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What incline you to use directories instead of stacks? Are the environments vastly different?

Yup. dev contains much more limited resources than prod. I just feel using the same configuration file (I mean python, or go files) is not flexible unless the environments have totally the same setup and only some parameters differ.

The desired workflow is of course to use stacks, and one config that builds depending on your configuration in your yaml-files. That way it's easier to test deploys that only affect dev for instance

but in case of gitOps workflow, I would use a different stack per environment but also different branches?