1) == '\n')
        i += 2;
      else
        ++i;

      start = i;
    }
    return lines;
  }

  private static int toLines_nextLineBreak(String s, int start) {
    for (int i = start; i < s.length(); i++) {
      char c = s.charAt(i);
      if (c == '\r' || c == '\n')
        return i;
    }
    return -1;
  }

  public static String fromLines(List<String> lines) {
    StringBuilder buf = new StringBuilder();
    for (String line : lines) {
      buf.append(line).append('\n');
    }
    return buf.toString();
  }

  private static File applyTranslators(File x, List<String> translators, List<File> libraries_out) throws Exception {
    for (String translator : translators)
      x = applyTranslator(x, translator, libraries_out);
    return x;
  }

  // also takes a library
  private static File applyTranslator(File x, String translator, List<File> libraries_out) throws Exception {
    if (verbose)
      System.out.println("Using translator " + translator + " on sources in " + x.getPath());

    File newDir = runTranslatorOnInput(translator, null, x, !verbose, libraries_out);

    if (!new File(newDir, "main.java").exists()) {
      throw new Exception("Translator " + translator + " did not generate main.java");
      // TODO: show translator output
    }
    if (verbose)
      System.out.println("Translated with " + translator + " from " + x.getPath() + " to " + newDir.getPath());
    x = newDir;
    return x;
  }

  private static File luaPrintToJavaPrint(File x) throws IOException {
    File newDir = TempDirMaker_make();
    String code = loadTextFile(new File(x, "main.java").getPath(), null);
    code = luaPrintToJavaPrint(code);
    if (verbose)
      System.out.println(code);
    saveTextFile(new File(newDir, "main.java").getPath(), code);
    return newDir;
  }

  public static String luaPrintToJavaPrint(String code) {
    return ("\n" + code).replaceAll(
      "(\n\\s*)print (\".*\")",
      "$1System.out.println($2);").substring(1);
  }

  public static File loadSnippetAsMainJava(String snippetID) throws IOException {
    File srcDir = TempDirMaker_make();
    saveTextFile(new File(srcDir, "main.java").getPath(), loadSnippet(snippetID));
    return srcDir;
  }

  public static File loadSnippetAsMainJavaVerified(String snippetID, String hash) throws IOException {
    File srcDir = TempDirMaker_make();
    saveTextFile(new File(srcDir, "main.java").getPath(), loadSnippetVerified(snippetID, hash));
    return srcDir;
  }

  /** returns output dir */
  private static File runTranslatorOnInput(String snippetID, String hash, File input, boolean silent,
                                           List<File> libraries_out) throws Exception {
    File libraryFile = DiskSnippetCache_getLibrary(parseSnippetID(snippetID));
    if (libraryFile != null) {
      loadLibrary(snippetID, libraries_out, libraryFile);
      return input;
    }

    File srcDir = hash == null ? loadSnippetAsMainJava(snippetID)
      : loadSnippetAsMainJavaVerified(snippetID, hash);

    long mainJavaSize = new File(srcDir, "main.java").length();

    if (mainJavaSize == 0) { // no text in snippet? assume it's a library
      loadLibrary(snippetID, libraries_out, libraryFile);
      return input;
    }

    List<File> libraries = new ArrayList<File>();
    srcDir = defaultTranslate(srcDir, libraries);
    boolean runInProcess = false;
    File ioBaseDir = TempDirMaker_make();

    if (virtualizeTranslators) {
      if (verbose) System.out.println("Virtualizing translator");

      //srcDir = applyTranslator(srcDir, "#2000351"); // I/O-virtualize the translator
      // that doesn't work because it recurses infinitely...

