Yes, it was me that reached out to you @seancorfield, and here is the issue (https://github.com/polyfy/polylith/issues/66) including a discussion with Alex about the #polylith workspace structure.
Yeah, every time I've looked at Polylith it's just looked like overkill formalism -- and I think the rigidity you've adopted is part of what's causing you problems with deps.edn
and tooling. I agree with Alex's comment that you're aiming at an "easy" solution instead of "simple" as well and that's also causing you headaches.
BTW @tengstrand I notice that your #polylith channel here does not have either @logbot or @zulip-mirror-bot as members so none of that conversation is being logged anywhere, and therefore isn't searchable. You might want to add both of those bots to improve the discoverability of your discussions.