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Currently, cider complains when the dependencies are wrong in profile.clj. I understand the reasons for this, but it would be nice if Cider offered the ability to update your profile for you.
Another possibility would be for cider to check whether pomegranate is present and if not, inject the correct dependencies. Don't know if that is possible with plugins, but worth thinking about.
This would be great for me when I am switching Emacs' -- sometimes using melpa-stable, sometimes melpa normal. Then I have to continually re-edit my profile.clj. Painful.