Perform jekyll-paginate deprecation warning correctly.

Fixes #3393

lib/jekyll/configuration.rb

@@ -262,11 +262,6 @@ module Jekyll
           "be removed in 3.0.0. We recommend you switch to Kramdown."
       end
 
-      if config.key?('paginate') && config['paginate'] && !(config['gems'] || []).include?('jekyll-paginate')
-        Jekyll::Deprecator.deprecation_message "You appear to have pagination " +
-          "turned on, but you haven't included the `jekyll-paginate` gem. " +
-          "Ensure you have `gems: [jekyll-paginate]` in your configuration file."
-      end
       config
     end
 

lib/jekyll/plugin_manager.rb

@@ -17,6 +17,7 @@ module Jekyll
     def conscientious_require
       require_plugin_files
       require_gems
+      deprecation_checks
     end
 
     # Require each of the gem plugins specified.
@@ -88,5 +89,14 @@ module Jekyll
       end
     end
 
+    def deprecation_checks
+      pagination_included =  (!(site.config['gems'] || []).include?('jekyll-paginate') || !defined?(Jekyll::Paginate))
+      if site.config['paginate'] && pagination_included
+        Jekyll::Deprecator.deprecation_message "You appear to have pagination " +
+          "turned on, but you haven't included the `jekyll-paginate` gem. " +
+          "Ensure you have `gems: [jekyll-paginate]` in your configuration file."
+      end
+    end
+
   end
 end