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Are you inserting your appd configuration as the very first line of your application code?
Please check the docs for the same -
Typically the file you provide to node-js in order to get your the application code running.
Incase you are injecting at the root and still seeing the agent is not getting connected please check if the following folder is getting created '/tmp/appd' ? If yes, please zip the folder and share it here for us to help resolve the issue.
I am facing a similar issue here. I have node.js v6.11.3 version running on windows.
I have run locally npm install appdynamics***.tgz and copied the appdynamics folder under the node_modules directory. Also added the require statement in a server.js file at first line.
The application is started but the agent couldn't hook up with the Application node.
I see you have already started a support ticket for the same, lets explore this togther there.