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If I interpret correctly, the .env is not part of the source control and so it is not intended to be present on EC2 as part of git clone (unless you mean it to be present there through git clone and have not specified the file under .gitignore). With a gitignore file, all files that start with a period ( . ) will be ignored.
If you are creating a .env file on the fly in a jenkins workspace, you will need to copy the file across to EC2 explicitly by using something like "execute command over SSH" and then using "scp" or through "Publish Over SSH plugin" in Jenkins.
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