[BUG] project scoped mcp servers not listed

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

I added supabase and sentry mcp servers to my project scope but they are not shown where listing it either through the command line or through /mcp which means I can't authenticate.

See:

✗ claude mcp get supabase
supabase:
  Scope: Project config (shared via .mcp.json)
  Status: ⚠ Needs authentication
  Type: http
  URL: https://mcp.supabase.com/mcp?project_ref=foo

To remove this server, run: claude mcp remove "supabase" -s project
✗ claude mcp list
Checking MCP server health...

github: https://api.githubcopilot.com/mcp (HTTP) - ✓ Connected
context7: https://mcp.context7.com/mcp (HTTP) - ✓ Connected

Now... when I do /mcp inside claude code I also only see github and context7. I think this might be a 2.0.55 regression because I think it was working in 2.0.54.

What Should Happen?

I should see all mcp servers and be able to authenticate.

Error Messages/Logs

Steps to Reproduce

Described above.

Claude Model

None

Is this a regression?

Yes, this worked in a previous version

Last Working Version

2.0.54

Claude Code Version

2.0.55

Platform

Anthropic API

Operating System

Other Linux

Terminal/Shell

Other

Additional Information

_No response_