      // So we do it right here:
      String s = loadTextFile(new File(srcDir, "main.java").getPath(), null);
      s = s.replaceAll("new\\s+File\\(", "virtual.newFile(");
      s = s.replaceAll("new\\s+FileInputStream\\(", "virtual.newFileInputStream(");
      s = s.replaceAll("new\\s+FileOutputStream\\(", "virtual.newFileOutputStream(");
      s += "\n\n" + loadSnippet("#2000355"); // load class virtual

      // change baseDir
      s = s.replace("virtual_baseDir = \"\";",
        "virtual_baseDir = " + javaQuote(ioBaseDir.getAbsolutePath()) + ";");

      // forward snippet cache
      s = s.replace("static File DiskSnippetCache_dir;",
        "static File DiskSnippetCache_dir = new File(" + javaQuote(DiskSnippetCache_dir.getAbsolutePath()) + ");");
      s = s.replace("static boolean preferCached = false;", "static boolean preferCached = true;");

      if (verbose) {
        System.out.println("==BEGIN VIRTUALIZED TRANSLATOR==");
        System.out.println(s);
        System.out.println("==END VIRTUALIZED TRANSLATOR==");
      }
      saveTextFile(new File(srcDir, "main.java").getPath(), s);

      // TODO: silence translator also
      runInProcess = true;
    }

    return runJavaX(ioBaseDir, srcDir, input, silent, runInProcess, libraries);
  }

  private static void loadLibrary(String snippetID, List<File> libraries_out, File libraryFile) throws IOException {
    if (verbose)
      System.out.println("Assuming " + snippetID + " is a library.");

    if (libraryFile == null) {
      byte[] data;
      try {
        URL url = new URL("http://eyeocr.sourceforge.net/filestore/filestore.php?cmd=serve&file=blob_" + parseSnippetID(snippetID)
          + "&contentType=application/binary");
        System.err.println("Loading library: " + url);
        data = loadBinaryPage(url.openConnection(), url);
        if (verbose)
          System.err.println("Bytes loaded: " + data.length);
      } catch (FileNotFoundException e) {
        throw new IOException("Binary snippet #" + snippetID + " not found or not public");
      }
      DiskSnippetCache_putLibrary(parseSnippetID(snippetID), data);
      libraryFile = DiskSnippetCache_getLibrary(parseSnippetID(snippetID));
    }

    if (!libraries_out.contains(libraryFile))
      libraries_out.add(libraryFile);
  }

  /** returns output dir */
  private static File runJavaX(File ioBaseDir, File originalSrcDir, File originalInput,
                               boolean silent, boolean runInProcess,
                               List<File> libraries) throws Exception {
    File srcDir = new File(ioBaseDir, "src");
    File inputDir = new File(ioBaseDir, "input");
    File outputDir = new File(ioBaseDir, "output");
    copyInput(originalSrcDir, srcDir);
    copyInput(originalInput, inputDir);
    javax2(srcDir, ioBaseDir, silent, runInProcess, libraries);
    return outputDir;
  }

  private static void copyInput(File src, File dst) throws IOException {
    copyDirectory(src, dst);
  }

  public static boolean hasFile(File inputDir, String name) {
    return new File(inputDir, name).exists();
  }

  public static void copyDirectory(File src, File dst) throws IOException {
    if (verbose) System.out.println("Copying " + src.getAbsolutePath() + " to " + dst.getAbsolutePath());
    dst.mkdirs();
    File[] files = src.listFiles();
    if (files == null) return;
    for (File file : files) {
      File dst1 = new File(dst, file.getName());
      if (file.isDirectory())
        copyDirectory(file, dst1);
      else {
        if (verbose) System.out.println("Copying " + file.getAbsolutePath() + " to " + dst1.getAbsolutePath());
        copy(file, dst1);
      }
    }
  }

  /** Quickly copy a file without a progress bar or any other fancy GUI... :) */
  public static void copy(File src, File dest) throws IOException {
    FileInputStream inputStream = new FileInputStream(src);
    FileOutputStream outputStream = new FileOutputStream(dest);
    try {
      copy(inputStream, outputStream);
      inputStream.close();
    } finally {
      outputStream.close();
    }
  }

  public static void copy(InputStream in, OutputStream out) throws IOException {
    byte[] buf = new byte[65536];
    while (true) {
      int n = in.read(buf);
      if (n <= 0) return;
      out.write(buf, 0, n);
    }
  }

