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I created a 'server' directory next to public_html and in case I needed to add to it, designated a codeigniter directory within containing all the codeigniter files.
Then I found adding this useful in index.php:
Code:
define("CI_ROOT", rtrim($_SERVER["DOCUMENT_ROOT"], "/public_html") . "/server/codeigniter");
then for example in Pages:
Code:
if (!file_exists(CI_ROOT . '/application/views/pages/' . $page . '.php')) {