Replace assert_empty with assert_equal using explicit literals

Due to overly aggressive detection by RuboCop Minitest, the distinction between `[]` and `{}` was uniformly replaced with `assert_empty`,
making it impossible to differentiate between them.
As a result of https://github.com/rubocop/rubocop-minitest/issues/344, where the `Minitest/AssertEmptyLiteral` cop was disabled,
the return value has been expressed using explicit literal forms.

test/mcp/server/transports/stdio_notification_integration_test.rb

@@ -213,7 +213,7 @@ module MCP
           # This test verifies the complete integration from server to transport
 
           # Start with no output
-          assert_empty @mock_stdout.output
+          assert_equal([], @mock_stdout.output)
 
           # Add a prompt and notify
           @server.define_prompt(