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You can do it with Chef if you have that level of automation, if not you can write a script. Assuming you're going to the same controller and don't want to do anything fancy with hierarchies and are fine with grabbing default server/node names, then the controller-info.xml file will be the same for all agents.
.Net Script documentation: https://docs.appdynamics.com/display/PRO45/Unattended+Installation+for+.NET
Java Documentation: https://docs.appdynamics.com/display/PRO45/Automate+Java+Agent+Deployment