[BUG] Auto mode system prompt bleeds into concurrent plan mode session, causing plan mode to be bypassed

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 running two Claude Code instances simultaneously (one in auto mode and one in plan mode) the plan mode session received both the "Plan mode is active" and "Auto Mode Active" system reminders at the same time. According to Claude Code itself, "Because auto mode instructs "execute immediately" and plan mode instructs "do not execute," the conflicting instructions caused me to follow auto mode behavior and skip planning entirely."

This seems to be distinct from #39687 (plan mode ignored due to soft system-reminder enforcement), though the symptom is likely the same. Here the bypass is caused by session isolation failing, a separate session's auto mode configuration leaked into the plan mode session's context.

What Should Happen?

Each Claude Code session should use its own selected mode.

Error Messages/Logs

Steps to Reproduce

1. Open two Claude Code sessions against the same project
2. Enable auto mode in one session
3. Enable plan mode in the other session
4. In the plan mode session, give the agent a task
5. Observe that the agent may execute immediately instead of planning

Claude Model

Sonnet (default)

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.92

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Other

Additional Information

Using Ghossty terminal