This is how I solved it
First of all make sure your glossaries are working within the moodle, i.e all the setting are correct (lots of posts here to this effect including Chiang Sabrinas' above). ie must be switched on, global glossaries etc.
Your external stuff, must be a php file rather than straight HTML as it has to run a couple of things past moodle.
At the top of your php file include the line
where "the_path" is the route from your files to the main config.php
gather all your page in a variable say $b
the run it through the following function
then something like
to put it on the screen.
I hope this works for you as well feel free to get back to me if I have not explained properly