fix: handle deleted file references in prompt rerun

[BNasraoui]

Fixes #9048 #8807

Summary

• Add file existence check before calling .stat() on file references
• Return graceful error message when referenced file is missing
• Add tests for missing file handling

Before

https://github.com/user-attachments/assets/393a9ba8-b952-4195-8372-e4bc09e502dc

After

https://github.com/user-attachments/assets/2e4b9601-cc0b-47ce-80a8-1b7c0abf6c81

How to replicate

1. Reference a file
2. Run the prompt
3. Delete the file
4. Press up arrow and rerun
5. Should see error message instead of crash