  /** writes safely (to temp file, then rename) */
  public static void saveTextFile(String fileName, String contents) throws IOException {
    File file = new File(fileName);
    File parentFile = file.getParentFile();
    if (parentFile != null)
      parentFile.mkdirs();
    String tempFileName = fileName + "_temp";
    FileOutputStream fileOutputStream = new FileOutputStream(tempFileName);
    OutputStreamWriter outputStreamWriter = new OutputStreamWriter(fileOutputStream, charsetForTextFiles);
    PrintWriter printWriter = new PrintWriter(outputStreamWriter);
    printWriter.print(contents);
    printWriter.close();
    if (file.exists() && !file.delete())
      throw new IOException("Can't delete " + fileName);

    if (!new File(tempFileName).renameTo(file))
      throw new IOException("Can't rename " + tempFileName + " to " + fileName);
  }

  /** writes safely (to temp file, then rename) */
  public static void saveBinaryFile(String fileName, byte[] contents) throws IOException {
    File file = new File(fileName);
    File parentFile = file.getParentFile();
    if (parentFile != null)
      parentFile.mkdirs();
    String tempFileName = fileName + "_temp";
    FileOutputStream fileOutputStream = new FileOutputStream(tempFileName);
    fileOutputStream.write(contents);
    fileOutputStream.close();
    if (file.exists() && !file.delete())
      throw new IOException("Can't delete " + fileName);

    if (!new File(tempFileName).renameTo(file))
      throw new IOException("Can't rename " + tempFileName + " to " + fileName);
  }

  public static String loadTextFile(String fileName, String defaultContents) throws IOException {
    if (!new File(fileName).exists())
      return defaultContents;

    FileInputStream fileInputStream = new FileInputStream(fileName);
    InputStreamReader inputStreamReader = new InputStreamReader(fileInputStream, charsetForTextFiles);
    return loadTextFile(inputStreamReader);
  }

  public static String loadTextFile(Reader reader) throws IOException {
    StringBuilder builder = new StringBuilder();
    try {
      BufferedReader bufferedReader = new BufferedReader(reader);
      String line;
      while ((line = bufferedReader.readLine()) != null)
        builder.append(line).append('\n');
    } finally {
      reader.close();
    }
    return builder.length() == 0 ? "" : builder.substring(0, builder.length()-1);
  }

  static File DiskSnippetCache_dir;

  public static void initDiskSnippetCache(File dir) {
    DiskSnippetCache_dir = dir;
    dir.mkdirs();
  }

  // Data files are immutable, use centralized cache
  public static synchronized File DiskSnippetCache_getLibrary(long snippetID) throws IOException {
    File file = new File(getGlobalCache(), "data_" + snippetID + ".jar");
    if (verbose)
      System.out.println("Checking data cache: " + file.getPath());
    return file.exists() ? file : null;
  }

  public static synchronized String DiskSnippetCache_get(long snippetID) throws IOException {
    return loadTextFile(DiskSnippetCache_getFile(snippetID).getPath(), null);
  }

  private static File DiskSnippetCache_getFile(long snippetID) {
    return new File(DiskSnippetCache_dir, "" + snippetID);
  }

  public static synchronized void DiskSnippetCache_put(long snippetID, String snippet) throws IOException {
    saveTextFile(DiskSnippetCache_getFile(snippetID).getPath(), snippet);
  }

  public static synchronized void DiskSnippetCache_putLibrary(long snippetID, byte[] data) throws IOException {
    saveBinaryFile(new File(getGlobalCache(), "data_" + snippetID).getPath() + ".jar", data);
  }

  public static File DiskSnippetCache_getDir() {
    return DiskSnippetCache_dir;
  }

  public static void initSnippetCache() {
    if (DiskSnippetCache_dir == null)
      initDiskSnippetCache(getGlobalCache());
  }

  private static File getGlobalCache() {
    File file = new File(System.getProperty("user.home"), ".tinybrain/snippet-cache");
    file.mkdirs();
    return file;
  }

