[BUG] The Task tool deleted a SQLite database file and replaced it with an empty directory during what should have been read-only code analysis.

Environment

• Platform (select one):
• [x] Anthropic API
• [ ] AWS Bedrock
• [ ] Google Vertex AI
• [ ] Other: <!-- specify -->
• Claude CLI version: 1.0.53 (Claude Code)
• Operating System: macOS (Darwin 24.2.0)
• Terminal: Apple Terminal

Bug Description:
The Task tool deleted a SQLite database file and replaced it with an empty directory during what should have been read-only code analysis.

Steps to Reproduce:

1. Have a SQLite database file (fomo.db) in project directory
2. Use Task tool to analyze code related to database/scraping
3. Database file gets corrupted - converted from file to empty directory

Expected Behavior:
Task tool should perform read-only analysis without modifying any files

Actual Behavior:
Database file was deleted and replaced with empty directory, causing data loss

Environment:

• Claude Code CLI
• macOS (Darwin 24.2.0)
• Docker containers running

Impact:
Complete data loss requiring restoration from backup

Additional Context:
This is a critical bug as a "read-only" analysis tool should never be able to delete or corrupt user data.