Program: 42322
Project: 42322
Buggy source:
@Override public int run(List<XValue> args) throws Exception {
  Options opts=new Options("String_Node_Str",SerializeOpts.getOptionDefs());
  opts.parse(args);
  String optdef=opts.getOptString("String_Node_Str",null);
  String passthrough=opts.getOptString("String_Node_Str",null);
  String ignore=opts.getOptString("String_Node_Str",null);
  boolean bSerialize=opts.getOptFlag("String_Node_Str",true);
  boolean bPassSerialize=opts.getOptFlag("String_Node_Str",true);
  boolean bArgIndex=opts.hasOpt("String_Node_Str");
  args=opts.getRemainingArgs();
  if (optdef == null) {
    if (args.size() == 0) {
      usage();
      return 1;
    }
    if (passthrough != null)     optdef=passthrough;
 else     optdef=args.remove(0).toString();
  }
  boolean bNoArgs=opts.hasOpt("String_Node_Str");
  boolean bNoValues=opts.hasOpt("String_Node_Str");
  List<OptionDef> ignore_opts=null;
  Options prog_opts=new Options(optdef,bSerialize ? SerializeOpts.getOptionDefs() : null);
  if (ignore != null)   ignore_opts=prog_opts.addOptionDefs(ignore);
  if (passthrough != null && passthrough != optdef)   prog_opts.addOptionDefs(passthrough);
  List<OptionValue> prog_optvalues=prog_opts.parse(args);
  SerializeOpts serializeOpts=this.getSerializeOpts(opts);
  List<XValue> remaining_args=prog_opts.getRemainingArgs();
  int arg_index=remaining_args.isEmpty() ? args.size() : args.indexOf(remaining_args.get(0));
  if (passthrough == null)   writeOptions(opts,bNoArgs,bNoValues,prog_opts,prog_optvalues,ignore_opts);
 else {
    OutputPort stdout=getStdout();
    IXdmValueOutputStream out=stdout.asXdmValueOutputStream(serializeOpts);
    Options pass_opts=new Options(passthrough,bPassSerialize ? SerializeOpts.getOptionDefs() : null);
    List<OptionDef> pass_optdefs=pass_opts.getOptDefs();
    for (    OptionDef def : pass_optdefs) {
      OptionValue value=prog_opts.getOpt(def.name);
      if (value != null) {
        writeOption(stdout,serializeOpts,out,value);
      }
    }
    stdout.writeSequenceTerminator(serializeOpts);
    stdout.release();
  }
  return bArgIndex ? arg_index : 0;
}

Fixed version (ground truth):
@Override public int run(List<XValue> args) throws Exception {
  Options opts=new Options("String_Node_Str",SerializeOpts.getOptionDefs());
  opts.parse(args);
  String optdef=opts.getOptString("String_Node_Str",null);
  String passthrough=opts.getOptString("String_Node_Str",null);
  String ignore=opts.getOptString("String_Node_Str",null);
  boolean bSerialize=opts.getOptFlag("String_Node_Str",true);
  boolean bPassSerialize=opts.getOptFlag("String_Node_Str",true);
  boolean bArgIndex=opts.hasOpt("String_Node_Str");
  args=opts.getRemainingArgs();
  if (optdef == null) {
    if (passthrough != null)     optdef=passthrough;
 else {
      if (args.size() == 0) {
        usage();
        return 1;
      }
      optdef=args.remove(0).toString();
    }
  }
  boolean bNoArgs=opts.hasOpt("String_Node_Str");
  boolean bNoValues=opts.hasOpt("String_Node_Str");
  List<OptionDef> ignore_opts=null;
  Options prog_opts=new Options(optdef,bSerialize ? SerializeOpts.getOptionDefs() : null);
  if (ignore != null)   ignore_opts=prog_opts.addOptionDefs(ignore);
  if (passthrough != null && passthrough != optdef)   prog_opts.addOptionDefs(passthrough);
  List<OptionValue> prog_optvalues=prog_opts.parse(args);
  SerializeOpts serializeOpts=this.getSerializeOpts(opts);
  List<XValue> remaining_args=prog_opts.getRemainingArgs();
  int arg_index=remaining_args.isEmpty() ? args.size() : args.indexOf(remaining_args.get(0));
  if (passthrough == null)   writeOptions(opts,bNoArgs,bNoValues,prog_opts,prog_optvalues,ignore_opts);
 else {
    OutputPort stdout=getStdout();
    IXdmValueOutputStream out=stdout.asXdmValueOutputStream(serializeOpts);
    Options pass_opts=new Options(passthrough,bPassSerialize ? SerializeOpts.getOptionDefs() : null);
    List<OptionDef> pass_optdefs=pass_opts.getOptDefs();
    for (    OptionDef def : pass_optdefs) {
      OptionValue value=prog_opts.getOpt(def.name);
      if (value != null) {
        writeOption(stdout,serializeOpts,out,value);
      }
    }
    stdout.writeSequenceTerminator(serializeOpts);
    stdout.release();
  }
  return bArgIndex ? arg_index : 0;
}