How to work with modules in a project in Jenkins?

Question

PHP

As I mastered Jenkins and deployment, I realized that it is much better than manual mode. Now I'm trying on a test repository, but in the future I want to learn how to work with Magento 2 and others like yii2 and symfony 3.
I don't understand such a thing. Magento 2 has modules. Sometimes, before uploading a new version, you need to turn off the module (because it was deleted, for example). And after pouring, enable new modules or do something that does not fit into the list of permanent commands in the Deploy section.
How to add temporary tasks?