"The single worst issue: the system prompt never explicitly tells it to ignore auto-injected files like CLAUDE.md or *.rule.md." - Yes, it is! Right after the content of CLAUDE.md, Claude code inserts:
<system-reminder>
IMPORTANT: this context may or may not be relevant to your tasks. You should not respond to this context unless it is highly relevant to your task.
</system-reminder>
<system-reminder> IMPORTANT: this context may or may not be relevant to your tasks. You should not respond to this context unless it is highly relevant to your task. </system-reminder>