Program: 101512
Project: 101512
Buggy source:
private void parse(){
  int nargs=args.length;
  for (int i=0; i < nargs; i++) {
    String nextArg=args[i];
    if (nextArg.length() < 2 || nextArg.charAt(0) != '-') {
      nonOptionArgs.add(nextArg);
      continue;
    }
    if ("String_Node_Str".equals(nextArg)) {
      for (int j=i + 1; j < nargs; j++) {
        nonOptionArgs.add(args[j]);
      }
      return;
    }
    if (nextArg.charAt(1) == '-') {
      int equalPos=nextArg.indexOf('=');
      String flag=(equalPos != -1) ? nextArg.substring(2,equalPos) : nextArg.substring(2);
      List opts=programOptions.getLongOptions(flag);
      if (opts.size() == 0) {
        throw new IllegalArgumentException("String_Node_Str" + flag);
      }
      if (opts.size() > 1) {
        throw new IllegalArgumentException("String_Node_Str" + flag);
      }
      Option option=(Option)opts.get(0);
      if (option.getArgumentType().equals(ArgumentType.NO_ARGUMENT)) {
        suppliedOptions.put(option,null);
        continue;
      }
      if (equalPos != -1) {
        String argument=(equalPos + 1 < nextArg.length()) ? nextArg.substring(equalPos + 1) : "String_Node_Str";
        suppliedOptions.put(option,argument);
        continue;
      }
      if (option.getArgumentType().equals(ArgumentType.REQUIRED_ARGUMENT)) {
        if (i + 1 < nargs) {
          String argument=args[i++];
          suppliedOptions.put(option,argument);
          continue;
        }
        throw new IllegalArgumentException("String_Node_Str");
      }
    }
 else {
      int shortSeqSize=nextArg.length();
      for (int j=1; j < shortSeqSize; j++) {
        char curChar=nextArg.charAt(j);
        Option option=programOptions.getShortOption(curChar);
        if (option == null) {
          throw new IllegalArgumentException("String_Node_Str" + curChar);
        }
        if (option.getArgumentType().equals(ArgumentType.NO_ARGUMENT)) {
          suppliedOptions.put(option,null);
          continue;
        }
        if (j < shortSeqSize) {
          String argument=nextArg.substring(j + 1);
          suppliedOptions.put(option,argument);
          continue;
        }
        if (option.getArgumentType().equals(ArgumentType.REQUIRED_ARGUMENT)) {
          if (i + 1 < nargs) {
            String argument=args[i++];
            suppliedOptions.put(option,argument);
            continue;
          }
          throw new IllegalArgumentException("String_Node_Str");
        }
      }
    }
  }
}

Fixed version (ground truth):
private void parse(){
  int nargs=args.length;
  int skip=0;
  for (int i=0; i < nargs; i+=1 + skip) {
    skip=0;
    String nextArg=args[i];
    if (nextArg.length() < 2 || nextArg.charAt(0) != '-') {
      nonOptionArgs.add(nextArg);
      continue;
    }
    if ("String_Node_Str".equals(nextArg)) {
      for (int j=i + 1; j < nargs; j++) {
        nonOptionArgs.add(args[j]);
      }
      return;
    }
    if (nextArg.charAt(1) == '-') {
      int equalPos=nextArg.indexOf('=');
      String flag=(equalPos != -1) ? nextArg.substring(2,equalPos) : nextArg.substring(2);
      List opts=programOptions.getLongOptions(flag);
      if (opts.size() == 0) {
        throw new IllegalArgumentException("String_Node_Str" + flag);
      }
      if (opts.size() > 1) {
        throw new IllegalArgumentException("String_Node_Str" + flag);
      }
      Option option=(Option)opts.get(0);
      if (option.getArgumentType().equals(ArgumentType.NO_ARGUMENT)) {
        suppliedOptions.put(option,null);
        continue;
      }
      if (equalPos != -1) {
        String argument=(equalPos + 1 < nextArg.length()) ? nextArg.substring(equalPos + 1) : "String_Node_Str";
        suppliedOptions.put(option,argument);
        continue;
      }
      if (option.getArgumentType().equals(ArgumentType.REQUIRED_ARGUMENT)) {
        if (i + 1 < nargs) {
          String argument=args[i];
          skip=1;
          suppliedOptions.put(option,argument);
          continue;
        }
        throw new IllegalArgumentException("String_Node_Str");
      }
    }
 else {
      int shortSeqSize=nextArg.length();
      for (int j=1; j < shortSeqSize; j++) {
        char curChar=nextArg.charAt(j);
        Option option=programOptions.getShortOption(curChar);
        if (option == null) {
          throw new IllegalArgumentException("String_Node_Str" + curChar);
        }
        if (option.getArgumentType().equals(ArgumentType.NO_ARGUMENT)) {
          suppliedOptions.put(option,null);
          continue;
        }
        if (j < shortSeqSize) {
          String argument=nextArg.substring(j + 1);
          suppliedOptions.put(option,argument);
          continue;
        }
        if (option.getArgumentType().equals(ArgumentType.REQUIRED_ARGUMENT)) {
          if (i + 1 < nargs) {
            String argument=args[i];
            skip=1;
            suppliedOptions.put(option,argument);
            continue;
          }
          throw new IllegalArgumentException("String_Node_Str");
        }
      }
    }
  }
}