Sencha CMD 4 app.js script creation issue

I am having an issue with the app.js file that is output as a result of the build process. The app.js file that is produced has the content of my config.js file in a location that is after where it needs to be and this results in script errors when it executes in a browser. How can I make sure that the contents of the config.js file are included correctly by Sencha CMD? I am using 4.2 of EXTJS with Sencha CMD 4.

I have reviewed the Sencha CMD documentation but it is not clear to me how this script creation process actually is intended to work and how I can control it through configuration files. Any help is greatly appreciated.

Here is the compile block that is part of my index.html file.

<!-- <x-compile> -->

<!-- <x-bootstrap> -->

<script src="ext/ext-dev.js"></script>

<script src="bootstrap.js"></script>

<!-- </x-bootstrap> -->

<script type="text/javascript" src="app/config.js"></script>

<script type="text/javascript" src="app.js"></script>

<!-- </x-compile> -->