I am working on a bootstrap and php , i am using jquery to add animation to and hover effects, i added scriptwith other scripts files in footer , but due to this file my php login code stop working ,i remove it and my code start working but hover effect on my thumbnails vanished, i only added login functionality yet . when i remove jquery-latest.min link from my code , thumbnails having hover animation stop working but php code works fine , how can i remove this conflict from my code ?? i am adding these as header and footer. In short both codes are fine but not working with each other.
    <!DOCTYPE html>
    <html lang="en">
    <head>
        <meta charset="utf-8">
        <meta http-equiv="X-UA-Compatible" content="IE=edge">
        <meta name="viewport" content="width=device-width, initial-scale=1">
        <meta name="description" content="Bootstrap 3 Tutorial from auto-hire.com">
        <meta name="author" content="BootstrapBay.com">
        <title>Auto Hire Edge</title>
        <link href="css/bootstrap.min.css" rel="stylesheet">
        <link href="css/custom.css" rel="stylesheet">
        <link href="css/screen.css" rel="stylesheet">
         <script src="js/respond.js"></script>
        <link href="js/bootstrap.js" rel="javascript">
        <link href="http://netdna.bootstrapcdn.com/font-awesome/4.0.3/css/font-awesome.css" rel="stylesheet">
        <link href='http://fonts.googleapis.com/css?family=Open+Sans' rel='stylesheet' type='text/css'>
        <link href='http://fonts.googleapis.com/css?family=Oswald' rel='stylesheet' type='text/css'>
      </head>
      <body>
    this is footer , it has latest jquery link , wherever i added this , my php code stop working , buttons seem to un clickable
     <!-- Fixed footer -->
        <div class="navbar navbar-default " role="navigation">
            <div class="navbar-text pull-left">
              <p>© 2015 AutoHireEdge.</p>
            </div>
            <div class="navbar-text pull-right">
              <a href="#"><i class="fa fa-facebook-square fa-2x"></i></a>
              <a href="#"><i class="fa fa-twitter fa-2x"></i></a>
              <a href="#"><i class="fa fa-google-plus fa-2x"></i></a>
            </div>
        </div>
          <script src="http://code.jquery.com/jquery-latest.min.js"></script>
            <script src="js/bootstrap.min.js"></script>
            <script src="js/bootstrap.js"></script>
            <!-- Menu Toggle Script -->
        <script>
        $("#menu-toggle").click(function(e) {
            e.preventDefault();
            $("#wrapper").toggleClass("toggled");
        });
        </script>
      </div><!--container-->
    </body>
    </html>
    Here is my thumbnail code:it only work due to jquery latest.min file , added above in footer , if i remove that , hover effevt vanished
       <div class="container">
       <div class="container">
    <!---------------------------->
    <div class="text-center">
      <label class="row">Features</label>
        <h1><strong>Auto Hire Edge</strong></h1>
        </div>
           <!--thumbnail-1---->
        <ul class="thumbnails" id="hover-cap-4col">
          <li class="span3">
            <div class="thumbnail">
             <div class="caption">
               <h1>Tap To Register</h1>
               <p><a href="#" class="btn btn-inverse" rel="tooltip" title="Preview"><i class="icon-eye-open"></i></a> <a href="#" rel="tooltip" title="Visit Website" class="btn btn-inverse"><i class="icon-share"></i></a></p>
              </div>
               <img src="images/img-thum1.jpg" alt=""> 
             </div>
        </li>
     </ul>
     </div>
    </div><!-- /.container -->
this is working fine , but when i add php functionality , it stop working with each other: here is my php files of code
<html>
<?php
    include 'core/init.php';
    include 'includes/head.php';
    include 'includes/aside.php';
    if(empty($_POST)===false)
    {
        $username= $_POST['username'];
        $password= $_POST['password'];
        if(empty($username)===true || empty($password)===true) {
            $errors[]='you need to enter user name and passwords';
        } 
        //check user exists or nots
        else if(user_exists($username)===false){
            $errors[]='we cant find the user with this name. have u registered?';
        }
        else if(user_active($username)===false){
            $errors[]='you haven\' t activated your account yet';
        }else{
            //check for string length
            if(strlen($password)  >32)
            {
                $errors[]='password is too long';
            }
            $login=login($username,$password);
                 if($login===false){
                $errors='this combination is false';
            }
            else
            {
                //set sessions
                $_SESSION['user_id']=$login;
                //redirect to home page
                header('Location:index.php');//redirects to home page with logged inn
                exit();
            }
         }
    }
    else
    {
        $errors[]='no data received';
    }
    include 'includes/header.php';
    if(empty($errors)===false){
        ?>
        <h2>we tried you to login but...</h2>
        <?php
        echo output_errors($errors);
    }
    include'includes/footer.php';
    ?>
    </html>
file 2: loggedin
<!--added to index.php-->
<div id="wrapper">
<div class="navbar navbar-default navbar-fixed-top pull-right ">
    <a href="#menu-toggle" class="btn btn-primary btn-lg " id="menu-toggle" ><span class="glyphicon glyphicon-tasks"></span>Menu </a>
    <img src="images/logo.png" alt="auto-hire-edge">
        <div class="loginbutton">
             <li> <h4> <?php echo $user_data['first_name']; ?> </h4></li>
             <li><button class="btn btn-sm"><a href="logout.php">Logout</a></button></li>
             <li><a href="register.php">Register</a></li>
        </div>
       <!----includes menu list ----->
    </div>
</div>
<?php include 'includes/overall/head.php'; ?>
<?php include 'core/init.php'; ?>
<?php //include 'includes/header.php'; ?>
<?php include 'includes/aside.php';
      include 'includes/slider.php';
      include 'includes/customer-thumbs.php';
?>
<?php
      include 'includes/footer.php';
?>
         <div id="wrapper">
         <div class="navbar navbar-default navbar-fixed-top pull-right ">
         <a href="#menu-toggle" class="btn btn-primary btn-lg " id="menu-toggle" ><span class="glyphicon glyphicon-tasks"></span>Menu </a>
              <img src="images/logo.png" alt="auto-hire-edge">
              <div class="loginbutton">
                  <form  action="login.php" method="post" >
                     <ul id="login">    
                      <li><input type="text" name="username"  placeholder="Username" ></li>
                      <li><input type="password" name="password"  placeholder="Password"></li>
                     <li><button type="submit" class="btn btn-sm" id="submit">Login</button></li>
                     <li><a href="register.php">Register</a></li>
                     </ul>
                </form> 
             </div>
             <!----includes menu list ------>
         </div>
     </div>
 
    