In the Sencha Cmd docs it states that there are different options you specify for the compiler when it is handling JavaScript files in app.json.
What is the difference between the "bundle" and "includeInBundle" options?
From the forums:
Apologies for the delay in response - I recognize this is confusing, here's a quick explanation:
only one of your js resources should be marked bundle: true - it tells Sencha Cmd "this is the file to use as the bundle - concatenate anything else that is a part of the build into this file"
includeInBundle says "include this file in the bundle via concatenation / minification"
I hope that clarifies things! There's also some documentation here if you'd like to read more: