This page lists sample tools created by AppDynamics users to deploy Java Agents automatically. You can use these samples for ideas on how to automate AppDynamics agent deployment for your own environment.
In the samples, the agents are deployed independently of the application deployment:
ChefExample1 and ChefExample2 use Opscode Chef recipes and provide examples of automating deployment on Java platforms. See Chef website.
JavaExample1 uses a script, configuration file, and a package repository.