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From an architecture perspective, I'm trying to get a better understand of how and where files deployed to eb (t2) server are stored.

I see some .zip files in s3 that show when I upload something via the eb interface, though how/where exactly does this get end up on my ec2(t2) server?

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It's within the /tmp/deployment/application folder during deployment and then moved to /var/app/current subsequently.

In case you search them, the node logs are in /var/log/nodejs/nodejs.log and therefore the application can bind to 8081 regardless of what PORT environment variable you set within the Environment Variables in the console.

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