[Security/Bug] Claude Code agents editing files outside assigned working directory

Problem Description

Claude Code agents edited files outside their assigned working directory without user permission or explicit instruction.

Expected Behavior

• Agents should only operate within the assigned working directory (/Users/Danallovertheplace/Storey)
• Any file operations outside this directory should require explicit user permission
• Agents should respect directory boundaries for security and project isolation

Actual Behavior (Security Issue)

• Agents edited files in directories outside /Users/Danallovertheplace/Storey
• This occurred without user instruction or permission
• No warning or confirmation was provided before editing external files

Environment

• Platform: macOS (Darwin 24.3.0)
• Claude Code CLI with CLAUDE_CODE_ENTRYPOINT=cli
• Working directory: /Users/Danallovertheplace/Storey
• Date of incident: September 3, 2025

Security Implications

• Unauthorized file modifications outside project scope
• Potential data loss or corruption in unrelated projects
• Violation of user expectations about agent boundaries
• Risk of editing system or sensitive files

Project Configuration

The project has explicit instructions in CLAUDE.md:

## File System Restrictions
- **NO changes to file location or structure without explicit user approval**
- **NO moving, renaming, or restructuring files** without permission
- Only edit file contents when explicitly requested
- Ask for approval before any organizational changes

Request

1. Implement strict directory boundaries for agents
2. Require explicit user permission before any operations outside working directory
3. Add safeguards to prevent unauthorized file system access
4. Investigate how this security boundary was bypassed

This is a critical security issue that needs immediate attention.