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Er, well I'd recommend you don't. Since your PaaS (in this case, Fly) should let you specify environment variables. In Fly's case, for non-secret ones, put them in fly.toml in the [env] block. For secret ones, use the separate fly secrets command to set them. Either way, they will be environment variables in your app and be nice and secure.
But if you really need to include an .env ... you could do that by modifying both the .dockerignore (to not ignore it) and then the Dockerfile to copy .env it to the image.
So add a line there for !.env (use ! to invert. Why? As I've previously ignored all files with *, so then add back only the files we don't want ignored, so in this case you don't want your .env ignored).
How to add .env to Dockerfile ? maybe can simple for setup
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