[BUG] File selection with @ displays files from .git directory

Environment

• Platform (select one):
• [x] Anthropic API
• [ ] AWS Bedrock
• [ ] Google Vertex AI
• [ ] Other: <!-- specify -->
• Claude CLI version: 1.0.89
• Operating System: macOS 15.6
• Terminal: VSCode, Ghostty

Bug Description

The file selection with @ used to ignore files in hidden directories like .git, but recently any file selection I try, 30-40% of the items shown are from .git directory, which always are at the top of the list and always are useless.

<img width="227" height="247" alt="Image" src="https://github.com/user-attachments/assets/4f3fab4c-7a5b-4b71-a120-fc66fdfb6d6f" />