[BUG] Claude Desktop: Research mode can't use local (stdio) MCP servers, and nothing warns before the run starts

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet (closest: #85498, closed, different cause)
• [x] This is a single bug report
• [x] I am using the latest version of Claude Code (versions below; this report is about Claude Desktop's Research mode, not the CLI)

What's Wrong?

In Claude Desktop, a local stdio MCP server configured in claude_desktop_config.json is connected, and its tools work in a normal chat. Reproduced with Google's analytics-mcp (Google Analytics 4).

When Research is turned on in that chat:

• The research run can't reach the local server's tools. Only web-hosted connectors are available to it; a hosted connector returned data in the same run.
• Nothing warns before the run starts. The connector still shows as connected, and the model launches the research anyway.
• The gap only shows up in the final report, after the run's time is spent: "the analytics connector wasn't available in this session".
• The model can't fall back to the local connector either. It reported that while Research is on, it can only use the research tool in that chat.

Turning Research off restores the local tools in the same chat immediately; the server never stopped. This happened twice this week, with two different requests.

What Should Happen?

In order of preference:

1. Research can call local MCP tools, routed through the desktop client the way normal chats are.
2. If that isn't possible, show before the run which connectors it can and can't use (for example, grey out local connectors as "not available in Research"), and warn when the request needs one.
3. At minimum, tell the model which tools the research run can reach, so it warns before launching; and document the limitation in the Research help article.

Why it matters: the connector UI says "connected", so users reasonably expect Research to use it. A report that quietly lacks data the user believes was included is worse than an error. Today the only workaround is splitting every task by hand: Research for web sources, then a separate non-Research chat for local data.

Error Messages/Logs

Research report: "GA4 didn't: the analytics connector wasn't available in this session"
Model, same chat, earlier run: "while Research is on, I can only use the research tool in this chat"

Steps to Reproduce

1. In Claude Desktop on Windows, add any local stdio MCP server to claude_desktop_config.json and restart the app.
2. In a new chat with Research off, ask for data from that server. It works.
3. In the same chat, turn Research on and ask a question that needs that server's data.
4. The research run starts with no warning; the final report says the connector wasn't available.
5. Turn Research off in the same chat; the local tools work immediately.

Claude Model

Not sure / Multiple models

Is this a regression?

I don't know

Claude Code Version

Claude Desktop 2.9939.2.0 (Microsoft Store package); Claude Code 2.1.270. The bug is in the Desktop chat's Research mode.

Platform

Other (Claude Desktop, claude.ai account)

Operating System

Windows (Windows 11 Pro, build 26200)

Terminal/Shell

Other (Claude Desktop chat, not a terminal)

Additional Information

Hosted connectors work in Research and only local stdio servers are unavailable, which is consistent with the research run executing server-side. Related theme (a local MCP server shown as connected but unusable in some context): #95184, #80516.