You are better off referencing your assets relative to a known point on your site.
There are several techniques for this... like:
Use the document root as your starting point
include ($_SERVER["DOCUMENT_ROOT"] . "/includes/myfunctions.php");
or set up a constant
define("APP_ROOT", $_SERVER["DOCUMENT_ROOT"]);
or even in a .htaccess file
SetEnv APP_ROOT "/path/to/myroot";
For URL based includes (js /css/ hrefs)
Always use absolute paths when referring to assets on your site (beginning with a /) except for images and fonts loaded from within a css file, those can be loaded relative to the css file.