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claude-code - 💡(How to fix) Fix Custom MCP server tools not discovered after update to 2.1.116 [1 comments, 2 participants]

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anthropics/claude-code#51736•Fetched 2026-04-22 07:54:13
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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.

Root Cause

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.

Fix Action

Workaround

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

Code Example

echo '{"jsonrpc":"2.0","id":1,"method":"tools/list"}' | /opt/homebrew/bin/google-mcp-server serve
RAW_BUFFERClick to expand / collapse

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: 
    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.

extent analysis

TL;DR

The issue is likely due to a compatibility problem between Claude Code version 2.1.116 and custom MCP servers, preventing tool discovery and loading into the deferred tools registry.

Guidance

  • Verify that the custom MCP server is correctly configured in .mcp.json and that the server is running and accessible.
  • Check the JSON-RPC response from the custom server to ensure it is returning the expected tool list, as shown in the example command: echo '{"jsonrpc":"2.0","id":1,"method":"tools/list"}' | /opt/homebrew/bin/google-mcp-server serve.
  • Investigate potential changes in the Claude Code 2.1.116 update that may affect custom MCP server compatibility, such as changes to the tool discovery mechanism or JSON-RPC handling.
  • Consider downgrading Claude Code to a previous version to see if the issue persists, which could help determine if the problem is specific to version 2.1.116.

Example

No code snippet is provided as the issue seems to be related to compatibility and configuration rather than a specific code problem.

Notes

The issue may be specific to the combination of Claude Code version 2.1.116 and custom MCP servers, and further investigation is needed to determine the root cause. The fact that built-in claude.ai connectors work suggests that the problem is not with the ToolSearch functionality itself, but rather with the integration of custom MCP servers.

Recommendation

Apply a workaround by downgrading Claude Code to a previous version where custom MCP servers were working correctly, until a fix for version 2.1.116 is available. This is because the custom MCP server was working correctly before the update, suggesting a regression in the new version.

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claude-code - 💡(How to fix) Fix Custom MCP server tools not discovered after update to 2.1.116 [1 comments, 2 participants]