[Bug] MCP server settings from claude.ai persist and override Claude Code configuration

Bug Description
MCP servers from claude.ai (web) are showing up in claude code. Despite disabling them inside Claude Code they get re-enabled in every new project. Claude web MCP server configuration should be seperate from Claude Code.

Environment Info

• Platform: darwin
• Terminal: ghostty
• Version: 2.1.104
• Feedback ID: ef32ee3f-1bd8-4e64-a459-4ea0a950b958

Errors

[]

  Manage MCP servers
  7 servers

    User MCPs (/Users/samm/.claude.json)
  ❯ dev-tools · ✔ connected
    excalidraw · ✔ connected

    claude.ai
    claude.ai Atlassian · ✔ connected
    claude.ai Gmail · △ needs authentication
    claude.ai Google Calendar · △ needs authentication
    claude.ai Last.FM · △ needs authentication

Above shows claude.ai web MCP servers configured and enabled despite never being added to Claude Code - and also being disabled in a previous Claude Code session.