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Lambda container images does not support layers. Layers are only a way to add dependencies, so all you have to do is include those dependencies in your docker image. Layers use the /opt. When you use docker, you don't have to use /opt and you can deploy your dependencies in the regular location.
I don't think you need to use FROM twice. Just use the second, npm install, and copy the application files.
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I don't know in JS, but in Python what I would do is use the docker image provided by lambda to install my packages into a specific folder. Zip that, store it in S3, job done. So yes, I suppose a multi-stages build works as well. But again, I am not familiar with the specific inner workings of NPM to achieve that.
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