Program: 89200
Project: 89200
Buggy source:
protected void processRequest(final Request request,final Link link){
  boolean requestLogged=false;
  Response response=null;
  try {
    final Command[] cmds=request.getCommands();
    final Answer[] answers=new Answer[cmds.length];
    for (int i=0; i < cmds.length; i++) {
      final Command cmd=cmds[i];
      Answer answer;
      try {
        if (s_logger.isDebugEnabled()) {
          if ((cmd instanceof ModifySshKeysCommand)) {
            s_logger.debug("String_Node_Str");
          }
 else {
            if (!requestLogged) {
              s_logger.debug("String_Node_Str" + request.toString());
              requestLogged=true;
            }
          }
          s_logger.debug("String_Node_Str" + cmd.toString());
        }
        if (cmd instanceof CronCommand) {
          final CronCommand watch=(CronCommand)cmd;
          scheduleWatch(link,request,watch.getInterval() * 1000,watch.getInterval() * 1000);
          answer=new Answer(cmd,true,null);
        }
 else         if (cmd instanceof UpgradeCommand) {
          final UpgradeCommand upgrade=(UpgradeCommand)cmd;
          answer=upgradeAgent(upgrade.getUpgradeUrl(),upgrade);
        }
 else         if (cmd instanceof ShutdownCommand) {
          ShutdownCommand shutdown=(ShutdownCommand)cmd;
          s_logger.debug("String_Node_Str" + shutdown.getReason());
          cancelTasks();
          _reconnectAllowed=false;
          answer=new Answer(cmd,true,null);
        }
 else         if (cmd instanceof AgentControlCommand) {
          answer=null;
synchronized (_controlListeners) {
            for (            IAgentControlListener listener : _controlListeners) {
              answer=listener.processControlRequest(request,(AgentControlCommand)cmd);
              if (answer != null) {
                break;
              }
            }
          }
          if (answer == null) {
            s_logger.warn("String_Node_Str" + cmd.toString());
            answer=new AgentControlAnswer(cmd);
          }
        }
 else {
          _inProgress.incrementAndGet();
          try {
            answer=_resource.executeRequest(cmd);
          }
  finally {
            _inProgress.decrementAndGet();
          }
          if (answer == null) {
            s_logger.debug("String_Node_Str" + cmd.toString());
            answer=Answer.createUnsupportedCommandAnswer(cmd);
          }
        }
      }
 catch (      final Throwable th) {
        s_logger.warn("String_Node_Str",th);
        final StringWriter writer=new StringWriter();
        th.printStackTrace(new PrintWriter(writer));
        answer=new Answer(cmd,false,writer.toString());
      }
      answers[i]=answer;
      if (!answer.getResult() && request.stopOnError()) {
        for (i++; i < cmds.length; i++) {
          answers[i]=new Answer(cmds[i],false,"String_Node_Str");
        }
        break;
      }
    }
    response=new Response(request,answers);
  }
  finally {
    if (s_logger.isDebugEnabled()) {
      s_logger.debug(response != null ? response.toString() : "String_Node_Str");
    }
    if (response != null) {
      try {
        link.send(response.toBytes());
      }
 catch (      final ClosedChannelException e) {
        s_logger.warn("String_Node_Str" + response.toString());
      }
    }
  }
}

Fixed version (ground truth):
protected void processRequest(final Request request,final Link link){
  boolean requestLogged=false;
  Response response=null;
  try {
    final Command[] cmds=request.getCommands();
    final Answer[] answers=new Answer[cmds.length];
    for (int i=0; i < cmds.length; i++) {
      final Command cmd=cmds[i];
      Answer answer;
      try {
        if (s_logger.isDebugEnabled()) {
          if ((cmd instanceof ModifySshKeysCommand)) {
            s_logger.debug("String_Node_Str");
          }
 else {
            if (!requestLogged) {
              s_logger.debug("String_Node_Str" + request.toString());
              requestLogged=true;
            }
          }
          s_logger.debug("String_Node_Str" + cmd.toString());
        }
        if (cmd instanceof CronCommand) {
          final CronCommand watch=(CronCommand)cmd;
          scheduleWatch(link,request,watch.getInterval() * 1000,watch.getInterval() * 1000);
          answer=new Answer(cmd,true,null);
        }
 else         if (cmd instanceof UpgradeCommand) {
          final UpgradeCommand upgrade=(UpgradeCommand)cmd;
          answer=upgradeAgent(upgrade.getUpgradeUrl(),upgrade);
        }
 else         if (cmd instanceof ShutdownCommand) {
          ShutdownCommand shutdown=(ShutdownCommand)cmd;
          s_logger.debug("String_Node_Str" + shutdown.getReason());
          cancelTasks();
          _reconnectAllowed=false;
          answer=new Answer(cmd,true,null);
        }
 else         if (cmd instanceof MaintainCommand) {
          s_logger.debug("String_Node_Str");
          cancelTasks();
          _reconnectAllowed=false;
          answer=new MaintainAnswer((MaintainCommand)cmd);
        }
 else         if (cmd instanceof AgentControlCommand) {
          answer=null;
synchronized (_controlListeners) {
            for (            IAgentControlListener listener : _controlListeners) {
              answer=listener.processControlRequest(request,(AgentControlCommand)cmd);
              if (answer != null) {
                break;
              }
            }
          }
          if (answer == null) {
            s_logger.warn("String_Node_Str" + cmd.toString());
            answer=new AgentControlAnswer(cmd);
          }
        }
 else {
          _inProgress.incrementAndGet();
          try {
            answer=_resource.executeRequest(cmd);
          }
  finally {
            _inProgress.decrementAndGet();
          }
          if (answer == null) {
            s_logger.debug("String_Node_Str" + cmd.toString());
            answer=Answer.createUnsupportedCommandAnswer(cmd);
          }
        }
      }
 catch (      final Throwable th) {
        s_logger.warn("String_Node_Str",th);
        final StringWriter writer=new StringWriter();
        th.printStackTrace(new PrintWriter(writer));
        answer=new Answer(cmd,false,writer.toString());
      }
      answers[i]=answer;
      if (!answer.getResult() && request.stopOnError()) {
        for (i++; i < cmds.length; i++) {
          answers[i]=new Answer(cmds[i],false,"String_Node_Str");
        }
        break;
      }
    }
    response=new Response(request,answers);
  }
  finally {
    if (s_logger.isDebugEnabled()) {
      s_logger.debug(response != null ? response.toString() : "String_Node_Str");
    }
    if (response != null) {
      try {
        link.send(response.toBytes());
      }
 catch (      final ClosedChannelException e) {
        s_logger.warn("String_Node_Str" + response.toString());
      }
    }
  }
}