Copilot CLI loses todos and edits the wrong plan after forked

### Describe the bug

If Copilot is asked to update the plan and the todo list, it will update the old plan in the forked session and reports the todo list being empty.

This is likely a problem not only for the plan mode, but whenever it needs to edit a file in the session folder.

### Affected version

1.0.78

### Steps to reproduce the behavior

1. Ask the agent to create a plan with todos
2. Fork the session
3. Ask it to update the plan and todos

### Expected behavior

The agent should edit the plan file and the todo list under the new session folder. The todo list should be copied over for the new session

### Additional context

_No response_

Reproduce the issue by creating a plan with todos, forking the session, and asking the agent to update both. Trace how the forked session selects its plan file and todo list under the new session folder, then verify that the todo list is copied and both files are updated in the forked session rather than the original.

Written by the indexing model from the issue text.