[BUG] Global MCPs Not Available in Chat

Environment

• Claude CLI version: 1.0.72 (Claude Code)
• Operating System: macOS 15.6
• Terminal: zsh

Bug Description

Running claude mcp list and asking claude to use the mcps are not synced.

[redacted] % claude
╭───────────────────────────────────────────────────╮
│ ✻ Welcome to Claude Code!                         │
│                                                   │
│   /help for help, /status for your current setup  │
│                                                   │
│   cwd: [redacted]  │
╰───────────────────────────────────────────────────╯

 ※ Tip: Run claude --continue or claude --resume to resume a conversation

> check mcps

⏺ I'll check the available MCP servers for you.

⏺ listMcpResources(List all MCP resources)
  ⎿  (No resources found)                                                                                                                                  

⏺ No MCP resources are currently available. This means either no MCP servers are configured or connected, or they don't expose any resources at the moment.

[redacted] % claude mcp list
Checking MCP server health...

playwright: npx @playwright/mcp@latest - ✓ Connected
github: docker run -i --rm -e GITHUB_PERSONAL_ACCESS_TOKEN ghcr.io/github/github-mcp-server - ✓ Connected
firecrawl-mcp: npx -y firecrawl-mcp - ✓ Connected
reddit: uvx reddit-mcp - ✓ Connected
[redacted] % 

Steps to Reproduce

1. Add "mcpServers" to the root of /Users/[redacted]/.claude.json
2. Run claude and ask check mcps -> Shows no available MCPs.
3. Run claude mcp list -> Shows available MCPs connected.

Expected Behavior

Global MCPs should be available in any folder.

Actual Behavior

Something is causing claude to not see the available MCPs.