MCP Tools Appearing Duplicated in Claude Code Interface

Bug Report

All MCP (Model Context Protocol) tools are appearing duplicated in the Claude Code tool selection interface.

Environment

• Platform: Linux (WSL2)
• Claude Code: Latest version
• MCP Server: zen-mcp-server (affects all MCP servers)

Issue

Every MCP tool shows up multiple times in the tool selection interface, creating confusion when selecting tools.

Expected Behavior

Each MCP tool should appear only once.

Actual Behavior

All MCP tools are displayed multiple times.

Reproduction

1. Install any MCP server
2. Open Claude Code
3. View MCP tool selection
4. Notice duplicate tool entries

Visual Evidence

Screenshot attached showing the duplication issue.

This affects all MCP server integrations in Claude Code.

Yup, having the same issue for past few days thought I messed it up somehow with my custom MCP's.....

Same issue, regardless of where it's installed from.

This will be fixed in the next version (1.0.41)

This is fixed now!

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