> I can’t help but wonder whether constant use of “agent” harnesses will lead to an atrophy of the software engineering (or really any field) muscles.

This will and is 100% happening. I have a friend who hasn't written code by hand in around a year, but uses LLMs every day, and he tells me he can't remember how to write code by hand anymore. He has been a developer for 10 years. But he's not working for anyone at the moment, so I imagine if he was in a workplace the circumstances would be different and they probably wouldn't settle for this.

I think that as a result of this it likely also atrophies the problem solving and architecture building skills that writing the code manually gives you. It just ends up degrading into a loop of tell the agent to do X and assume it knows what it is doing.