[BUG] Settings file being continuously rewritten during tool execution, destroying pre-configured permissions

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?

Report this issue at: https://github.com/anthropics/claude-code/issues

Include in your report:

1. Summary: Settings file being continuously rewritten during tool execution, destroying pre-configured permissions
2. Details:

• Parent settings at /Users/.../.claude/settings.json have full permissions configured
• Local settings at ./.claude/settings.json get stripped down and rewritten with only the minimum permissions for each tool call
• Every tool execution (Read, Bash, etc.) modifies settings.json, removing your configured rules
• Makes it impossible to persist the permission configuration

1. Expected behavior: The Settings file should be a read-only configuration that doesn't change based on tool execution
2. Steps to reproduce:

• Configure comprehensive permissions in settings.json
• Run any tool
• Check settings.json - it will be overwritten with minimal permissions

1. Environment:

• Claude Code version: [check]
• macOS 25.1.0

Also, mention you can see the symlink structure issue: settings.local.json → settings.json, but the local version gets stripped instead of inheriting parent settings.

This is definitely a legitimate bug that needs to be fixed in Claude Code.

What Should Happen?

Report this issue at: https://github.com/anthropics/claude-code/issues

Include in your report:

1. Summary: Settings file being continuously rewritten during tool execution, destroying pre-configured permissions
2. Details:

• Parent settings at /Users/.../.claude/settings.json have full permissions configured
• Local settings at ./.claude/settings.json get stripped down and rewritten with only the minimum permissions for each tool call
• Every tool execution (Read, Bash, etc.) modifies settings.json, removing your configured rules
• Makes it impossible to persist the permission configuration

1. Expected behavior: The Settings file should be a read-only configuration that doesn't change based on tool execution
2. Steps to reproduce:

• Configure comprehensive permissions in settings.json
• Run any tool
• Check settings.json - it will be overwritten with minimal permissions

1. Environment:

• Claude Code version: [check]
• macOS 25.1.0

Also, mention you can see the symlink structure issue: settings.local.json → settings.json, but the local version gets stripped instead of inheriting parent settings.

This is definitely a legitimate bug that needs to be fixed in Claude Code.

Error Messages/Logs

Steps to Reproduce

Report this issue at: https://github.com/anthropics/claude-code/issues

Include in your report:

1. Summary: Settings file being continuously rewritten during tool execution, destroying pre-configured permissions
2. Details:

• Parent settings at /Users/.../.claude/settings.json have full permissions configured
• Local settings at ./.claude/settings.json get stripped down and rewritten with only the minimum permissions for each tool call
• Every tool execution (Read, Bash, etc.) modifies settings.json, removing your configured rules
• Makes it impossible to persist the permission configuration

1. Expected behavior: The Settings file should be a read-only configuration that doesn't change based on tool execution
2. Steps to reproduce:

• Configure comprehensive permissions in settings.json
• Run any tool
• Check settings.json - it will be overwritten with minimal permissions

1. Environment:

• Claude Code version: [check]
• macOS 25.1.0

Also, mention you can see the symlink structure issue: settings.local.json → settings.json, but the local version gets stripped instead of inheriting parent settings.

This is definitely a legitimate bug that needs to be fixed in Claude Code.

Claude Model

Sonnet (default)

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

1.0.123

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_