So I got around the issue by including my plugin/module as a dependancy rather than part of the application.
Since it's a good idea to have a main config file for your app, I told r.js
to use this but then spoofed the URL for my plugin/module to the special empty:
value.
This then stopped r.js
trying to find all the dependancies of the already optimised plugin/module and allowed me to include it as a dependancy; all is now well.