[BUG] Claude code does not respect .gitignore and project rules while exploring

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?

The agent regularly calls "Glob" tool as well as find and grep bash command listing and reading sensitive and ignored files like .env and node_modules. The files were included in the .gitignore and the agent was explicitly told not to in the CLAUDE.md to respect the .gitignore and to not touch the sensitive files. Closer investigation revealed that
1) .gitignore is not respected in the Glob (file listing / search) tool
2) The agent uses the built-in "Explore" sub-agent which ignores the project and user level CLAUDE.md and does not respect the project's .gitignore file.

What Should Happen?

1. All agents should either respect the CLAUDE.md file or have another option to inject system prompt into them
2. All agents and tools should respect .gitignore or at least be instructed to use it in for commands like find and others.

Error Messages/Logs

Steps to Reproduce

Create a test repo containing .gitignore, put some files there and ask the agent to explore the project.

Claude Model

Opus

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

v2.1.42

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

VS Code integrated terminal

Additional Information

_No response_