[BUG] Model ignores CLAUDE.md priority over skill instructions

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?

CLAUDE.md contains the rule: "Do not commit implementation plan documents." A superpowers skill (writing-plans) has a workflow that includes committing plan/design documents. The skill itself documents the priority order:

1. CLAUDE.md — highest priority
2. Skills — middle
3. Default system prompt — lowest

Despite this, the model followed the skill's workflow and committed two plan documents, violating the CLAUDE.md rule. The model did not cross-check the skill's steps against project instructions before acting.

What Should Happen?

When a skill workflow step conflicts with a CLAUDE.md rule, the model should skip or adapt that step to comply with CLAUDE.md.

Error Messages/Logs

Steps to Reproduce

1. Add a rule to CLAUDE.md (e.g., "Do not commit plan documents")
2. Use a skill whose workflow includes a step that violates that rule (e.g., writing-plans skill that commits plan files)
3. The model follows the skill and violates the CLAUDE.md rule

Claude Model

Opus

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.86

Platform

Anthropic API

Operating System

Ubuntu/Debian Linux

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_