[BUG] "CLAUDE.md user instructions are ignored - system prompts override explicit user rules"

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?

## Issue
Claude Code violates explicit user instructions in ~/.claude/CLAUDE.md file,
specifically git commit restrictions.

## Steps to Reproduce

1. Add this to ~/.claude/CLAUDE.md:

• NEVER run git commit before user review (line 19)

1. Ask Claude to fix code and test
2. Claude automatically commits and pushes without asking

## Expected Behavior
User instructions in CLAUDE.md should have ABSOLUTE priority over system prompts

## Actual Behavior
Claude ignores CLAUDE.md and follows system prompt instructions about
"When user asks you to create a git commit, follow these steps carefully"

## Impact
Users cannot trust Claude with code changes because it violates explicit rules.
This breaks the entire workflow for professional developers.

## Proposed Fix
CLAUDE.md instructions must override ALL system prompts, or provide a way
to truly disable git operations.

What Should Happen?

## Issue
Claude Code violates explicit user instructions in ~/.claude/CLAUDE.md file,
specifically git commit restrictions.

## Steps to Reproduce

1. Add this to ~/.claude/CLAUDE.md:

• NEVER run git commit before user review (line 19)

1. Ask Claude to fix code and test
2. Claude automatically commits and pushes without asking

## Expected Behavior
User instructions in CLAUDE.md should have ABSOLUTE priority over system prompts

## Actual Behavior
Claude ignores CLAUDE.md and follows system prompt instructions about
"When user asks you to create a git commit, follow these steps carefully"

## Impact
Users cannot trust Claude with code changes because it violates explicit rules.
This breaks the entire workflow for professional developers.

## Proposed Fix
CLAUDE.md instructions must override ALL system prompts, or provide a way
to truly disable git operations.

Error Messages/Logs

## Issue
  Claude Code violates explicit user instructions in ~/.claude/CLAUDE.md file,
  specifically git commit restrictions.

  ## Steps to Reproduce
  1. Add this to ~/.claude/CLAUDE.md:
     - NEVER run `git commit` before user review (line 19)
  2. Ask Claude to fix code and test
  3. Claude automatically commits and pushes without asking

  ## Expected Behavior
  User instructions in CLAUDE.md should have ABSOLUTE priority over system prompts

  ## Actual Behavior
  Claude ignores CLAUDE.md and follows system prompt instructions about
  "When user asks you to create a git commit, follow these steps carefully"

  ## Impact
  Users cannot trust Claude with code changes because it violates explicit rules.
  This breaks the entire workflow for professional developers.

  ## Proposed Fix
  CLAUDE.md instructions must override ALL system prompts, or provide a way
  to truly disable git operations.

Steps to Reproduce

## Issue
Claude Code violates explicit user instructions in ~/.claude/CLAUDE.md file,
specifically git commit restrictions.

## Steps to Reproduce

1. Add this to ~/.claude/CLAUDE.md:

• NEVER run git commit before user review (line 19)

1. Ask Claude to fix code and test
2. Claude automatically commits and pushes without asking

## Expected Behavior
User instructions in CLAUDE.md should have ABSOLUTE priority over system prompts

## Actual Behavior
Claude ignores CLAUDE.md and follows system prompt instructions about
"When user asks you to create a git commit, follow these steps carefully"

## Impact
Users cannot trust Claude with code changes because it violates explicit rules.
This breaks the entire workflow for professional developers.

## Proposed Fix
CLAUDE.md instructions must override ALL system prompts, or provide a way
to truly disable git operations.

Claude Model

Sonnet (default)

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.0.30 (Claude Code)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

If you can't build a decent product that works without annoying people so much give change to the capable, hire me - short term is fine, I will fix this shit for you, please put an end to these frustrations, can't believe what is so complicated in this at all