Inconsistent configuration requirements for different MCP server installation methods

[ChanMeng666]

Describe the bug
There is an inconsistency in the required configuration for MCP servers in claude_desktop_config.json depending on how they were installed. Specifically:

• Servers installed via npm install -g require "command": "D:\\Program\\nvm\\node.exe" configuration
• Servers installed via npx @smithery/cli install require "command": "npx" configuration

Using the wrong configuration type results in MCP connection errors, but this requirement is not documented and may cause confusion for users.

To Reproduce
Steps to reproduce the behavior:

1. Install MCP servers using different methods:

   # Method 1: Global NPM install
   npm install -g @modelcontextprotocol/server-sequential-thinking
   npm install -g exa-mcp-server
   
   # Method 2: Smithery CLI install
   npx @smithery/cli install mcp-obsidian --client claude
   npx @smithery/cli install @browserbasehq/mcp-browserbase --client claude

2. Try configuring all servers with "command": "npx"
3. Try configuring all servers with "command": "D:\\Program\\nvm\\node.exe"
4. Observe that each installation method requires its specific configuration approach

Expected behavior

• Configuration method should be consistent regardless of installation method
• If different configuration methods are required, this should be clearly documented in the README
• Ideally, there should be a single recommended way to configure MCP servers to avoid confusion

Logs
System information:

Microsoft Windows [Version 10.0.26100.2605]
Node location: D:\Program\nvm\node.exe
Global npm root: D:\Program\nvm\node_modules

Installation logs and configuration file:

C:\Users\0>npm install -g @modelcontextprotocol/server-sequential-thinking
added 32 packages in 13s

C:\Users\0>npm install -g exa-mcp-server
added 25 packages in 5s

C:\Users\0>npx @smithery/cli install mcp-obsidian --client claude
[...]
✓ Successfully installed package 'mcp-obsidian' for claude

C:\Users\0>npx -y @smithery/cli install @browserbasehq/mcp-browserbase --client claude
[...]
✓ Successfully installed package '@browserbasehq/mcp-browserbase' for claude

Current working configuration in claude_desktop_config.json:

{
    "sequential-thinking": {
      "command": "D:\\Program\\nvm\\node.exe",
      "args": [
        "D:\\Program\\nvm\\node_modules\\@modelcontextprotocol\\server-sequential-thinking\\dist\\index.js"
      ]
    },
    "exa": {
      "command": "D:\\Program\\nvm\\node.exe",
      "args": [
        "D:\\Program\\nvm\\node_modules\\exa-mcp-server\\build\\index.js"
      ],
      "env": {
        "EXA_API_KEY": ""
      }
    },
    "mcp-obsidian": {
      "command": "npx",
      "args": [
        "-y",
        "mcp-obsidian",
        "D:\\github_repository\\obsidian"
      ]
    },
    "@browserbasehq-mcp-browserbase": {
      "command": "npx",
      "args": [
        "-y",
        "@browserbasehq/mcp-browserbase"
      ],
      "env": {
        "BROWSERBASE_API_KEY": "",
        "BROWSERBASE_PROJECT_ID": ""
      }
    }
}

Additional context
This inconsistency makes it difficult for users to set up multiple MCP servers, as they need to remember or figure out which configuration method to use based on how each server was installed. A unified configuration approach would greatly improve the user experience.

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Configuration information for MCP applications installed using npm install -g :

Configuration information for successful connection:

Configuration information when the connection fails:

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Configuration information for MCP applications installed using npx -y @smithery/cli install :

Configuration information for successful connection:

Configuration information when the connection fails:

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CMD operation log: