[BUG] Claude Desktop silently destroys claude_desktop_config.json when MCP server uses url field

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?

When claude_desktop_config.json contains an MCP server configured with a url field (for Streamable HTTP transport per the MCP 2025-03-26 spec), Claude Desktop silently destroys the entire mcpServers section and strips some preferences keys on startup. No error is shown to the user — the config is simply rewritten with the offending entries removed.

This is a data loss bug. The app should either support the field or reject it with a visible error — not silently rewrite the user's config file.

Config Before Startup

{
  "mcpServers": {
    "brain-mcp": {
      "url": "http://127.0.0.1:7677/mcp"
    }
  },
  "preferences": {
    "quickEntryShortcut": "off",
    "launchPreviewPersistSession": true,
    "allowAllBrowserActions": false,
    "coworkScheduledTasksEnabled": true,
    "ccdScheduledTasksEnabled": true,
    "sidebarMode": "code",
    "bypassPermissionsModeEnabled": true,
    "coworkWebSearchEnabled": true
  }
}

Config After Startup (rewritten by the app)

{
  "preferences": {
    "coworkScheduledTasksEnabled": true,
    "ccdScheduledTasksEnabled": true,
    "sidebarMode": "code",
    "coworkWebSearchEnabled": true,
    "bypassPermissionsModeEnabled": true,
    "launchPreviewPersistSession": true
  }
}

Note:

• The entire mcpServers key is gone
• quickEntryShortcut and allowAllBrowserActions preferences were also stripped
• No error dialog, no log message, no indication that the config was modified

What Should Happen?

One of:

1. Support the url field for Streamable HTTP transport, as the MCP spec defines it and Claude Code CLI already supports it via "type": "http" in ~/.claude/settings.json
2. Show an error ("Unknown MCP server configuration: missing 'command' field") and leave the config file intact
3. Ignore the unrecognized entry but preserve it in the file

Silently deleting user configuration is never acceptable behavior.

Context

The url field is the natural way to configure a Streamable HTTP MCP server. The MCP 2025-03-26 specification replaces the old HTTP+SSE transport with Streamable HTTP, where the server exposes a single endpoint that accepts POST requests with JSON-RPC bodies. This is how shared MCP daemons (one process serving multiple Claude sessions) should be configured — spawning a separate stdio process per session is wasteful when the server maintains shared state like a database connection pool.

Claude Code CLI already supports this via ~/.claude/settings.json:

{
  "mcpServers": {
    "brain-mcp": {
      "type": "http",
      "url": "http://127.0.0.1:7677/mcp"
    }
  }
}

This works correctly. The gap is that Claude Desktop's claude_desktop_config.json doesn't support the same configuration format.

Current Workaround

Using mcp-remote as a stdio-to-HTTP bridge in claude_desktop_config.json:

{
  "mcpServers": {
    "brain-mcp": {
      "command": "npx",
      "args": ["mcp-remote", "http://127.0.0.1:7677/mcp"]
    }
  }
}

This works but defeats the purpose — it spawns a Node.js process per session to bridge between stdio and HTTP, adding latency and process overhead that the Streamable HTTP transport was designed to eliminate.

Related Issues

• #32708 — Claude Code CLI ignores "type": "streamable-http", falls back to SSE
• #33288 — Claude Code CLI sends GET instead of POST for Streamable HTTP
• #27142 — MCP Streamable HTTP client doesn't re-initialize after session invalidation

Steps to Reproduce

1. Edit ~/Library/Application Support/Claude/claude_desktop_config.json
2. Add an MCP server with a url field (no command):

``json
{"mcpServers": {"test": {"url": "http://127.0.0.1:8080/mcp"}}}
``

1. Restart Claude Desktop
2. Observe that claude_desktop_config.json has been rewritten with mcpServers removed

Environment

• macOS 15.4
• Claude Desktop (latest as of 2026-03-21)
• Claude Code 2.1.78