There are a few parent application settings when dealing with modules. In your ColdBox.cfc you can have a modules structure with some configuration settings.
modules = {
// reload and unload modules in every request
// DEPRECATED in coldbox 5
autoReload = false,
// An array or list of the module names that will load ONLY
include = [],
// An array or list of the module names that will be EXCLUDED
exclude = ["paidModule1","paidModule2"]
};