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>

lib/mcp/protocol_deprecations.rb

@@ -0,0 +1,52 @@
+# frozen_string_literal: true
+
+require_relative "configuration"
+
+module MCP
+  module ProtocolDeprecations
+    extend self
+
+    ROOTS_MESSAGE =
+      "MCP Roots (`roots/list` and `notifications/roots/list_changed`) is deprecated as of protocol version " \
+        "2026-07-28 (SEP-2577). Use tool parameters, resource URIs, server configuration, or environment " \
+        "variables instead."
+    SAMPLING_MESSAGE =
+      "MCP Sampling (`sampling/createMessage`) is deprecated as of protocol version 2026-07-28 (SEP-2577). " \
+        "Use direct LLM provider APIs instead."
+    LOGGING_MESSAGE =
+      "MCP Logging (`logging/setLevel` and `notifications/message`) is deprecated as of protocol version " \
+        "2026-07-28 (SEP-2577). Use stderr or OpenTelemetry instead."
+
+    MESSAGES = {
+      roots: ROOTS_MESSAGE,
+      sampling: SAMPLING_MESSAGE,
+      logging: LOGGING_MESSAGE,
+    }.freeze
+
+    def deprecated_roots_sampling_logging?(protocol_version)
+      return false unless protocol_version
+
+      protocol_version >= Configuration::ROOTS_SAMPLING_LOGGING_DEPRECATED_PROTOCOL_VERSION
+    end
+
+    def warn_for(feature, protocol_version:, uplevel: 1)
+      return unless deprecated_roots_sampling_logging?(protocol_version)
+
+      Kernel.warn(MESSAGES.fetch(feature), uplevel: uplevel)
+    end
+
+    def warn_for_client_capabilities(capabilities, protocol_version:, uplevel: 1)
+      return unless deprecated_roots_sampling_logging?(protocol_version)
+      return unless capabilities
+
+      warn_for(:roots, protocol_version: protocol_version, uplevel: uplevel) if capability?(capabilities, :roots)
+      warn_for(:sampling, protocol_version: protocol_version, uplevel: uplevel) if capability?(capabilities, :sampling)
+    end
+
+    private
+
+    def capability?(capabilities, key)
+      capabilities.key?(key) || capabilities.key?(key.to_s)
+    end
+  end
+end