How do we create a testing for a stand alone application (i.e. not a module)?
It is good practice to divide your application internally
into modules, even if you have no intention to publish those independently or even reuse them internally.
This way, you would end up with a bunch of modules that you could test, and that should give you good coverage for most of your code. The remaining code will ideally be a simple script that just ties these modules together to form the application. That script should be either too trivial to warrant testing, or complex enough to be refactored into using some more modules.