Here's a custom MCP tool I use to run commands and parse stdout / stderr all the time:

    try {
        const execPromise = promisify(exec);
        const { stdout, stderr } = await execPromise(command);
        if (stderr) {
            return {
                content: [{
                    type: "text",
                    text: `Error: ${stderr}`
                }],
                isError: true
            };
        }
        return {
            content: [{
                type: "text",
                text: stdout
            }],
            isError: false
        };
    } catch (error: any) {
        return {
            content: [{
                type: "text",
                text: `Error executing command: ${error.message}`
            }],
            isError: true
        };
    }

Yeah, if you want to be super technical, it's Node that does the actual command running, but in my opinion, that's as good as saying the MCP client is...

The point is that MCP servers expose tools that can do whatever MCP servers want them to do, and it doesn’t have to have anything to do with stdio.