[Server] (Re-)Implement Manual Registration of Capabilities via ServerBuilder

[pronskiy]

Describe the bug
I'm trying to implement the most basic mcp server, but the tools list is empty.

To Reproduce

<?php

require __DIR__ . '/../vendor/autoload.php';

use Mcp\Server;
use Mcp\Server\Transport\StdioTransport;
use Psr\Log\NullLogger;

Server::make()
    ->withLogger(new NullLogger())
    ->withServerInfo('Stdio Calculator', '1.1.0', 'Basic Calculator over STDIO transport.')
    ->withTool(function (float $a, float $b, string $operation = 'add'): float {
        return match ($operation) {
            'add' => $a + $b,
            'subtract' => $a - $b,
            'multiply' => $a * $b,
            'divide' => $a / $b,
            default => throw new InvalidArgumentException('Invalid operation'),
        };
    }, name: 'calculator', description: 'Perform basic math operations (add, subtract, multiply, divide)')
    ->build()
    ->connect(new StdioTransport());

npx @modelcontextprotocol/inspector php calc.php

Expected behavior
There should be calculator tool in the list.

[chr-hertel]

Yup, true, that's know atm - focused on discovery first. I wanted to level up example for example in #5. So you can see there what makes sense to test :)