I was able to determine my issue. It turns out, I was using a Debian Base Image with the alpine .Net agent for linux. I think it would have been nice to understand from the docs how agents start on their own. Once I fixed my base image, the agent simply started when I started my application which is pretty cool. I probably also would've been able to figure this out if I were able to download the agent of my choosing. I pulled the agent from a co worker who had downloaded it before but they didn't know what OS it supported. I tired downloading from the AppDynamics download center but even after creating an account and starting a free trial the download link just looks back and no download ever starts.
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