[BUG] Project-level MCP's not available in /mcp

Environment

• Platform (select one):
• [x] Anthropic API
• [ ] AWS Bedrock
• [ ] Google Vertex AI
• [ ] Other: <!-- specify -->
• Claude CLI version: 1.0.54
• Operating System: macos 15.5
• Terminal: iTerm2

Bug Description

claude-code is unable to see project level MCP's.

Given this .mcp.json in project root:

{
  "mcpServers": {
    "filesystem": {
      "type": "stdio",
      "command": "bunx",
      "args": [
        "@modelcontextprotocol/server-filesystem",
        "/tmp"
      ]
    }
  }
}

Steps to Reproduce

Add any project-level mcp server.
Start claude-code.
Check /mcp command.

Expected Behavior

Project-level MCP to be visible

Actual Behavior

No MCP from the project level is available

Additional Context

<!-- Add any other context about the problem here, such as screenshots, logs, etc. -->