When I use pgp require it moves the head content on the included file into the body tags, I've explored questions somewhat related to my problem but none have solved my problem.
index.php:
<!DOCTYPE html>
<html>
<head></head>
<body></body>
</html>
<?php
require '/home/sethfreeman/public_html/subdomains/gwd/navigation/header/header.html';
?>
Included File:
<!DOCTYPE html>
<html lang="en">
<head>
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<link rel="stylesheet" href="http://sethjfreeman.com/subdomains/gwd/assets/css/header.css" type="text/css">
<link rel="stylesheet" href="http://sethjfreeman.com/subdomains/gwd/assets/libs/bootstrap/css/bootstrap.css" media="screen">
<link rel="stylesheet" href="http://sethjfreeman.com/subdomains/gwd/assets/libs/bootstrap/css/bootstrap-responsive.css" media="screen">
</head>
<body>
<div class="container"></div>
<script src="http://sethjfreeman.com/subdomains/gwd/assets/js/jquery-3.1.1.js"></script>
<script src="http://sethjfreeman.com/subdomains/gwd/assets/libs/bootstrap/js/bootstrap.min.js"></script>
</body>
</html>
Chrome Output:
<!DOCTYPE html>
<html lang="en">
<head></head>
<body>
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<link rel="stylesheet" href="http://sethjfreeman.com/subdomains/gwd/assets/css/header.css" type="text/css">
<link rel="stylesheet" href="http://sethjfreeman.com/subdomains/gwd/assets/libs/bootstrap/css/bootstrap.css" media="screen">
<link rel="stylesheet" href="http://sethjfreeman.com/subdomains/gwd/assets/libs/bootstrap/css/bootstrap-responsive.css" media="screen">
<div class="container"></div>
<script src="http://sethjfreeman.com/subdomains/gwd/assets/js/jquery-3.1.1.js"></script>
<script src="http://sethjfreeman.com/subdomains/gwd/assets/libs/bootstrap/js/bootstrap.min.js"></script>
</body>
</html>
"Require isn't smart. It's simply going to dump the contents of the required file where it's invoked. If you want some code in the head portion, put that in a separate file and require it in the correct place." - Major Productions LLC
To close this question.