[BUG] Sub agents can't use tools properly: `Permission to use xxx has been auto-denied in dontAsk mode` even with `--dangerously-skip-permissions`

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

Sub agents (like Explore) aren't much use at the moment, because they keep hitting Permission to use xxx has been auto-denied in dontAsk mode. This happens even with --dangerously-skip-permissions. It makes Claude Code much less effective because it can no longer explore codebases, use various commands to read files etc.

What Should Happen?

When --dangerously-skip-permissions is used, sub agents should be able to do whatever they want. No Permission to use xxx has been auto-denied in dontAsk mode error messages.

Error Messages/Logs

Steps to Reproduce

Open Claude Code, go into Plan mode and ask it to do something comprehensive which uses the Explore agent. Explore the codebase + check certain files + go online and do some research. You'll see the sub agent constantly hits the "denied in dontAsk mode" errors.

Claude Model

None

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.0.46

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

Windows Terminal

Additional Information

_No response_