The dotenv-deployment readme mentions how you can use it in a production environment:
If you are using Capistrano 3+:
Just add .env to the list of related files:
set :linked_files, %w{.env}
If you are using Capistrano 2.xx version:
In your config/deploy.rb :
require "dotenv/capistrano"
It symbolizes the .env link located in /path/to/shared in the new version.
Remember to add :production group to the dotenv-rails stone in the Gemfile application:
gem 'dotenv-rails', :groups => [:development, :test, :production]
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