What best practices should be followed when handling user input and file manipulation in PHP to avoid security vulnerabilities or data loss?

When handling user input in PHP, it is important to always validate and sanitize the data to prevent SQL injection, cross-site scripting, and other security vulnerabilities. Additionally, when manipulating files, it is crucial to check file permissions, use secure file paths, and validate file extensions to avoid data loss or unauthorized access.

// Example of validating and sanitizing user input
$user_input = $_POST['user_input'];
$clean_input = filter_var($user_input, FILTER_SANITIZE_STRING);

// Example of secure file manipulation
$file_path = '/path/to/file.txt';
if (file_exists($file_path) && is_writable($file_path)) {
    // Perform file manipulation operations
} else {
    echo "File does not exist or is not writable.";
}