//Completely changing the book tree markup
function mskcc_preprocess_book_tree(&$variables) {

  //strings in need of insertion
  $replacementBeginning = '<li class="left-navigation__item"><a class="left-navigation__item__link" ';
  $replacementMiddle = '<span class="left-navigation__item__link__txt">';
  $replacementEnd = '</span><span class="arrow-right"></span></a></li>';

  //split up the block by link for easy loop through
  $tree_array = explode("\n", $variables['tree']);

  $tree_array_length = count($tree_array);
//reset tree for when markup will be placed back in
  $variables['tree'] = '';


  //loop through each link and replace the markup
  for ($i = 0; $i < $tree_array_length - 1; $i++) {

    $length = strpos( $tree_array[$i], "href");
    $tree_array[$i] = substr_replace($tree_array[$i], $replacementBeginning, 0, $length );
    $start = strpos ($tree_array[$i], "</a>");
    $tree_array[$i] = substr_replace($tree_array[$i], $replacementEnd, $start );

    //prep the individual links for insertion of the middle String ($replacementMiddle)
    $sub_tree_array = explode(">",  $tree_array[$i] );
    $sub_tree_array_length = count($sub_tree_array);

    $tree_array[$i] = '';
    for ($j = 0; $j < $sub_tree_array_length - 1; $j++) {

      $sub_tree_array[$j] = $sub_tree_array[$j] . ">";

     $tree_array[$i] = $tree_array[$i] . $sub_tree_array[$j];

      if ( $j == 1) {
        $tree_array[$i] = $tree_array[$i] . $replacementMiddle;
      }
    }

    //put everything back together
    $variables['tree'] = $variables['tree'] . "\n" . $tree_array[$i];
  }
}