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

[binaryfire]

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

[github-actions[bot]]

Found 3 possible duplicate issues:

1. https://github.com/anthropics/claude-code/issues/11881
2. https://github.com/anthropics/claude-code/issues/5466
3. https://github.com/anthropics/claude-code/issues/10906

This issue will be automatically closed as a duplicate in 3 days.

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🤖 Generated with Claude Code

[LeonardMH]

Related to #11881, fix allegedly incoming. In the meantime seems like rolling back to 2.0.42 helps some users.

[github-actions[bot]]

This issue has been inactive for 30 days. If the issue is still occurring, please comment to let us know. Otherwise, this issue will be automatically closed in 30 days for housekeeping purposes.