I would recommend using a constant with an absolute base path, like so:
(in your front-end files)
Code:
// index.php
define('ROOT_PATH', dirname(__FILE__));
// [...]
include ROOT_PATH . '/includes/mydirectory/myfile.php';
(deeper inside your application, front-end file in a subdirectory)
Code:
// subdirectory/index.php
define('ROOT_PATH', dirname(dirname(__FILE__)));
// [...]
include ROOT_PATH . '/includes/mydirectory/myfile.php';
You can also use that deeper in your code to maintain clear and understandable include paths, as well. Since all includes would be from the perspective of your forward-facing files, it'd mimic the behavior of using the include_path while still allowing yourself adaptability. To maintain your root path, just adjust your constant delcaration (and instead of using .. in the root path, use
dirname to go up a directory in the string)