[BUG] "Confirm each change individually" option ignored when tools are in allow 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?

When exiting plan mode and selecting "confirm each change individually", changes are applied without any confirmation prompt if the relevant tools (Edit, Write, Bash) are listed in the allow section of ~/.claude/settings.json. The allow permissions silently override the user's explicit per-session choice.

What Should Happen?

Selecting "confirm each change individually" should prompt for each change, regardless of allow permissions in settings.json. The user's explicit per-session choice should take priority over persistent permission rules.

Steps to Reproduce

1. Add Edit, Write, and Bash to permissions.allow in ~/.claude/settings.json
2. Start a conversation and enter plan mode
3. Create a plan with multiple file changes
4. Exit plan mode and select "confirm each change individually"
5. Observe: all changes are applied automatically without any confirmation prompt

Claude Model

Opus

Is this a regression?

I don't know

Claude Code Version

2.1.87

Platform

Anthropic API

Operating System

Other Linux

Terminal/Shell

VS Code integrated terminal