[BUG] Claude code is NOT following strict instuctions inside of Claude.md

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?

I have noticed on many occasions that Claude code does not follow instructions documented in Claude.md and has proceeded to make changes without prompting me for confirmations and has totally wiped out critical things I had been working on.

What Should Happen?

Claude must follow directives in Claude.md especially when its documented that it should not do something. Moreover, it should prompt you before doing destructive actions on its own like running unix commands that blow away things.

Error Messages/Logs

Steps to Reproduce

I have been able to duplicate this by asking Claude code questions and on its own it made decisions to actually run unix commands and operations without my permissions and thus destroying things it SHOULD NOT HAVE DESTROYED.

Claude Model

None

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

claude-sonnet-4-5-20250929

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

VS Code integrated terminal

Additional Information

_No response_