Claude Desktop launches command args incorrectly

[hemna]

Describe the bug
Trying to launch my own mcp.py script as an Claude Desktop MCP server.

Claude Desktop for Mac
Version 0.9.3

To Reproduce
Steps to reproduce the behavior:

1. Edit claude_desktop_config.json and add entry to mcpServers with args.
2. Launch Claude Desktop

Expected behavior
A clear and concise description of what you expected to happen.
I expect the mcp server to get called. It doesn't because of a weird args issue.

Logs
Why is it using 2 foward slashes before the args? //foo.py was not in my config?

│2025-05-30T14:54:14.103-0400 2025-05-30T18:54:14.100Z [weather] [info] Message from client: {"method":"initialize","params":{"protocolVersion":"2024-11-05","capabilities":{},"clientInfo":{"name":"c│
│2025-05-30T14:54:14.254-0400 /Users/I530566/devel/mine/hamradio/haminfo/.venv/bin/python: can't open file '//foo.py': [Errno 2] No such file or directory                                            │
│2025-05-30T14:54:14.257-0400 2025-05-30T18:54:14.257Z [weather] [info] Server transport closed                                                                                                       │
│2025-05-30T14:54:14.258-0400 2025-05-30T18:54:14.257Z [weather] [info] Client transport closed

Additional context
My claude_desktop_config.json

{
  "mcpServers": {
    "weather": {
      "command": "/Users/I530566/devel/mine/hamradio/haminfo/.venv/bin/python",
      "args": [
        "foo.py"
      ],
      "env": {
        "VIRTUAL_ENV":"/Users/I530566/devel/mine/hamradio/haminfo/.venv"
      }
    }
  },
  "logging": {
    "level": "DEBUG"
  },
  "globalShortcut": "Ctrl+Q"
}

[hemna]

Also, it seems that the env is completely ignored.

I have a python virtual environment setup at the location provided by VIRTUAL_ENV and it's ignored.

[hemna]

I've also tried this setup.

{
  "mcpServers": {
    "weather": {
      "command": "/Users/I530566/devel/mine/hamradio/haminfo/.venv/bin/haminfo",
      "args": [
        "mcp-server",
        "-c /Users/I530566/docker/haminfo/config/haminfo.conf",
        "--loglevel DEBUG"
      ],
      "env": {
        "VIRTUAL_ENV":"/Users/I530566/devel/mine/hamradio/haminfo/.venv"
      }
    }
  },
  "logging": {
    "level": "DEBUG"
  },
  "globalShortcut": "Ctrl+Q"
}

which results in this error

│2025-05-30T15:13:00.533-0400 2025-05-30T19:13:00.462Z [weather] [info] Initializing server...                                                                                                        │
│2025-05-30T15:13:00.538-0400 2025-05-30T19:13:00.536Z [weather] [info] Server started and connected successfully                                                                                     │
│2025-05-30T15:13:00.538-0400 2025-05-30T19:13:00.537Z [weather] [info] Message from client: {"method":"initialize","params":{"protocolVersion":"2024-11-05","capabilities":{},"clientInfo":{"name":"c│
│2025-05-30T15:13:02.958-0400 Usage: haminfo mcp-server [OPTIONS]                                                                                                                                     │
│2025-05-30T15:13:02.958-0400 Try "haminfo mcp-server -h" for help.                                                                                                                                   │
│2025-05-30T15:13:02.958-0400                                                                                                                                                                         │
│2025-05-30T15:13:02.958-0400 Error: no such option: --loglevel DEBUG                                                                                                                                 │
│2025-05-30T15:13:03.074-0400 2025-05-30T19:13:03.073Z [weather] [info] Server transport closed                                                                                                       │
│2025-05-30T15:13:03.074-0400 2025-05-30T19:13:03.073Z [weather] [info] Client transport closed

Launching the app from the command line in the same way described by the weather mcp server works fine.

╭─I530566 HFF2W62GTV in ~/Library/Application Support/Claude   
└─> /Users/I530566/devel/mine/hamradio/haminfo/.venv/bin/haminfo mcp-server -c /Users/I530566/docker/haminfo/config/haminfo.conf --loglevel DEBUG

[hemna]

this is why I suspected the launching of the app with the args from Claude Desktop were broken...which is shown in my first post with the failure of //foo.py example.

That same exact setup as described in #1971 (comment) works just fine in the Cursor IDE.