Windows: /upgrade on a winget install replaces the WinGet\Links alias and leaves winget/Add-Remove Programs on the old version

[ImperiumTakp]

Describe the bug

On Windows, when Copilot CLI is installed with winget (GitHub.Copilot) and then updated with the built-in updater (/upgrade), the update bypasses winget. The new binary is written over winget's command alias instead of the winget package, so the install record is never updated:

• winget list and Add/Remove Programs keep reporting the old version, and winget offers an "upgrade" to the version that is already running.
• Software inventory tooling that relies on install records (Uninstall registry keys / winget) reports the wrong version.
• The winget package folder and the binary that actually runs are out of sync.

Affected version

GitHub Copilot CLI 1.0.91 (updated from 1.0.89 via /upgrade)

Steps to reproduce the behavior

1. Install with winget: winget install --id GitHub.Copilot -e (here this installed 1.0.89).
2. Run copilot and use /upgrade.
3. copilot --version reports 1.0.91.
4. winget list --id GitHub.Copilot still shows the old version, with the running version offered as an update:

   Name        Id             Version Available Source
   Copilot CLI GitHub.Copilot v1.0.89 v1.0.91   winget
   

5. The Uninstall entry HKCU:\Software\Microsoft\Windows\CurrentVersion\Uninstall\GitHub.Copilot_Microsoft.Winget.Source_8wekyb3d8bbwe still has DisplayVersion = v1.0.89.
6. Compare the two binaries:

   $links = "$env:LOCALAPPDATA\Microsoft\WinGet\Links\copilot.exe"
   $pkg   = "$env:LOCALAPPDATA\Microsoft\WinGet\Packages\GitHub.Copilot_Microsoft.Winget.Source_8wekyb3d8bbwe\copilot.exe"
   (Get-Item $links).LinkType                      # empty: no longer a symlink
   (Get-Item $links).VersionInfo.ProductVersion    # 1.0.91
   (Get-Item $pkg).VersionInfo.ProductVersion      # 1.0.89 (unchanged)

   The other winget portable packages in WinGet\Links are still symbolic links into WinGet\Packages; for Copilot CLI the link has been replaced by a regular file containing the new version.

Expected behavior

Either of:

• The updater detects a winget-managed install and defers to the package manager (for example: "Copilot CLI was installed with winget; run winget upgrade GitHub.Copilot"), or
• The update is applied in a way that keeps the winget install consistent (package folder, WinGet\Links alias and install record reflect the running version).

The same question likely applies to other package-manager installs (Homebrew, npm) where a self-update can diverge from what the package manager reports.

Additional context

• OS: Windows 11, x64
• Shell: PowerShell 7
• Install method: winget (portable package, user scope)
• The old 1.0.89 binary remains in the winget package folder; only the WinGet\Links\copilot.exe alias was replaced.