You should see your commands when using the Craft CLI.
First thing to check would be that the module is registered in
app.php, both in the
bootstrap arrays. Craft's documentation on that is here.
I find the best way to quickly validate that your module is registered, is by dumping something out from the module
Craft::dd('Registered') does the trick. If you don't see anything on the frontend, your module isn't getting loaded into Craft.
Secondly, I would check that you are correctly setting the
controllerNamespace, so that Craft knows where to look for controllers, depending on your request. Their documentation on that is here.
Finally, check that you have some valid functions setup in your controllers. Each function name should be prefixed with
action. For example:
actionRun() in a
JobController.php file will be run with
php craft mymodule/job/run.