Fix GH-746 - Loading config files order with APP_INSTANCE

[sgaestel]

This will fix the loading order when having different file extensions and working with APP_INSTANCE as well.
Instead of doing a forEach on basenames and extensions, then adding the APP_INSTANCE, the filename using the APP_INSTANCE is defined before going through all extensions, so that it is loaded after all extensions without the APP_INSTANCE being defined.

Did a console.log (that I removed) for the allowedFiles object when running the added test to show the difference:
Before the fix:

After the fix:

[lorenwest]

This looks really good. I'm surprised it took this long to discover - probably because mixed file types with instances isn't very common.

Thank you for finding, fixing, and writing the test! I'll bring it in and so some local testing, then push a new release with this asap.