  public static String loadSnippetVerified(String snippetID, String hash) throws IOException {
    String text = loadSnippet(snippetID);
    String realHash = getHash(text.getBytes("UTF-8"));
    if (!realHash.equals(hash)) {
      String msg;
      if (hash.isEmpty())
        msg = "Here's your hash for " + snippetID + ", please put in your program: " + realHash;
      else
        msg = "Hash mismatch for " + snippetID + ": " + realHash + " (new) vs " + hash + " - has tinybrain.de been hacked??";
      throw new RuntimeException(msg);
    }
    return text;
  }

  public static String getHash(byte[] data) {
    return bytesToHex(getFullFingerprint(data));
  }

  public static byte[] getFullFingerprint(byte[] data) {
    try {
      return java.security.MessageDigest.getInstance("MD5").digest(data);
    } catch (java.security.NoSuchAlgorithmException e) {
      throw new RuntimeException(e);
    }
  }

  public static String bytesToHex(byte[] bytes) {
    return bytesToHex(bytes, 0, bytes.length);
  }

  public static String bytesToHex(byte[] bytes, int ofs, int len) {
    StringBuilder stringBuilder = new StringBuilder(len*2);
    for (int i = 0; i < len; i++) {
      String s = "0" + Integer.toHexString(bytes[ofs+i]);
      stringBuilder.append(s.substring(s.length()-2, s.length()));
    }
    return stringBuilder.toString();
  }

  public static String loadSnippet(String snippetID) throws IOException {
    return loadSnippet(parseSnippetID(snippetID));
  }

  public static long parseSnippetID(String snippetID) {
    return Long.parseLong(shortenSnippetID(snippetID));
  }

  private static String shortenSnippetID(String snippetID) {
    if (snippetID.startsWith("#"))
      snippetID = snippetID.substring(1);
    String httpBlaBla = "http://tinybrain.de/";
    if (snippetID.startsWith(httpBlaBla))
      snippetID = snippetID.substring(httpBlaBla.length());
    return snippetID;
  }

  public static boolean isSnippetID(String snippetID) {
    snippetID = shortenSnippetID(snippetID);
    return isInteger(snippetID) && Long.parseLong(snippetID) != 0;
  }

  public static boolean isInteger(String s) {
    return Pattern.matches("\\-?\\d+", s);
  }

  public static String loadSnippet(long snippetID) throws IOException {
    String text = memSnippetCache.get(snippetID);
    if (text != null)
      return text;

    if (preferCached) {
      initSnippetCache();
      text = DiskSnippetCache_get(snippetID);
      if (text != null)
        return text;
    }

    try {
      URL url = new URL("http://tinybrain.de:8080/getraw.php?id=" + snippetID);
      text = loadPage(url);
    } catch (FileNotFoundException e) {
      throw new IOException("Snippet #" + snippetID + " not found or not public");
    }

    memSnippetCache.put(snippetID, text);

    try {
      initSnippetCache();
      DiskSnippetCache_put(snippetID, text);
    } catch (IOException e) {
      System.err.println("Minor warning: Couldn't save snippet to cache ("  + DiskSnippetCache_getDir() + ")");
    }

    return text;
  }

  private static String loadPage(URL url) throws IOException {
    System.err.println("Loading: " + url.toExternalForm());
    URLConnection con = url.openConnection();
    return loadPage(con, url);
  }

  public static String loadPage(URLConnection con, URL url) throws IOException {
    String contentType = con.getContentType();
    if (contentType == null)
      throw new IOException("Page could not be read: " + url);
    //Log.info("Content-Type: " + contentType);
    String charset = guessCharset(contentType);
    Reader r = new InputStreamReader(con.getInputStream(), charset);
    StringBuilder buf = new StringBuilder();
    while (true) {
      int ch = r.read();
      if (ch < 0)
        break;
      //Log.info("Chars read: " + buf.length());
      buf.append((char) ch);
    }
    return buf.toString();
  }

  public static byte[] loadBinaryPage(URLConnection con, URL url) throws IOException {
    ByteArrayOutputStream buf = new ByteArrayOutputStream();
    InputStream inputStream = con.getInputStream();
    while (true) {
      int ch = inputStream.read();
      if (ch < 0)
        break;
      buf.write(ch);
    }
    inputStream.close();
    return buf.toByteArray();
  }

  public static String guessCharset(String contentType) {
    Pattern p = Pattern.compile("text/html;\\s+charset=([^\\s]+)\\s*");
    Matcher m = p.matcher(contentType);
    /* If Content-Type doesn't match this pre-conception, choose default and hope for the best. */
    return m.matches() ? m.group(1) : "ISO-8859-1";
  }

