What takes priority, System ENV or .env file?

Yes, that was done intentionally, though it does only check "local only" variables which limits the scope a little bit.

What variables are you talking about in the .htaccess? The only one that I recall being in there was the CI_ENVIRONMENT, and that's only there because a number of people were having issues where they didn't have access to other locations to set it. I believe that's old though and could probably be removed, as it's now intended to be in the .env file.

Unfortunately, I am not involved in the more real-time chat options as I'm too slammed with the day job to be able to really help that way.

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