Custom MCP server tools not discovered after update to 2.1.116

Description

After updating Claude Code to version 2.1.116, custom MCP server tools are no longer being discovered and loaded into the deferred tools registry, even though the servers are connected and working correctly.

Steps to Reproduce

1. Have a custom MCP server configured in .mcp.json (e.g., google-mcp-server from ngs/homebrew-tap)
2. Update Claude Code to 2.1.116 (npm update -g @anthropic-ai/claude-code)
3. Start a new session
4. Run claude mcp list — server shows as "✓ Connected"
5. Try to use ToolSearch to find the custom server's tools — they don't appear
6. Only built-in claude.ai remote MCP connectors appear in the deferred tools list

Expected Behavior

Custom MCP server tools should be discovered and available via ToolSearch, prefixed with mcp__{server_name}__ (e.g., mcp__google__calendar_events_list).

Actual Behavior

• claude mcp list shows custom server as connected
• Querying the server directly via JSON-RPC confirms it exposes tools correctly:

``bash
echo '{"jsonrpc":"2.0","id":1,"method":"tools/list"}' | /opt/homebrew/bin/google-mcp-server serve
``
Returns 50+ tools (calendar_events_list, gmail_messages_list, etc.)

• But ToolSearch returns "No matching deferred tools found" for any custom server tools
• Only claude.ai built-in remote connectors appear in the registry

Environment

• Claude Code version: 2.1.116
• OS: macOS (Darwin 24.6.0, arm64)
• Custom MCP server: google-mcp-server v0.4.0 (from ngs/homebrew-tap)
• Shell: zsh

Additional Context

• The custom MCP server was working correctly before this update
• Re-adding the server via claude mcp remove + claude mcp add does not fix the issue
• Restarting the session does not fix the issue (tool discovery seems broken at startup)

Workaround

None currently — built-in claude.ai connectors work but custom stdio MCP servers do not have their tools loaded.