  /** runs a transpiled set of sources */
  public static void javax2(File srcDir, File ioBaseDir, boolean silent, boolean runInProcess,
                            List<File> libraries) throws Exception {
    // collect sources

    List<File> sources = new ArrayList<File>();
    if (verbose) System.out.println("Scanning for sources in " + srcDir.getPath());
    scanForSources(srcDir, sources, true);
    if (sources.isEmpty()) {
      System.out.println("No sources found");
      return;
    }

    // compile

    File optionsFile = File.createTempFile("javax", "");
    File classesDir = TempDirMaker_make();
    if (verbose) System.out.println("Compiling " + sources.size() + " source(s) to " + classesDir.getPath());
    String options = "-d " + bashQuote(classesDir.getPath());
    writeOptions(sources, libraries, optionsFile, options);
    classesDir.mkdirs();
    String javacOutput = invokeJavac(optionsFile);

    // run

    if (verbose) System.out.println("Running program (" + srcDir.getAbsolutePath()
      + ") on io dir " + ioBaseDir.getAbsolutePath() + (runInProcess ? "[in-process]" : "") + "\n");
    runProgram(javacOutput, classesDir, ioBaseDir, silent, runInProcess, libraries);
  }

  private static void runProgram(String javacOutput, File classesDir, File ioBaseDir,
                                 boolean silent, boolean runInProcess,
                                 List<File> libraries) throws Exception {
    // print javac output if compile failed and it hasn't been printed yet
    boolean didNotCompile = !hasFile(classesDir, "main.class");
    if (verbose || didNotCompile)
      System.out.println(javacOutput);
    if (didNotCompile)
      return;

    if (runInProcess
      || (ioBaseDir.getAbsolutePath().equals(new File(".").getAbsolutePath()) && !silent)) {
      runProgramQuick(classesDir, libraries);
      return;
    }

    boolean echoOK = false;
    // TODO: add libraries to class path
    String bashCmd = "(cd " + bashQuote(ioBaseDir.getAbsolutePath()) + " && (java -cp "
      + bashQuote(classesDir.getAbsolutePath()) + " main" + (echoOK ? "; echo ok" : "") + "))";
    if (verbose) System.out.println(bashCmd);
    String output = backtick(bashCmd);
    if (verbose || !silent)
      System.out.println(output);
  }

  private static void runProgramQuick(File classesDir, List<File> libraries) throws Exception {
    // collect urls
    URL[] urls = new URL[libraries.size()+1];
    urls[0] = classesDir.toURI().toURL();
    for (int i = 0; i < libraries.size(); i++)
      urls[i+1] = libraries.get(i).toURI().toURL();

    // make class loader
    URLClassLoader classLoader = new URLClassLoader(urls);

    // load JavaX main class
    Class<?> mainClass = classLoader.loadClass("main");

    // run main method
    java.lang.reflect.Method main = mainClass.getMethod("main", String[].class);
    main.invoke(null, (Object) new String[0]);
  }

  private static String invokeJavac(File optionsFile) throws IOException {
    String output;
    try {
      output = invokeEcj(optionsFile);
    } catch (NoClassDefFoundError e) {
      if (verbose) {
        System.err.println("ecj not found - using javac");
        e.printStackTrace();
      }
      output = backtick("javac " + bashQuote("@" + optionsFile.getPath()));
    }
    if (verbose) System.out.println(output);
    return output;
  }

