Allow $ref in Tool::Schema for protocol version 2025-11-25

`Tool::Schema` rejected `$ref` with an `ArgumentError`.
Earlier MCP spec versions (2024-11-05 through 2025-06-18) did not define
a JSON Schema dialect or reference the `$ref` keyword. `inputSchema` was described
only as "JSON Schema defining expected parameters" with no further constraints:

- https://modelcontextprotocol.io/specification/2024-11-05/server/tools
- https://modelcontextprotocol.io/specification/2025-06-18/server/tools

The MCP spec 2025-11-25 introduced a "JSON Schema Usage" section that adopts
JSON Schema 2020-12 as the default dialect. Since `$ref` is a core keyword in 2020-12,
it is now allowed for protocol version 2025-11-25 and later.

- https://modelcontextprotocol.io/specification/2025-11-25/basic#json-schema-usage
- https://modelcontextprotocol.io/specification/2025-11-25/server/tools
- https://json-schema.org/draft/2020-12/release-notes

For backward compatibility with older protocol versions (2025-06-18 and earlier),
`Server#validate!` continues to raise `ArgumentError` when a tool input schema contains `$ref`.
This preserves the existing behavior for servers targeting those spec versions.

lib/mcp/server.rb

@@ -219,6 +219,14 @@ module MCP
           message = "Error occurred in server_info. `description` is not supported in protocol version 2025-06-18 or earlier"
           raise ArgumentError, message
         end
+
+        tools_with_ref = @tools.each_with_object([]) do |(tool_name, tool), names|
+          names << tool_name if schema_contains_ref?(tool.input_schema_value.to_h)
+        end
+        unless tools_with_ref.empty?
+          message = "Error occurred in #{tools_with_ref.join(", ")}. `$ref` in input schemas is supported by protocol version 2025-11-25 or higher"
+          raise ArgumentError, message
+        end
       end
 
       if @configuration.protocol_version <= "2025-03-26"
@@ -259,6 +267,17 @@ module MCP
       raise ToolNotUnique, duplicated_tool_names unless duplicated_tool_names.empty?
     end
 
+    def schema_contains_ref?(schema)
+      case schema
+      when Hash
+        schema.any? { |key, value| key.to_s == "$ref" || schema_contains_ref?(value) }
+      when Array
+        schema.any? { |element| schema_contains_ref?(element) }
+      else
+        false
+      end
+    end
+
     def handle_request(request, method)
       handler = @handlers[method]
       unless handler

lib/mcp/tool/schema.rb

@@ -31,10 +31,6 @@ module MCP
         case schema
         when Hash
           schema.each_with_object({}) do |(key, value), result|
-            if key.casecmp?("$ref")
-              raise ArgumentError, "Invalid JSON Schema: $ref is not allowed in tool schemas"
-            end
-
             result[yield(key)] = deep_transform_keys(value, &block)
           end
         when Array