Skill tool invocation triggers bypass_permissions_gate_blocked, downgrading session from bypassPermissions to acceptEdits

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 a Skill tool is invoked in a session running in Bypass Permissions mode, the session automatically downgrades to Accept Edits mode. The error banner reads: "Bypass Permissions mode isn't enabled. The session started in Accept Edits — enable Bypass Permissions in Settings to use it."

What Should Happen?

Skill invocation should not alter the session permission mode.

Error Messages/Logs

Steps to Reproduce

Start Claude Code Desktop with defaultMode: bypassPermissions in global settings
Open a project session — mode shows "Bypass Permissions" ✓
Invoke any Skill tool
Mode switches to "Accept Edits" and error banner appears

Claude Model

Opus

Is this a regression?

No, this never worked

Last Working Version

_No response_

Claude Code Version

v1.9659.2

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

Root cause (from app source): The CLI subprocess checks whether --dangerously-skip-permissions is available and emits bypass_permissions_gate_blocked when not in a Docker/sandbox container. The app's Redux store catches this event and downgrades the session mode.

Workaround: Add drv-brain script patterns to permissions.allow in project settings.json — commands run without prompts even in Accept Edits mode, but the mode switch and error banner remain.