[BUG] Cowork auto-start on launch wipes the entire `mcpServers` block from `claude_desktop_config.json` (Windows MSIX)

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?

On launch, Claude Desktop opens directly in the Cowork tab. When it does, it rewrites the entire claude_desktop_config.json, replacing the whole file with a coworkUserFilesPath + preferences-only structure and removing the complete mcpServers block — silently, with no warning, no error, and no backup.

Because Cowork is entered automatically at startup, the mcpServers block is destroyed on every launch, before the user can even switch to the Chat tab. This affects the entire mcpServers block, not any single server — all locally configured stdio MCP servers are lost at once (cf. #32345, where 36 servers were wiped).

Related to #32345 and #26073, but this describes a distinct trigger: automatic Cowork start on launch, not a manual tab open.

What Should Happen?

The mcpServers block should be preserved across launches. If the preferences system needs to write to the file, it should merge its keys into the existing JSON rather than replacing the whole file.

Error Messages/Logs

No error message or log file is generated. The failure is completely silent — the config file is simply overwritten and MCP tools become unavailable with no indication in the UI.

Steps to Reproduce

1. Manually add a valid mcpServers entry (local stdio server) to claude_desktop_config.json at the virtualized MSIX path: C:\Users\<user>\AppData\Local\Packages\Claude_pzs8sxrjxfjjc\LocalCache\Roaming\Claude\claude_desktop_config.json
2. Fully quit Claude Desktop (tray icon → Quit) and relaunch.
3. Observe that the app opens in the Cowork tab automatically.
4. Re-open the config file — the mcpServers block is gone.

Additional finding: setting "sidebarMode": "chat" in preferences as a workaround did not prevent the automatic Cowork start — the value appears to be ignored (see attached screenshot).

Claude Model

None

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

N/A — this is a Claude Desktop app bug (Electron/GUI), not the Claude Code CLI. Desktop app version: Claude 1.19367.0 (1a5be1) 2026-07-07T05:45:41.000Z

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

Other

Additional Information

This is a Claude Desktop app configuration bug, not a Claude Code CLI issue — some form fields above don't map cleanly since this template is CLI-oriented.