It is important to understand the differences between your local and web context. Specific limitations are described here: http://msdn.microsoft.com/en-us/library/windows/apps/hh465373.aspx - it is worth noting that you can only include external script files from pages running in a web context.
In addition, your application should always have a top-level page that is in your package. This page should be in the local context and loaded via the ms-appx schema. This external page can select iframe pages loaded into the web context (via ms-appx-web for in-package files or via http / https for pages hosted on the Internet.)
What you should keep in mind is that even if you can upload an external script to the context web page, the script will not be able to access the Windows Runtime APIs. If you want your external script to be able to call WinRT, you can create a communication channel using the HTML5 Web Messaging API .
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