feat: deprecate roots sampling and logging

Warn when Roots, Sampling, or Logging APIs are used with MCP protocol version 2026-07-28 or newer.

Add a shared protocol deprecation helper, YARD deprecation notes, and regression tests covering warnings at and after the deprecation threshold and no warnings for older or never-established protocol versions.

Closes https://github.com/modelcontextprotocol/ruby-sdk/issues/390

Co-authored-by: Qlaw <noreply@qlaw.quick.shopify.io>

test/mcp/server_roots_test.rb

@@ -4,6 +4,8 @@ require "test_helper"
 
 module MCP
   class ServerRootsTest < ActiveSupport::TestCase
+    include DeprecationWarningTestHelper
+
     class MockTransport < Transport
       attr_reader :requests
 
@@ -62,6 +64,36 @@ module MCP
       assert callback_called
     end
 
+    test "notifications/roots/list_changed warns when negotiated protocol version is 2026-07-28" do
+      server = Server.new(name: "test", version: "1.0")
+      server.handle({
+        jsonrpc: "2.0",
+        method: "initialize",
+        id: 1,
+        params: {
+          protocolVersion: "2026-07-28",
+          capabilities: { roots: { listChanged: true } },
+          clientInfo: { name: "test-client", version: "1.0" },
+        },
+      })
+
+      assert_deprecation_warning(/MCP Roots .*2026-07-28/) do
+        server.handle({
+          jsonrpc: "2.0",
+          method: "notifications/roots/list_changed",
+        })
+      end
+    end
+
+    test "notifications/roots/list_changed does not warn when negotiated protocol version is older" do
+      assert_no_deprecation_warning do
+        @server.handle({
+          jsonrpc: "2.0",
+          method: "notifications/roots/list_changed",
+        })
+      end
+    end
+
     test "notifications/roots/list_changed is handled as no-op by default" do
       result = @server.handle({
         jsonrpc: "2.0",
@@ -144,6 +176,21 @@ module MCP
       assert_silent { session.list_roots(related_request_id: "req-1") }
     end
 
+    test "ServerSession#list_roots warns when negotiated protocol version is 2026-07-28 and client lacks roots" do
+      session = ServerSession.new(server: @server, transport: @mock_transport)
+      session.store_client_info(client: { name: "test-client" }, capabilities: {})
+      session.mark_initialized!(protocol_version: "2026-07-28")
+
+      error = nil
+      assert_deprecation_warning(/MCP Roots .*2026-07-28/) do
+        error = assert_raises(RuntimeError) do
+          session.list_roots(related_request_id: "req-1")
+        end
+      end
+
+      assert_equal("Client does not support roots.", error.message)
+    end
+
     test "ServerSession#client_capabilities falls back to server global capabilities" do
       transport = MCP::Server::Transports::StreamableHTTPTransport.new(@server)
 
@@ -219,5 +266,31 @@ module MCP
       end
       assert_equal("No active stream for roots/list request.", error.message)
     end
+
+    test "ServerSession#list_roots warns when session negotiated protocol version is 2026-07-28" do
+      server = Server.new(name: "test", version: "1.0")
+      transport = MockTransport.new(server)
+
+      session = ServerSession.new(server: server, transport: transport, session_id: "s1")
+      server.handle(
+        {
+          jsonrpc: "2.0",
+          method: "initialize",
+          id: 1,
+          params: {
+            protocolVersion: "2026-07-28",
+            capabilities: { roots: {} },
+            clientInfo: { name: "http-client", version: "1.0" },
+          },
+        },
+        session: session,
+      )
+
+      assert_deprecation_warning(/MCP Roots .*2026-07-28/) do
+        session.list_roots(related_request_id: "req-1")
+      end
+
+      assert_equal Methods::ROOTS_LIST, transport.requests.first[:method]
+    end
   end
 end