[BUG] Windows-MCP tools available but not discoverable in Cowork project sessions — works when explicitly invoked

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 tools (PowerShell, Process, Screenshot, etc.) are installed, enabled, and functional — but are not discoverable via ToolSearch at the start of a new Cowork project conversation. ToolSearch returns "No matching deferred tools found" for queries like select:mcp__Windows-MCP__PowerShell.
However, the tools do work when explicitly invoked mid-conversation. If I tell Claude "use the Windows MCP connector," it successfully loads the tools and runs PowerShell commands on my machine.
This means Claude defaults to asking the user to copy-paste PowerShell commands manually, even though it has direct access to the machine.

What Should Happen?

Windows-MCP tools should be discoverable via ToolSearch at conversation start, or ideally listed as deferred tools in the system prompt, so Claude can use them proactively without the user having to explicitly request it.

Error Messages/Logs

Steps to Reproduce

Install and enable Windows-MCP extension (local mode) in Claude Desktop
Create a Cowork project with custom instructions referencing Windows-MCP
Verify Windows-MCP is toggled ON in the project's Connectors panel
Start a new conversation in the project
Send a message like "My CPU is at 70°C, diagnose it"
Claude calls ToolSearch for Windows-MCP tools → returns "No matching deferred tools found"
Claude falls back to providing manual PowerShell commands
In the same conversation, send "use the windows mcp connector"
Claude successfully loads tools and runs commands directly on the machine

Claude Model

Opus

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

1.3561.0

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

Other

Additional Information

The same behavior occurs with scheduled tasks: the task runs but cannot find the Windows-MCP tools, aborting diagnostics (related to #40835)
The tools work reliably in the same session once loaded — the issue is purely discovery/initialization
Project custom instructions explicitly naming the tools and providing ToolSearch queries do not help
Standalone Cowork sessions (without a project) show the same behavior — tools work when requested but aren't auto-discovered