There are no standard "Java EE commands", most projects use some kind of build tool, an IDE like NetBeans, or a command line tool like
ANT or Maven.
Additionally, there is no standard way of deploying Java EE applications across application servers, each application server deployment may be different from another.
To answer your question, since the book is focused on NetBeans, deployment is explained from the assumption that the reader is using NetBeans to develop and deploy the application.
In my other book, "Java EE 5 Development Using GlassFish Application Server", Maven is used as the build tool for the examples, and the different ways of deploying an application into GlassFish are explained.
David