[BUG] Local MCP tool calls approved but never forwarded to server (Desktop + Claude Code in Desktop)

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?

Summary

Local custom MCP servers initialize and list tools successfully, but tools/call messages never reach the server process. Tool permissions are granted in the UI, but the actual invocation is silently dropped. Remote MCPs (e.g., Atlassian) work fine.

Environment

• Claude Desktop 2.1.92 (macOS Darwin 25.4.0)
• Node.js 24.14.0 (system and built-in identical)
• MCP SDK: @modelcontextprotocol/sdk ^1.10.0
• Custom MCP server: stdio transport, node command

Evidence

Server initializes correctly — mcp-server-aha.log shows successful initialize, notifications/initialized, and tools/list handshakes. 21 tools registered.

Permissions granted — main.log shows:

Emitted tool permission request ... for mcp__aha__aha_list_epics
Received permission response ... always

Calls never reach server — Zero tools/call entries in the entire 880-line mcp-server-aha.log. Grep for tools/call, error, Error, fail returns nothing.

Remote MCPs work — Same main.log shows Atlassian remote MCP succeeding:

Making remote MCP tool call: fetchAtlassian
Remote tool call succeeded: fetchAtlassian

No equivalent Making local MCP tool call log line exists for the local aha server.

Claude Code CLI works — The same MCP server, same config, same auth token successfully returns data when called from the Claude Code CLI process (within Desktop). The failure is specific to Desktop's conversation-to-MCP routing path.

API is reachable — curl to the Aha API from the same machine returns HTTP 200.

Repro steps

1. Configure a local stdio MCP server in claude_desktop_config.json
2. Restart Desktop, open a new Claude Code session
3. Ask Claude to call one of the MCP tools
4. Tool permission prompt appears, approve it
5. Claude reports "fetch failed" — server logs show no tools/call received

Additional context

• First noticed around 2026-04-09, initially in Cowork sessions (where custom MCP forwarding was already broken)
• Now also affects regular Claude Code in Desktop sessions
• Previously working — the same MCP server worked in Desktop prior to early April 2026

What Should Happen?

The Aha! connector was working fine when initially built - so it should work again :)

Error Messages/Logs

Steps to Reproduce

1. Configure a local stdio MCP server in claude_desktop_config.json
2. Restart Desktop, open a new Claude Code session
3. Ask Claude to call one of the MCP tools
4. Tool permission prompt appears, approve it
5. Claude reports "fetch failed" — server logs show no tools/call received

Claude Model

Sonnet (default)

Is this a regression?

Yes, this worked in a previous version

Last Working Version

Unsure - there's been almost daily updates to Claude Desktop

Claude Code Version

2.1.92

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_