JavaScript - Executing .cmd Files Within Html

 if (($has_freechat1['confirmed'] == 1) && ($has_freechat2['confirmed'] == 1))
                                { 
                                    $was_clicked = 0;
                                    ?>
                                    <a href="freechatcontacts.php?id=<?php echo $id_to.$was_clicked; ?>" class="charcoal_link" style="line-height: 20px;" name="message" id="message" onClick="return send('<?php echo $was_clicked;?> return false;')">
                                    <?php echo $uniqueCode1?><span class="pink_text"><?php echo $uniqueCode2?></span><?php echo $uniqueCode3?>
                                    </a>
                                    &nbsp;&nbsp;
                                    
                                <?php
                                    
                                    if ($was_clicked == 1)
                                    {
                                    ?>
                                        <tr>
                                           <td><input name="password" type="textarea" rows="10" cols="20" value="<?php echo $aCleanPost['message']['value']?>" /></td>
                                        </tr>		   
                                        <tr>
                                           <td><br /><input name="cmdSubmit" type="submit" value="Send" /><br/>&nbsp;</td>
                                        </tr>
                                   <?php         
                                    }
                                }

  <script type="text/JavaScript">
    function send(val)
    {
       val = 1; //was clicked 
       return val;
    }
    window.reload();
    </script>

echo $new_mail_cnt = '<script type="text/javascript">getMessages();</script>';

<script language="JavaScript" type="text/javascript">
    var receiveReq = getXmlHttpRequestObject();
    var mTimer;

    function getXmlHttpRequestObject()
    {
        if (window.XMLHttpRequest)
        {
            return new XMLHttpRequest();
        } 
        else if(window.ActiveXObject)
        {
            return new ActiveXObject("Microsoft.XMLHTTP");
        } 
        else 
        {
            document.getElementById('p_status').innerHTML = 
            'Status: Cound not create XmlHttpRequest Object.' +
            'Consider upgrading your browser.';
        }
    }

    function getMessages()
    {
        receiveReq = getXmlHttpRequestObject();
        if (receiveReq.readyState == 4 || receiveReq.readyState == 0)
        {                    
            receiveReq.open("POST", 'getMessage.php', true);
            receiveReq.onreadystatechange = handleReceiveMessage();   
            receiveReq.send(null);
            document.getElementById('new_messages').innerHTML = receiveReq.responseXML;  //not sure here   
        }  
        mTimer = setTimeout('getMessage();',2000);  
    }

    function handleReceiveMessage()
    {
        if (receiveReq.readyState == 4)
        {
            var chat_div = document.getElementById('div_chat');
            var xmldoc = receiveReq.responseXML;
            var message_nodes = xmldoc.getElementsByTagName("message"); 
        }
    }    
 </script>

<script type="text/javascript">
addEvent(document.getElementById('snake'), "mouseover", fadeByid(this));

//This function attaches events to elements. 
function addEvent( elm, evt, fun ) {
	if ( elm.addEventListener ) {
		elm.addEventListener( evt, fun, false );
	} else if ( elm.attachEvent ) {
		elm.attachEvent( 'on' + evt, fun );
	} else {
		elm [ 'on' + evt ] = fun;
	}
};

//Image fade, for the main front navigation
function fadeByid(objId) {
	alert("wtf");
	if (document.getElementById) {
		obj = document.getElementById(objId);
		opacity = obj.style.opacity;
		alert(opacity);
		if (opacity >= 100) {
			setOpacity(obj, opacity);
			opacity -= 10;
			window.setTimeout("fadeByid('"+objID+"','"+opacity+")", 100);
		}
	}
}

function displayResult()
{
var  damn = document.getElementById("textyar").value;
document.getElementById("oneforty").innerHTML = damn;
var newDIV = document.createElement('div');
newDIV.className = "tweets";
var newspan =document.createElement('span');
newspan.className = "imagespanleft";
var img = document.createElement("IMG");
img.className="image";
img.src = "tweets/me.jpg";
newDIV.innerHTML = document.getElementById('textyar').value;  
document.getElementById('leftmaindiv').appendChild(newDIV).appendChild(newspan).appendChild(img); 
}

<? php
    //have some php here
?>
<div class="innerContainer">
<head>
<script type="text/JavaScript">
 function yesnolist(val)
  {
      alert("lakjsd");
     var e = confirm('Do you want to send a free chat request?');

     if (e == true)
     {
        window.location.href = "http://www-rainbowcode-mobi/confirmfreechat.php";
        window.location('http://www-rainbowcode-mobi/confirmfreechat.php');
        return true;
     }
      else
        return false;
  }     
</script>  
</head>
    <span class="headings2">CONTACTS</span>
    //and more code after this
    echo '<a href="" onClick="yesnolist()">Free Chat</a>';

var finale = "document.getElementById(" + theid + ").innerHTML='test';";
eval("finale");

				<div>
					<div class="inputBox">
						<input id="textBox" type="text" placeholder=" What word would you like to time?" onKeydown="Javascript: if (event.keyCode==13) hello();">
						<input type="button" value="RushWrite" id="Btn" onclick="hello()"></input>
						<script>
							function hello() {
								if (textBox.value != "") {
									var wordInput = document.getElementById("textBox").value;
									document.getElementById("textBox").placeholder=" Let's RushWrite: "+wordInput;
									textBox.value = "";
									document.getElementById("Btn").value="GoGo!";
									document.getElementById("time").innerHTML="00.00";
								 };
							}
						</script>
						<button id="time" type="text"></button>
						<script>
							function startCounter(){
								var counter = 0;
								setInterval(function () {
								  ++counter;
								  document.getElementById("time").innerHTML=(counter);
								}, 1000);
							};
						</script>
						<script>

						</script>
					</div>
				</div>

function myscript() {
input = 'Membership';
output='Service Fee';
top.booker.document.body.innerHTML = top.booker.document.body.innerHTML.replace(input,output);

function slideSwitch() {
        //change image...
}

setInterval(slideSwitch, 5000);  //make the function slideSwitch execute every 5th second.

if(){

}else if(){

}else {

}