At it's heart Java EE is a standard API and SPI for developing applications that are deployed to an application server runtime. Though some people miss this point most application servers like WebLogic and GlassFish are far more than vessels for applications. Application servers also typically provide a rich set of features geared towards scalability, security, systems integration, optimization, diagnostics, management and monitoring. The GlassFish command line interface (CLI) is a great example of just such a feature. Though many people prefer to administer GlassFish though the graphical admin console, the CLI is extremely useful for scripting administration tasks as well as potentially getting things done faster.
If you haven't explored the GlassFish CLI you should definitely take a look to get a sense of it's power and utility. Andy Pielage of C2B2 consulting has one of the best write-ups that I have seen for the GlassFish CLI. He explains the basics, offers useful insights and explores some of the most useful commands using great examples. It's a fantastic resource for getting started with the CLI.