[BUG] MCP Desktop Extensions Fail on MSIX-Packaged Claude Desktop (Windows)

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

"Windows-MCP" cant start when claude dekstop is installed using MSIX

What Should Happen?

Environment
Claude Desktop version: 1.1617.0.0 (MSIX package ID: Claude_pzs8sxrjxfjjc)
OS: Windows (Enterprise, managed via Microsoft Intune)
Extension: Windows-MCP (ant.dir.cursortouch.windows-mcp)
Deployment: MSIX distributed via Intune to corporate devices
Error Message
Unable to connect to extension server. Please try disabling and re-enabling the extension.
Relevant Log (mcp-server-Windows-MCP.log)
[Windows-MCP] [info] Using MCP server command: uv with args and path
'uv' is not recognized as an internal or external command, operable program or batch file.
[Windows-MCP] [error] spawn uv ENOENT
at ChildProcess._handle.onexit (node:internal/child_process:294:12)
[Windows-MCP] [error] Server disconnected.
Root Cause Analysis
The MSIX packaging format runs Claude Desktop in a virtualized sandbox via the Windows App Model runtime. This sandbox constructs a minimal process environment that includes only machine-level PATH entries (HKLM) and excludes user-level PATH entries (HKCU).
uv (the Python package manager required by most MCP extensions) installs itself to %USERPROFILE%\.local\bin and registers only in user-level PATH — making it invisible to Claude Desktop despite being correctly installed and accessible from any normal terminal session.
Additionally, the MSIX package virtualizes %APPDATA%, causing the "Edit Config" button in Claude Desktop to open the wrong config file (%APPDATA%\Claude\claude_desktop_config.json which doesn't exist), instead of the correct virtualized path:
%LOCALAPPDATA%\Packages\Claude_pzs8sxrjxfjjc\LocalCache\Roaming\Claude\claude_desktop_config.json
Impact
Affects all enterprise customers deploying Claude Desktop via Intune/MSIX
Every MCP extension that relies on uv (Python) or npx/node (JavaScript) fails out of the box
No workaround is available to end users without admin rights
Current Workaround Copy runtimes to a machine-level PATH location visible to the sandbox:
powershell
Copy-Item "$env:USERPROFILE\.local\bin\uv.exe" "C:\Windows\System32\uv.exe" -Force
Copy-Item "$env:USERPROFILE\.local\bin\uvx.exe" "C:\Windows\System32\uvx.exe" -Force
This must be deployed via an Intune remediation script on every managed device — it is not scalable.
Proposed Fix
Add <desktop6:EnvironmentVariables> to the AppxManifest.xml to expose user PATH to the sandboxed process:
xml
<desktop6:EnvironmentVariables>
<desktop6:EnvironmentVariable Name="PATH" Value="%USERPROFILE%\.local\bin;[EXISTING_PATH]"/>
</desktop6:EnvironmentVariables>
Alternatively, Claude Desktop could resolve the runtime path at startup by scanning common install locations (%USERPROFILE%\.local\bin, %APPDATA%\npm, etc.) and injecting them into the child process env before spawning MCP servers — similar to how VS Code handles this.

Error Messages/Logs

Relevant Log (mcp-server-Windows-MCP.log)

[Windows-MCP] [info] Using MCP server command: uv with args and path
'uv' is not recognized as an internal or external command, operable program or batch file.
[Windows-MCP] [error] spawn uv ENOENT
    at ChildProcess._handle.onexit (node:internal/child_process:294:12)
[Windows-MCP] [error] Server disconnected.

Steps to Reproduce

on a device with claude desktop app installed using MSIX (we use intune) try to install and enable extension "Windows-MCP"

Claude Model

None

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

1.1617.0.0

Platform

Other

Operating System

Windows

Terminal/Shell

Other

Additional Information

_No response_