Two functions to help:
<?php
function add_include_path ($path)
{
    foreach (func_get_args() AS $path)
    {
        if (!file_exists($path) OR (file_exists($path) && filetype($path) !== 'dir'))
        {
            trigger_error("Include path '{$path}' not exists", E_USER_WARNING);
            continue;
        }
        
        $paths = explode(PATH_SEPARATOR, get_include_path());
        
        if (array_search($path, $paths) === false)
            array_push($paths, $path);
        
        set_include_path(implode(PATH_SEPARATOR, $paths));
    }
}
function remove_include_path ($path)
{
    foreach (func_get_args() AS $path)
    {
        $paths = explode(PATH_SEPARATOR, get_include_path());
        
        if (($k = array_search($path, $paths)) !== false)
            unset($paths[$k]);
        else
            continue;
        
        if (!count($paths))
        {
            trigger_error("Include path '{$path}' can not be removed because it is the only", E_USER_NOTICE);
            continue;
        }
        
        set_include_path(implode(PATH_SEPARATOR, $paths));
    }
}
?>