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

[mjbiamonte]

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