[Custom Agent] New Created file is gone when call sub agent

[showpune]

Hi,

My application will run some process and create a progress.md files in folder .github of the repo.

In copilot 0.0.360, when I am using the copilot cli to run my prompt, the progress.md will be created, but my prompt is running in a custom agent which is activated by copilot cli, the progress.md will gone。

I can see the progress.md if I rollback to 0.0.358,