[UX] Claude Code inside Desktop App has invisible separate MCP config — no indication which environment is active

Preflight Checklist

• [x] I have searched existing requests and this feature hasn't been requested yet
• [x] This is a single feature request (not multiple features)

Problem Statement

When Claude Code runs inside the Claude Desktop application, it uses its own separate MCP configuration (~/.claude.json) rather than the Desktop app's config (~/Library/Application Support/Claude/claude_desktop_config.json). There is no indication anywhere in the UI that these are two separate MCP environments.

This leads to confusing situations:

1. User runs Claude Code inside Claude Desktop
2. User configures MCP servers in Claude Desktop's config
3. Those MCP servers are NOT available in the Claude Code session
4. User has no idea why — there's no indication that a different config is active

Conversely, MCP servers added to Claude Code's config (e.g. via claude mcp add) don't appear in the Claude Desktop interface.

Proposed Solution

• Display active MCP config path/context in the UI or /status output
• Document clearly that Claude Code and Claude Desktop have independent MCP registries even when Code runs inside Desktop
• Consider a unified config or at least cross-visibility between the two

Alternative Solutions

_No response_

Priority

Critical - Blocking my work

Feature Category

CLI commands and flags

Use Case Example

A user configures a custom remote MCP server in Claude Desktop's config. They then open Claude Code inside the Desktop app and ask which MCP servers are available — the custom server is absent with no explanation. The user has no way to know they need to re-add it via claude mcp add in a completely separate config file.

Additional Context

Related issues:

• #27527 — Claude gives wrong-context MCP config instructions
• #28144 — (closed duplicate) Claude should know its runtime environment

Platform: macOS

---
Issue drafted with the assistance of Claude AI (Claude Code within Claude Desktop)