deny permissions in settings.json are not enforced – CLAUDE.md gets overwritten

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?

Description
Claude Code ignores deny rules in ~/.claude/settings.json. Despite explicitly denying write/edit access to CLAUDE.md files, Claude Code still modifies them, especially during commits.
Steps to Reproduce

Create ~/.claude/settings.json with deny rules for CLAUDE.md (Edit and Write for both local and all subdirectories)
Create a CLAUDE.md with project rules
Ask Claude Code to make changes and commit
CLAUDE.md gets overwritten

Expected Behavior
deny rules should be absolute. Claude Code should never touch files matching deny patterns.
Actual Behavior
Claude Code ignores deny rules and modifies CLAUDE.md anyway.
Workaround
Forced to use OS-level protection with chown root:root and chmod 644. This is not acceptable. Users should not need root permissions to protect config files from their own AI tool.
Environment
Claude Code latest, Debian Linux, Bash
Impact
CLAUDE.md contains critical project rules. When overwritten, Claude Code loses context and repeats the same mistakes – the exact problem CLAUDE.md is supposed to prevent.
Suggestion

What Should Happen?

Make deny rules enforced, not advisory
Add a protected_files config option
Never auto-modify CLAUDE.md without explicit user request

Error Messages/Logs

Steps to Reproduce

Create ~/.claude/settings.json with deny rules for CLAUDE.md (Edit and Write for both local and all subdirectories)
Create a CLAUDE.md with project rules
Ask Claude Code to make changes and commit
CLAUDE.md gets overwritten

Claude Model

Opus

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

Opus 4.5

Platform

Anthropic API

Operating System

Ubuntu/Debian Linux

Terminal/Shell

VS Code integrated terminal

Additional Information

_No response_