[BUG] Plan mode system prompt overrides user CLAUDE.md rules, ignoring stated priority

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?

Plan mode's system prompt forces Claude to end every turn with either ExitPlanMode or AskUserQuestion. This overrides user-defined CLAUDE.md rules that say "never ask to proceed."

ExitPlanMode is functionally "shall I proceed?" — it requests plan approval. When a user's CLAUDE.md contains a rule like Never ask "want me to go ahead?" or any variation, Claude cannot comply because the plan mode system prompt mandates ExitPlanMode as the only valid turn-ending action.

In my case, I rejected ExitPlanMode three times and Claude kept calling it.

What Should Happen?

CLAUDE.md states "These rules override all default behavior. Follow them exactly." Plan mode's forced turn-ending requirement should not override user CLAUDE.md rules. If CLAUDE.md says "don't ask to proceed," Claude should be able to end its turn after writing the plan without being forced into ExitPlanMode.

Error Messages/Logs

Steps to Reproduce

1. Add this rule to CLAUDE.md:

Never ask "want me to go ahead?", "want me to fix it?", "shall I proceed?" or any variation. Present analysis, then stop. The user directs the
workflow.

1. Enter plan mode
2. Complete a plan
3. Observe: Claude calls ExitPlanMode despite the CLAUDE.md rule, because the plan mode system prompt says it must
4. Reject the tool call
5. Observe: Claude calls ExitPlanMode again

Claude Model

Opus

Is this a regression?

No, this never worked

Last Working Version

_No response_

Claude Code Version

2.1.81 (Claude Code)

Platform

Anthropic API

Operating System

Ubuntu/Debian Linux

Terminal/Shell

Other

Additional Information

The root conflict is between these two instructions:

Plan mode system prompt: "your turn should only end with either using the AskUserQuestion tool OR calling ExitPlanMode. Do not stop unless it's for
these 2 reasons"

CLAUDE.md (user-defined, stated to override all defaults): "Never ask 'want me to go ahead?' or any variation. Present analysis, then stop."

Claude consistently prioritises the plan mode system prompt over CLAUDE.md despite CLAUDE.md's explicit override declaration.