Auto-update applied during startup silently prevents custom agents from loading

### Describe the bug

When the Copilot CLI auto-updates itself during startup, custom agents fail to load for that session with no
indication that an update occurred or that a restart is needed. The startup message looks identical to a normal
healthy startup — only the version number differs — making it appear as though agents are simply broken.

### Affected version

GitHub Copilot CLI 1.0.48.

### Steps to reproduce the behavior

1. Run Copilot CLI when a newer version is available (copilot)
2. The CLI auto-updates in the background during startup
3. Observe the startup message — custom agents from .github/agents/ are absent
4. Exit and restart the CLI
5. Observe all agents load correctly on the second launch

### Expected behavior

When an auto-update is applied during startup, the CLI should display a notice in the terminal informing the user that an update was
applied and a restart is required to fully initialize the environment (including custom agents).

Something like:

● ✓ Updated to v1.0.48 — please restart to load all agents and tools

Actual behavior

First launch (update applied silently during startup):

● Environment loaded: 1 skill, 1 MCP server

Second launch (no update, normal startup):

● Environment loaded: 1 skill, 1 MCP server, 11 agents

There is no message indicating an update occurred. From the user's perspective, it simply looks like the agents
failed to load.

### Additional context

Log evidence

The auto-update activity is visible in the log (~/.copilot/logs/), but nothing surfaces to the terminal:

[INFO] Starting Copilot CLI: 1.0.47
[INFO] Successfully downloaded package, restart to update to version 1.0.48
[INFO] Downloading updated win32-x64 binary...
[INFO] Successfully updated binary
[INFO] Cleaned up 1 old package version(s): 1.0.40

Environment

- OS: Windows 11 (x64)
- Shell: PowerShell
- CLI version at first launch:
1.0.47
- CLI version after restart:
1.0.48
- Custom agents: 11 (defined in .github/agents/ in a remote repository)
- Node.js: v24.15.0

Reproduce the startup flow from the issue with a newer version available, then inspect ~/.copilot/logs/ for the auto-update sequence and the CLI startup entry point. Confirm the behavior on Windows PowerShell with custom agents in .github/agents/. Done means an update is surfaced in the terminal and the user is told to restart before agents and tools are fully initialized.

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