What are some best practices for separating HTML, CSS, and PHP code to avoid issues with formatting and variable values?

To avoid issues with formatting and variable values when separating HTML, CSS, and PHP code, it is best practice to use a templating system like PHP's built-in `include` function or a more robust templating engine like Twig. This allows you to keep your HTML, CSS, and PHP code separate in different files, making it easier to maintain and update. Additionally, using proper naming conventions for variables and functions can help prevent conflicts and ensure clarity in your code.

<?php
// index.php

$variable = "Hello, World!";

include 'header.php';
?>
<!DOCTYPE html>
<html>
<head>
    <link rel="stylesheet" type="text/css" href="styles.css">
</head>
<body>
    <h1><?php echo $variable; ?></h1>
</body>
</html>

<?php
include 'footer.php';
?>