Program: 42321
Project: 42321
Buggy source:
public int run(List<XValue> args) throws Exception {
  Options opts=new Options("String_Node_Str");
  opts.parse(args);
  Shell shell=getShell();
  if (!mTopShell)   shell=shell.clone();
  int ret=0;
  try {
    if (opts.hasOpt("String_Node_Str"))     shell.setOption("String_Node_Str",true);
    if (opts.hasOpt("String_Node_Str"))     shell.setOption("String_Node_Str",true);
    if (opts.hasOpt("String_Node_Str"))     shell.setOption("String_Node_Str",true);
    String command=null;
    if (opts.hasOpt("String_Node_Str"))     command=opts.getOptStringRequired("String_Node_Str").toString();
    args=opts.getRemainingArgs();
    if (args.size() == 0 && command == null) {
      String rcfile=opts.getOptString("String_Node_Str",null);
      if (rcfile == null) {
        XValue home=shell.getEnv().getVarValue("String_Node_Str");
        if (home != null) {
          rcfile=home.toString() + "String_Node_Str";
        }
      }
      ret=shell.interactive(rcfile);
    }
 else {
      if (command != null) {
        Command cmd=new EvalScriptCommand(command);
        ret=shell.exec(cmd);
      }
 else {
        String scmd=args.remove(0).toString();
        ICommand cmd=CommandFactory.getInstance().getScript(shell,scmd,true,getLocation());
        if (cmd == null) {
          SourceLocation loc=getLocation();
          if (loc != null)           shell.printErr(loc.toString());
          shell.printErr(scmd + "String_Node_Str");
        }
 else {
          shell.setArg0(scmd);
          shell.setArgs(args);
          ret=cmd.run(shell,scmd,null);
        }
      }
    }
  }
  finally {
    if (!mTopShell)     shell.close();
  }
  return ret;
}

Fixed version (ground truth):
public int run(List<XValue> args) throws Exception {
  Options opts=new Options("String_Node_Str");
  opts.parse(args);
  Shell shell=getShell();
  if (!mTopShell)   shell=shell.clone();
  int ret=0;
  try {
    if (opts.hasOpt("String_Node_Str"))     shell.setOption("String_Node_Str",true);
    if (opts.hasOpt("String_Node_Str"))     shell.setOption("String_Node_Str",true);
    if (opts.hasOpt("String_Node_Str"))     shell.setOption("String_Node_Str",true);
    String command=null;
    if (opts.hasOpt("String_Node_Str"))     command=opts.getOptStringRequired("String_Node_Str").toString();
    boolean bNoRc=opts.hasOpt("String_Node_Str");
    args=opts.getRemainingArgs();
    if (args.size() == 0 && command == null) {
      String rcfile=opts.getOptString("String_Node_Str",null);
      if (rcfile == null) {
        XValue home=shell.getEnv().getVarValue("String_Node_Str");
        if (home != null) {
          rcfile=home.toString() + "String_Node_Str";
        }
      }
      ret=shell.interactive(bNoRc ? null : rcfile);
    }
 else {
      if (command != null) {
        Command cmd=new EvalScriptCommand(command);
        ret=shell.exec(cmd);
      }
 else {
        String scmd=args.remove(0).toString();
        ICommand cmd=CommandFactory.getInstance().getScript(shell,scmd,true,getLocation());
        if (cmd == null) {
          SourceLocation loc=getLocation();
          if (loc != null)           shell.printErr(loc.toString());
          shell.printErr(scmd + "String_Node_Str");
        }
 else {
          shell.setArg0(scmd);
          shell.setArgs(args);
          ret=cmd.run(shell,scmd,null);
        }
      }
    }
  }
  finally {
    if (!mTopShell)     shell.close();
  }
  return ret;
}