Session data loss when agency copilot closes

### Describe the bug

I'll be in the middle of an hours-long session and for one reason or another, agency closes. Maybe I close it, maybe the codespace turns off. But the result is that when I immediately try to resume, the session is wiped. This issue has been present for some time but is sporadic enough that I thought it was fixed.

### Affected version

GitHub Copilot CLI 1.0.55-7

### Steps to reproduce the behavior

1. run `agency copilot`
2. Be in any long lived session. In my case this was a fresh session from when I started copilot
3. Close agency copilot either with ctrl+c or another command. In my case copilot was actively processing a command
4. Restart agency copilot
5. /resume, observe session is gone

### Expected behavior

Session should not be deleted

### Additional context

- OS: Linux codespaces-b92d36 6.8.0-1052-azure 58~22.04.1-Ubuntu SMP Thu Mar 26 05:02:21 UTC 2026 x86_64 x86_64 x86_64 GNU/Linux
- Shell: zsh

Reproduce the report by running `agency copilot`, ending a long-lived session during processing, restarting it, and using `/resume`. Trace the session persistence and shutdown behavior involved in that flow; done means a session remains available after agency Copilot is closed with Ctrl+C or the environment stops.

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