[BUG] `claude mcp add --scope user` does not make MCP servers available across all projects

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?

The --scope user flag on claude mcp add is documented to provide "cross-project accessibility, making them available across all projects on your machine." In practice, the server is only registered for the current project directory and must be re-added for each new project.

Actual Behavior

• The server only appears in the project directory where claude mcp add was run
• In ~/.claude.json, the server is stored under projects.<project-path>.mcpServers — scoped to that specific project path, not globally
• New project directories get "mcpServers": {} with no inheritance from user-scoped servers
• Debug logs (--debug) from the new project show "Loading MCP configs..." but the user-scoped server is never mentioned

Environment

• Claude Code version: 2.1.72
• Platform: macOS (Darwin 24.6.0)

What Should Happen?

Expected Behavior

A --scope user MCP server should be available in all project directories without re-registering.

What the documentation says

From the official MCP documentation:

User scope: "User-scoped servers are stored in ~/.claude.json and provide cross-project accessibility, making them available across all projects on your machine while remaining private to your user account."

Where are MCP servers stored? - User and local scope: ~/.claude.json (in the mcpServers field or under project paths)

Error Messages/Logs

Steps to Reproduce

Steps to Reproduce

1. From project directory A, add an MCP server with user scope:

cd /path/to/project-a
claude mcp add --scope user --transport stdio my-server -- /path/to/server

1. Verify it works: launch Claude Code from project A, run /mcp — server appears and connects.

1. Launch Claude Code from a different project directory B (which has never had this server registered):

cd /path/to/project-b
claude

1. Run /mcp — the server does NOT appear.

Claude Model

Opus

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.72 (Claude Code)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

Additional Notes

• Other account-level settings in ~/.claude/settings.json (like hooks and model) ARE respected globally across all projects — making the MCP behavior inconsistent
• Putting mcpServers in ~/.claude/settings.json does not work either (those are silently ignored for MCP, though that file is not the documented location for MCP config)

Workaround

Run claude mcp add from each new project directory:

cd /path/to/new-project
claude mcp add --scope user --transport stdio my-server -- /path/to/server