gistfile1.php

 <?php
  $dom = new \DOMDocument('1.0', 'UTF-8');
  // PHP will output warnings about non-standard HTML. Suppress it by "@".
  @$dom->loadHTML($source);

  // Iterate over all link-elements.
  foreach ($dom->getElementsByTagName('link') as $node) {
    // Copy the element to be able to replace it.
    $updated_element = $node;
    $href_value = $updated_element->getAttribute( 'href' );
    // Checks if the value contains a standard violating character.
    if (is_int(strpos($href_value, ']=within'))) {
      // Encodes the URL to valid href value.
      $href_value = drupal_urlencode($href_value);
      $updated_element->setAttribute('href', $href_value);

      // Replace the wrong html markup.
      $node->parentNode->replaceChild($updated_element, $node);
    }
  }

  // Get the HTML markup.
  $html_markup_with_wrappers = $dom->saveHtml();
  // Remove the unnecessary wrappers.
  $my_html_markup = preg_replace('~<(?:!DOCTYPE|/?(?:html|head|body))[^>]*>\s*~i', '',
    $html_markup_with_wrappers);