I've tried changing the order of elements in the json file, combining the third-party libs into one file and all manner of other options.
As soon as the system/app has been compiled, third-party libs cease to be seen by the app. However, the libs are loaded as if there is a syntax error in the files, webkit will output an error and the app may even stop working.
That's why I'm totally confused. WebKit loads the files but the app cannot see their contents.