[BUG] Local MCP servers (npx/url) from ~/.claude/settings.json missing from Claude Code desktop app local code sessions

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?

MCP servers configured in ~/.claude/settings.json under mcpServers are not being started or made available in Claude Code desktop app local code sessions.

When a local session starts, the app only loads its built-in app-level connectors (Claude in Chrome, mcp-registry, Claude Preview, ccd_session, etc.). The servers defined in settings.json (e.g. ado, sql-server, figma) are completely absent from the session — no tools are registered, no launch attempt is logged, no error is shown.

The main.log confirms this — replaceRemoteMcpServers reports only 7 servers, all app-level connectors, with no mention of settings.json servers:

[CCD] [replaceRemoteMcpServers] Calling SDK with 7 total servers {
serverNames: ['Claude in Chrome', 'mcp-registry', 'Claude Preview',
'ccd_session', 'ccd_directory', 'ccd_session_mgmt', 'scheduled-tasks']
}
The same settings.json configuration works correctly when Claude Code is launched via CLI (claude command from terminal) — all MCP servers start and tools are available.

What Should Happen?

MCP servers in settings.json should be started and their tools should be available in desktop app sessions, the same way they are in CLI sessions.

Error Messages/Logs

[CCD] [replaceRemoteMcpServers] Calling SDK with 7 total servers {
  serverNames: ['Claude in Chrome', 'mcp-registry', 'Claude Preview', 
                'ccd_session', 'ccd_directory', 'ccd_session_mgmt', 'scheduled-tasks']
}

Steps to Reproduce

Install Claude Code desktop app (version 2.1.138)
Add one or more MCP servers to ~/.claude/settings.json under mcpServers, e.g.:
{
"mcpServers": {
"ado": {
"command": "npx",
"args": ["-y", "@azure-devops/mcp", "bcgapplabs", "--authentication", "pat"],
"env": {
"AZURE_DEVOPS_TOKEN": "<your-pat>"
}
}
}
}
Open Claude Code desktop app
Open a local code session (open a project folder)
Try to use any tool from the configured MCP server

Claude Model

None

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.138

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

Windows Terminal

Additional Information

_No response_