Copilot wrote codes to wrong files in Agent mode

**Describe the bug**

**Versions**
- Copilot for Xcode: 0.41.0
- Xcode: 26.0 beta 5 (17A5295f)
- macOS: 26.0 Beta (25A5338b)

**Steps to reproduce**
When using Agent mode to fix bugs, sometimes Copilot will write code to the wrong file and make content duplicated.

For example, with a SPM project, Copilot wrote codes of Package.swift to swift file in sources. And it could not found this was bug until I pointed out.

It also happened with normal .xcodeproj project between .swift files.

When this happens, the whole file content will be replaced. You will lost one file and have two duplicated files.

Can you investigate and fix it?

**Screenshots**

**Logs**

**Additional context**