  // throws ClassNotFoundError if ecj is not in classpath
  static String invokeEcj(File optionsFile) {
    StringWriter writer = new StringWriter();
    PrintWriter printWriter = new PrintWriter(writer);
    org.eclipse.jdt.core.compiler.CompilationProgress progress = null;
    org.eclipse.jdt.core.compiler.batch.BatchCompiler.compile(
      new String[] { "@" + optionsFile.getPath(), "-source", "1.7" },
      printWriter,
      printWriter,
      progress);
    return writer.toString();
  }

  private static void writeOptions(List<File> sources, List<File> libraries,
                                   File optionsFile, String moreOptions) throws IOException {
    FileWriter writer = new FileWriter(optionsFile);
    for (File source : sources)
      writer.write(bashQuote(source.getPath()) + " ");
    if (!libraries.isEmpty()) {
      List<String> cp = new ArrayList<String>();
      for (File lib : libraries)
        cp.add(lib.getAbsolutePath());
      writer.write("-cp " + bashQuote(join(File.pathSeparator, cp)) + " ");
    }
    writer.write(moreOptions);
    writer.close();
  }

  private static void scanForSources(File source, List<File> sources, boolean topLevel) {
    if (source.isFile() && source.getName().endsWith(".java"))
      sources.add(source);
    else if (source.isDirectory() && !isSkippedDirectoryName(source.getName(), topLevel)) {
      File[] files = source.listFiles();
      for (File file : files)
        scanForSources(file, sources, false);
    }
  }

  private static boolean isSkippedDirectoryName(String name, boolean topLevel) {
    if (topLevel) return false; // input or output ok as highest directory (intentionally specified by user, not just found by a directory scan in which case we probably don't want it. it's more like heuristics actually.)
    return name.equalsIgnoreCase("input") || name.equalsIgnoreCase("output");
  }

  public static String backtick(String cmd) throws IOException {
    ++processesStarted;
    File outFile = File.createTempFile("_backtick", "");
    File scriptFile = File.createTempFile("_backtick", isWindows() ? ".bat" : "");

    String command = cmd + ">" + bashQuote(outFile.getPath()) + " 2>&1";
    //Log.info("[Backtick] " + command);
    try {
      saveTextFile(scriptFile.getPath(), command);
      String[] command2;
      if (isWindows())
        command2 = new String[] { scriptFile.getPath() };
      else
        command2 = new String[] { "/bin/bash", scriptFile.getPath() };
      Process process = Runtime.getRuntime().exec(command2);
      try {
        process.waitFor();
      } catch (InterruptedException e) {
        throw new RuntimeException(e);
      }
      process.exitValue();
      return loadTextFile(outFile.getPath(), "");
    } finally {
      scriptFile.delete();
    }
  }

  /** possibly improvable */
  public static String javaQuote(String text) {
    return bashQuote(text);
  }

  /** possibly improvable */
  public static String bashQuote(String text) {
    if (text == null) return null;
    return "\"" + text
      .replace("\\", "\\\\")
      .replace("\"", "\\\"")
      .replace("\n", "\\n")
      .replace("\r", "\\r") + "\"";
  }

  public final static String charsetForTextFiles = "UTF8";

  static long TempDirMaker_lastValue;

  public static File TempDirMaker_make() {
    File dir = new File(System.getProperty("user.home"), ".javax/" + TempDirMaker_newValue());
    dir.mkdirs();
    return dir;
  }

  private static long TempDirMaker_newValue() {
    long value;
    do
      value = System.currentTimeMillis();
    while (value == TempDirMaker_lastValue);
    TempDirMaker_lastValue = value;
    return value;
  }

  public static String join(String glue, Iterable<String> strings) {
    StringBuilder buf = new StringBuilder();
    Iterator<String> i = strings.iterator();
    if (i.hasNext()) {
      buf.append(i.next());
      while (i.hasNext())
        buf.append(glue).append(i.next());
    }
    return buf.toString();
  }

  public static boolean isWindows() {
    return System.getProperty("os.name").contains("Windows");
  }
}

Began life as a copy of #2000359