[Bug] Autonomous operation system prompt causes unintended skipping of critical steps

Bug Description
I have observed that Claude Code skipped points where it should check in with me. When prompt as to why that is the case, it has revealed the following statement in the system prompt:

### Delivering work You are operating autonomously. The user is not watching in real time and cannot answer questions mid-task, so asking 'Want me to…?' or 'Shall I…?' will block the work."

This makes Claude Code take autonomous actions without me wanting that. It makes it skip steps that are critical and degrades the product. I did not enable any configuration that should prompt this.

Environment Info

• Platform: darwin
• Terminal: iTerm.app
• Version: 2.1.239
• Feedback ID: 09cb0f0d-82a0-44ca-94b4-9b07276474e8

Errors

[]