Program: 5742
Project: 5742
Buggy source:
private void registerCommands(){
  registerCommand("String_Node_Str",new BasicCommand("String_Node_Str","String_Node_Str"){
    public int executeCommand(    CommandContext context){
      if (context.getArgumentCount() == 0) {
        context.out.println("String_Node_Str");
        for (        Map.Entry<String,Command> entry : commands.entrySet()) {
          String name=entry.getKey();
          Command command=entry.getValue();
          String helpText=command.getCommandHelp(name);
          if (helpText != null) {
            String argHelp=command.getArgumentHelp(name);
            String prefix=argHelp != null ? (' ' + name + ' '+ argHelp) : (' ' + name);
            int n;
            if (helpText != null && (n=helpText.indexOf('\n')) > 0) {
              helpText=helpText.substring(0,n);
            }
            context.out.print(prefix);
            if (prefix.length() < 8) {
              context.out.print('\t');
            }
            if (prefix.length() < 16) {
              context.out.print('\t');
            }
            context.out.println("String_Node_Str" + helpText);
          }
        }
        return 0;
      }
      String cmd=context.getArgument(0);
      Command command=commands.get(cmd);
      if (command != null) {
        String helpText=command.getCommandHelp(cmd);
        String argHelp=command.getArgumentHelp(cmd);
        context.out.print(cmd);
        if (argHelp != null) {
          context.out.print(' ' + argHelp);
        }
        context.out.println();
        if (helpText != null && helpText.length() > 0) {
          context.out.println("String_Node_Str" + helpText);
        }
        return 0;
      }
      context.err.println("String_Node_Str" + cmd + '\'');
      return 1;
    }
  }
);
  registerCommand("String_Node_Str",new BasicCommand("String_Node_Str","String_Node_Str"){
    public int executeCommand(    CommandContext context){
      workaround=true;
      return 0;
    }
  }
);
  registerCommand("String_Node_Str",new BasicCommand("String_Node_Str","String_Node_Str"){
    public int executeCommand(    CommandContext context){
      for (int i=0; i < currentAsyncCommands.size(); i++) {
        CommandContext cmd=currentAsyncCommands.get(i)[0];
        context.out.println("String_Node_Str" + cmd);
      }
      return 0;
    }
  }
);
  registerCommand("String_Node_Str",new BasicCommand("String_Node_Str","String_Node_Str"){
    public int executeCommand(    CommandContext context){
      int pid=context.getArgumentAsInt(0);
      removePid(pid);
      return 0;
    }
  }
);
}

Fixed version (ground truth):
private void registerCommands(){
  registerCommand("String_Node_Str",new BasicCommand("String_Node_Str","String_Node_Str"){
    public int executeCommand(    CommandContext context){
      if (context.getArgumentCount() == 0) {
        context.out.println("String_Node_Str");
        for (        Map.Entry<String,Command> entry : commands.entrySet()) {
          String name=entry.getKey();
          Command command=entry.getValue();
          String helpText=command.getCommandHelp(name);
          if (helpText != null) {
            String argHelp=command.getArgumentHelp(name);
            String prefix=argHelp != null ? (' ' + name + ' '+ argHelp) : (' ' + name);
            int n;
            if ((n=helpText.indexOf('\n')) > 0) {
              helpText=helpText.substring(0,n);
            }
            context.out.print(prefix);
            if (prefix.length() < 8) {
              context.out.print('\t');
            }
            if (prefix.length() < 16) {
              context.out.print('\t');
            }
            context.out.println("String_Node_Str" + helpText);
          }
        }
        return 0;
      }
      String cmd=context.getArgument(0);
      Command command=commands.get(cmd);
      if (command != null) {
        String helpText=command.getCommandHelp(cmd);
        String argHelp=command.getArgumentHelp(cmd);
        context.out.print(cmd);
        if (argHelp != null && argHelp.length() > 0) {
          context.out.print(' ' + argHelp);
        }
        context.out.println();
        if (helpText != null && helpText.length() > 0) {
          context.out.println("String_Node_Str" + helpText);
        }
        return 0;
      }
      context.err.println("String_Node_Str" + cmd + '\'');
      return 1;
    }
  }
);
  registerCommand("String_Node_Str",new BasicCommand("String_Node_Str","String_Node_Str"){
    public int executeCommand(    CommandContext context){
      workaround=true;
      return 0;
    }
  }
);
  registerCommand("String_Node_Str",new BasicCommand("String_Node_Str","String_Node_Str"){
    public int executeCommand(    CommandContext context){
      for (int i=0; i < currentAsyncCommands.size(); i++) {
        CommandContext cmd=currentAsyncCommands.get(i)[0];
        context.out.println("String_Node_Str" + cmd);
      }
      return 0;
    }
  }
);
  registerCommand("String_Node_Str",new BasicCommand("String_Node_Str","String_Node_Str"){
    public int executeCommand(    CommandContext context){
      int pid=context.getArgumentAsInt(0);
      if (removePid(pid)) {
        return 0;
      }
      context.err.println("String_Node_Str");
      return 1;
    }
  }
);
}