[BUG] MCP Tools usage

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?

Title: [BUG] Claude Desktop 1.24012.1 (macOS): all local MCP tool calls fail — approval gate fires, tools/call never reaches servers

Version: 1.24012.1 (0adcae), built 2026-07-21T20:59:53Z, macOS (Apple Silicon)

Timeline: Local MCP worked for weeks. At 2026-07-22 01:55:41 UTC all three MCP child processes were killed un-gracefully (mcp-server logs: "Server transport closed unexpectedly... process exiting early") — consistent with the auto-updater installing this build, compiled ~3h earlier. All MCP tool execution broken since.

Symptoms:

• Every tool call from every conversation fails with a generic error
• Servers are healthy: initialize / notifications/initialized / tools/list all succeed on every app launch; tool schemas appear in conversations
• mcp-server-*.log contains ZERO tools/call entries — calls never reach the servers
• claude.ai-web.log shows [MCP] tool_approval_gate firing per call (approvalRequired:false, hasBufferedInput:false) with no subsequent forward to the server
• Followed by: [REACT_QUERY_CLIENT] 404 not_found_error / side_channel_waiting_key_absent on POST /chat_conversations/{id}/tool_result — "Tool result could not be submitted. The request may have expired"

Ruled out: valid config (3x official mcp-server-filesystem, absolute paths), multiple full Cmd+Q restarts, complete delete + fresh reinstall from claude.ai/download, 6+ brand-new conversations, different servers. All fail identically.

Likely related: #22451 (all MCP calls hang ~5 min then "No result received from client-side tool execution")

What Should Happen?

Tools should work fine

Error Messages/Logs

Steps to Reproduce

Steps to Reproduce:

1. macOS, Claude Desktop 1.24012.1 (0adcae). Configure one or more local stdio MCP servers in claude_desktop_config.json — e.g. the official filesystem server:

   {
     "mcpServers": {
       "regalcare": {
         "command": "/Users/<user>/.nvm/versions/node/v22.17.1/bin/mcp-server-filesystem",
         "args": ["/Users/<user>/Documents/GitHub/<repo>"]
       }
     }
   }

1. Launch Claude Desktop. Server starts and handshakes successfully — Settings shows "running", and ~/Library/Logs/Claude/mcp-server-*.log shows initialize, notifications/initialized, and tools/list all completing.
2. Open any conversation (new or existing) and ask Claude to call any tool from the server, e.g. list_allowed_directories (zero-argument, touches no path).
3. Observe: Claude receives a generic tool execution failure.

Expected: Tool call is forwarded to the MCP server over stdio and returns a result, as in all prior versions.

Actual:

• claude.ai-web.log logs [MCP] tool_approval_gate for the call (approvalRequired:false) — the call reaches the app
• The server log shows no tools/call entry — the app never forwards it (grep -c "tools/call" ~/Library/Logs/Claude/mcp-server-*.log returns 0)
• claude.ai-web.log then logs a 404 not_found_error (side_channel_waiting_key_absent) on POST .../tool_result
• Reproduces 100%: every tool, every server, every conversation, after full restarts and a clean reinstall

Claude Model

None

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

Claude 1.24012.1 (0adcae) 2026-07-21T20:59:53.000Z

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_

[filesystem] [info] Message from client: method="notifications/initialized"
Client does not support MCP Roots, using allowed directories set from server args: [ 'C:\Users\user-name\source\repos\target-repo' ]
[filesystem] [info] Message from client: method="tools/list" id=1 params
[filesystem] [info] Message from server: id=1 result