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Does it matter whether the app reads `.env` directly though?
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Maybe. How does the application unify different environment variables? Those inherited by the shell, those read from .profile, those set in the process that start the application (be that ./run.sh, a nodejs script, systemd etc...).
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Why would it want to? I'd say what you're asking for is actually a code smell. An app should not have a bazillion interlocking ways to be configured, unless there's a strong reason for this!
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It's not the app, it's the environment variables that have many ways to be configured.
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