Program: 12347
Project: 12347
Buggy source:
@Override public void run(){
  String javaBin="String_Node_Str";
  File binDir=(new File(jrePath)).toPath().resolve("String_Node_Str").toFile();
  if (binDir.exists()) {
    javaBin=binDir.toPath().resolve("String_Node_Str").toString();
  }
  StringBuilder sbClassPath=new StringBuilder();
  Path mcBinPath=parent.mcu.getMCFolder().resolve("String_Node_Str");
  sbClassPath.append(handleWhitespace(mcBinPath.resolve("String_Node_Str").toString()));
  sbClassPath.append(MCUpdater.cpDelimiter() + handleWhitespace(mcBinPath.resolve("String_Node_Str").toString()));
  sbClassPath.append(MCUpdater.cpDelimiter() + handleWhitespace(mcBinPath.resolve("String_Node_Str").toString()));
  sbClassPath.append(MCUpdater.cpDelimiter() + handleWhitespace(mcBinPath.resolve("String_Node_Str").toString()));
  String jlp="String_Node_Str" + handleWhitespace(mcBinPath.resolve("String_Node_Str").toString());
  String className="String_Node_Str";
  List<String> args=new ArrayList<String>();
  args.add(javaBin);
  args.add("String_Node_Str");
  args.add("String_Node_Str");
  args.add("String_Node_Str");
  args.add("String_Node_Str" + this.minMem);
  args.add("String_Node_Str" + this.maxMem);
  args.add("String_Node_Str");
  args.add(sbClassPath.toString());
  args.add(jlp);
  args.add(className);
  args.add(session.getUserName());
  args.add(session.getSessionId());
  if (!Version.isMasterBranch()) {
    parent.log("String_Node_Str");
    Iterator<String> itArgs=args.iterator();
    while (itArgs.hasNext()) {
      String entry=itArgs.next();
      parent.log(entry);
    }
  }
  ProcessBuilder pb=new ProcessBuilder(args);
  pb.redirectErrorStream(true);
  BufferedWriter buffWrite=null;
  try {
    buffWrite=new BufferedWriter(new OutputStreamWriter(new FileOutputStream(output)));
  }
 catch (  FileNotFoundException e) {
    log(e.getMessage() + "String_Node_Str");
    e.printStackTrace();
  }
  try {
    task=pb.start();
    BufferedReader buffRead=new BufferedReader(new InputStreamReader(task.getInputStream()));
    String line;
    buffRead.mark(1024);
    final String firstLine=buffRead.readLine();
    setReady();
    if (firstLine == null || firstLine.startsWith("String_Node_Str") || firstLine.startsWith("String_Node_Str")) {
      log("String_Node_Str");
      StringBuilder err=new StringBuilder(firstLine);
      while ((line=buffRead.readLine()) != null) {
        err.append('\n');
        err.append(line);
      }
      log(err + "String_Node_Str");
      JOptionPane.showMessageDialog(null,err);
    }
 else {
      buffRead.reset();
      minimizeFrame();
      log("String_Node_Str");
      int counter=0;
      while ((line=buffRead.readLine()) != null) {
        if (buffWrite != null) {
          buffWrite.write(line);
          buffWrite.newLine();
          counter++;
          if (counter >= 20) {
            buffWrite.flush();
            counter=0;
          }
        }
 else {
          System.out.println(line);
        }
        if (line.length() > 0) {
          log(line + "String_Node_Str");
        }
      }
    }
    buffWrite.flush();
    buffWrite.close();
    restoreFrame();
    log("String_Node_Str" + (forceKilled ? "String_Node_Str" : "String_Node_Str") + "String_Node_Str");
  }
 catch (  IOException ioe) {
    ioe.printStackTrace();
  }
}

Fixed version (ground truth):
@Override public void run(){
  String javaBin="String_Node_Str";
  File binDir=(new File(jrePath)).toPath().resolve("String_Node_Str").toFile();
  if (binDir.exists()) {
    javaBin=binDir.toPath().resolve("String_Node_Str").toString();
  }
  StringBuilder sbClassPath=new StringBuilder();
  Path mcBinPath=parent.mcu.getMCFolder().resolve("String_Node_Str");
  sbClassPath.append(handleWhitespace(mcBinPath.resolve("String_Node_Str").toString()));
  sbClassPath.append(MCUpdater.cpDelimiter() + handleWhitespace(mcBinPath.resolve("String_Node_Str").toString()));
  sbClassPath.append(MCUpdater.cpDelimiter() + handleWhitespace(mcBinPath.resolve("String_Node_Str").toString()));
  sbClassPath.append(MCUpdater.cpDelimiter() + handleWhitespace(mcBinPath.resolve("String_Node_Str").toString()));
  String jlp="String_Node_Str" + mcBinPath.resolve("String_Node_Str").toString();
  String className="String_Node_Str";
  List<String> args=new ArrayList<String>();
  args.add(javaBin);
  args.add("String_Node_Str");
  args.add("String_Node_Str");
  args.add("String_Node_Str");
  args.add("String_Node_Str" + this.minMem);
  args.add("String_Node_Str" + this.maxMem);
  args.add("String_Node_Str");
  args.add(sbClassPath.toString());
  args.add(jlp);
  args.add(className);
  args.add(session.getUserName());
  args.add(session.getSessionId());
  if (!Version.isMasterBranch()) {
    parent.log("String_Node_Str");
    Iterator<String> itArgs=args.iterator();
    while (itArgs.hasNext()) {
      String entry=itArgs.next();
      parent.log(entry);
    }
  }
  ProcessBuilder pb=new ProcessBuilder(args);
  pb.redirectErrorStream(true);
  BufferedWriter buffWrite=null;
  try {
    buffWrite=new BufferedWriter(new OutputStreamWriter(new FileOutputStream(output)));
  }
 catch (  FileNotFoundException e) {
    log(e.getMessage() + "String_Node_Str");
    e.printStackTrace();
  }
  try {
    task=pb.start();
    BufferedReader buffRead=new BufferedReader(new InputStreamReader(task.getInputStream()));
    String line;
    buffRead.mark(1024);
    final String firstLine=buffRead.readLine();
    setReady();
    if (firstLine == null || firstLine.startsWith("String_Node_Str") || firstLine.startsWith("String_Node_Str")) {
      log("String_Node_Str");
      StringBuilder err=new StringBuilder(firstLine);
      while ((line=buffRead.readLine()) != null) {
        err.append('\n');
        err.append(line);
      }
      log(err + "String_Node_Str");
      JOptionPane.showMessageDialog(null,err);
    }
 else {
      buffRead.reset();
      minimizeFrame();
      log("String_Node_Str");
      int counter=0;
      while ((line=buffRead.readLine()) != null) {
        if (buffWrite != null) {
          buffWrite.write(line);
          buffWrite.newLine();
          counter++;
          if (counter >= 20) {
            buffWrite.flush();
            counter=0;
          }
        }
 else {
          System.out.println(line);
        }
        if (line.length() > 0) {
          log(line + "String_Node_Str");
        }
      }
    }
    buffWrite.flush();
    buffWrite.close();
    restoreFrame();
    log("String_Node_Str" + (forceKilled ? "String_Node_Str" : "String_Node_Str") + "String_Node_Str");
  }
 catch (  IOException ioe) {
    ioe.printStackTrace();
  }
}