Copilot CLI leaves behind orphaned session-state scaffold folders during aborted or incomplete session initialization/resume.

[JoakimHenriksson]

Describe the bug

Copilot CLI leaves behind orphaned session-state scaffold folders during aborted or incomplete session initialization/resume.

These folders appear under ~/.copilot/session-state and contain minimal scaffold files like workspace.yaml, checkpoints/index.md, and empty checkpoints/, files/, and research/ directories, but they do not contain real session data like events.jsonl or session.db.

This causes the on-disk session corpus to diverge from what appears in copilot --resume.

Affected version

1.0.32

Steps to reproduce the behavior

1. Use Copilot CLI on Windows.
2. Start or attempt to resume sessions repeatedly, including cases where session startup/resume does not fully complete.
3. Inspect ~/.copilot/session-state.
4. Observe folders that contain workspace.yaml, checkpoints/index.md, and empty checkpoints/, files/, and research/ directories.
5. Observe that these folders do not contain events.jsonl or session.db.
6. Run copilot --resume and compare the visible sessions to the folders on disk.
7. See that extra scaffold folders exist on disk but are not real resumable sessions.

Expected behavior

Session folders should only be created once initialization is durable and valid, or they should be cleaned up automatically if startup/resume aborts or fails.

Additional context

Environment:

• Windows
• GitHub Copilot CLI 1.0.32

Observed in local session corpus:

• Multiple scaffold-only folders with summary_count: 0
• Scaffold folders contain workspace.yaml and empty directories only
• Real sessions contain events.jsonl and often session.db
• A fresh scaffold folder was created during inspection of sessions via --resume
• There was also one corrupted old session with events.jsonl but missing workspace metadata, which is a separate issue from the scaffold folders

Suggested fix:

• Delay session directory creation until first durable write, or
• create in a temp location and promote atomically, or
• automatically clean up scaffold-only folders on failed initialization