Overhaul tool handling (#89)

* Overhaul tool handling

- Renames [McpTool{Type}] to [McpServerTool{Type}], in order to distinguish representations of tools on the server from tools on the client.
- Enables [McpServerTool] methods to have arguments injected from DI, as well as a specific set of types from the implementation directly, like IMcpServer.
- Renames WithTools to WithToolsFromAssembly.
- All of the WithToolsXx methods now publish each individual McpServerTool into DI; other code can do so as well. The options setup code gathers all of the tools from DI and combines them into a collection which is then stored in McpServerOptions and used to construct the server.
- The server tools specified via DI as well as manually-provided handlers, using CallToolHandler as a fallback in case the requested tool doesn't exist in the tools collection, and ListToolsHandler augments the information for whatever tools exist.
- The tools are stored in McpServerOptions in a new McpServerToolCollection type, which is a thread-safe container that exposes add/removal notification. Adding/removing tools triggers a change notification that in turn sends a notification to the client about a tools update.
- The ServerOptions are exposed from the server instance.
- Removed cursor-based APIs from McpClientExtensions.
- Changed McpClientExtensions APIs to return `Task<IList<...>` rather than `IAsyncEnumerable<...>`.

I'm sure this will need to evolve further before we're "done", but it's a significant improvement from where we are now. One area I'm not super happy with is the notifying collection; that might work ok for a stdio server, where you can grab the created collection from the server's options and mutate it, but I don't know how well that's going to work for sse servers.

* Make McpServerTool{Collection} extensible

* Fix README.md example

* Add notifications test

* Address feedback

tests/ModelContextProtocol.Tests/Transport/StreamClientTransport.cs

@@ -0,0 +1,73 @@
+using Microsoft.Extensions.Logging.Abstractions;
+using ModelContextProtocol.Protocol.Messages;
+using ModelContextProtocol.Protocol.Transport;
+using ModelContextProtocol.Utils.Json;
+using System.Text.Json;
+
+namespace ModelContextProtocol.Tests.Transport;
+
+internal sealed class StreamClientTransport : TransportBase, IClientTransport
+{
+    private readonly JsonSerializerOptions _jsonOptions = McpJsonUtilities.DefaultOptions;
+    private Task? _readTask;
+    private CancellationTokenSource _shutdownCts = new CancellationTokenSource();
+    private readonly TextReader _stdin;
+    private readonly TextWriter _stdout;
+
+    public StreamClientTransport(TextReader stdin, TextWriter stdout)
+        : base(NullLoggerFactory.Instance)
+    {
+        _stdin = stdin;
+        _stdout = stdout;
+        _readTask = Task.Run(() => ReadMessagesAsync(_shutdownCts.Token), CancellationToken.None);
+        SetConnected(true);
+    }
+
+    public Task ConnectAsync(CancellationToken cancellationToken = default) => Task.CompletedTask;
+
+    public override async Task SendMessageAsync(IJsonRpcMessage message, CancellationToken cancellationToken = default)
+    {
+        string id = message is IJsonRpcMessageWithId messageWithId ?
+            messageWithId.Id.ToString() :
+            "(no id)";
+     
+        await _stdout.WriteLineAsync(JsonSerializer.Serialize(message)).ConfigureAwait(false);
+        await _stdout.FlushAsync(cancellationToken).ConfigureAwait(false);
+    }
+
+    private async Task ReadMessagesAsync(CancellationToken cancellationToken)
+    {
+        while (await _stdin.ReadLineAsync(cancellationToken).ConfigureAwait(false) is string line)
+        {
+            if (!string.IsNullOrWhiteSpace(line))
+            {
+                try
+                {
+                    if (JsonSerializer.Deserialize<IJsonRpcMessage>(line.Trim(), _jsonOptions) is { } message)
+                    {
+                        await WriteMessageAsync(message, cancellationToken).ConfigureAwait(false);
+                    }
+                }
+                catch (JsonException)
+                {
+                }
+            }
+        }
+    }
+
+    public override async ValueTask DisposeAsync()
+    {
+        if (_shutdownCts is { } shutdownCts)
+        {
+            await shutdownCts.CancelAsync().ConfigureAwait(false);
+            shutdownCts.Dispose();
+        }
+
+        if (_readTask is Task readTask)
+        {
+            await readTask.WaitAsync(TimeSpan.FromSeconds(5)).ConfigureAwait(false);
+        }
+
+        SetConnected(false);
+    }
+}