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Claude Desktop (Store): stdio MCP tools discovered but tools/call never reaches server (regression) #225

@cfrancisTimbercreek

Description

@cfrancisTimbercreek

Description
Local stdio MCP servers are discovered correctly (initialize + tools/list succeed), but tools/call messages never reach the server process. The model either falls back to built-in tools or responds "no matching tools found."

Remote MCP servers (HTTP-based, e.g. Microsoft 365, Context7) continue to work — only local stdio servers are affected.

Environment
Claude Desktop: Microsoft Store, v1.569.0.0
OS: Windows 11 Enterprise 10.0.26200
Confirmed on: 2 separate PCs, same Store version

Reproduction
Configure any stdio MCP server in %APPDATA%\Claude\claude_desktop_config.json (even a trivial ping server that just returns "Pong!")
Open Claude Desktop → Developer Settings → server shows as "running"
Ask Claude to call a tool from that server
Tool call never reaches the server — no log entry, no response
Minimal test server (test-ping-server.mjs):

import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
const server = new McpServer({ name: "test-ping", version: "1.0.0" });
server.tool("ping", "Returns Pong!", {}, async () => ({
content: [{ type: "text", text: "Pong!" }],
}));
const transport = new StdioServerTransport();
await server.connect(transport);
Config:

{
"mcpServers": {
"test-ping": {
"command": "node",
"args": ["path/to/test-ping-server.mjs"]
}
}
}
Timeline
Thu 2026-04-03: Working correctly (tools/call reached server, responses returned)
Sun 2026-04-06: Broken (tools/call never reaches server). A Claude Desktop auto-update occurred between these dates.
What we ruled out
Config path: Migrated from Store sandbox path (%LOCALAPPDATA%\Packages\Claude_pzs8sxrjjc...) to standard %APPDATA%\Claude\ — no change
Server code: Same servers work perfectly in Claude Code (VS Code extension) via .mcp.json
Auth/complexity: Even the trivial ping server above fails identically
Multiple PCs: Reproduced on 2 machines with independent installs
Expected behavior
tools/call messages should be routed to the stdio server process, and the response should be returned to the model.

Actual behavior
tools/call is silently dropped. The server process receives initialize and tools/list but never tools/call. The model behaves as if the tools don't exist.

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