Multiple copies of files in Java Agent zip

[Steven.Pearce]

Just trying to install AppDynamics for the first time. I have downloaded the agent and when I unzip I have the following structure

This screenshot shows I have 2x conf directories, 2 sets of jars, 2 javaagents, etc.

My questions are; what is this structure for, which conf and jar should I use, and what is the purpose of the second copy in a subdirectory with additional config files and src files?

Thanks.

^ edited by @Ryan.Paredez to make the post easier to read. 

[Peter.Holditch]

Steven,

A high level explanation is provided in the documentation: https://docs.appdynamics.com/display/PRO45/Java+Agent+Directory+Structure

Warm regards,

Peter