Stubbing out the configuration makes for much less warnings.

test/helper.rb

@@ -11,7 +11,11 @@ class Test::Unit::TestCase
   include RR::Adapters::TestUnit
 
   def dest_dir
-    File.join(File.dirname(__FILE__), *%w[dest])
+    File.join(File.dirname(__FILE__), 'dest')
+  end
+
+  def source_dir
+    File.join(File.dirname(__FILE__), 'source')
   end
 
   def clear_dest

test/test_generated_site.rb

@@ -4,9 +4,11 @@ class TestGeneratedSite < Test::Unit::TestCase
   context "generated sites" do
     setup do
       clear_dest
-      @source = File.join(File.dirname(__FILE__), *%w[source])
-      @configuration = Jekyll.configuration 'source' => @source, 'destination' => dest_dir
-      @site = Site.new(@configuration)
+      stub(Jekyll).configuration do
+        Jekyll::DEFAULTS.merge({'source' => source_dir, 'destination' => dest_dir})
+      end
+
+      @site = Site.new(Jekyll.configuration)
       @site.process
       @index = File.read(File.join(dest_dir, 'index.html'))
     end
@@ -16,9 +18,8 @@ class TestGeneratedSite < Test::Unit::TestCase
     end
 
     should "render post.content" do
-      latest_post = Dir[File.join(@source, '_posts/*')].last
-      post = Post.new(@site, @source, '', File.basename(latest_post))
-      #Jekyll.content_type = post.determine_content_type
+      latest_post = Dir[File.join(source_dir, '_posts/*')].last
+      post = Post.new(@site, source_dir, '', File.basename(latest_post))
       post.transform
       assert @index.include?(post.content)
     end

test/test_post.rb

@@ -2,7 +2,7 @@ require File.dirname(__FILE__) + '/helper'
 
 class TestPost < Test::Unit::TestCase
   def setup_post(file)
-    Post.new(@site, File.join(File.dirname(__FILE__), *%w[source]), '', file)
+    Post.new(@site, File.join(File.dirname(__FILE__), 'source'), '', file)
   end
 
   def do_render(post)

test/test_site.rb

@@ -3,10 +3,10 @@ require File.dirname(__FILE__) + '/helper'
 class TestSite < Test::Unit::TestCase
   context "creating sites" do
     setup do
-      @source = File.join(File.dirname(__FILE__), 'source')
-      @configuration = Jekyll.configuration(:source => @source, :destination => dest_dir)
-
-      @s = Site.new(@configuration)
+      stub(Jekyll).configuration do
+        Jekyll::DEFAULTS.merge({'source' => source_dir, 'destination' => dest_dir})
+      end
+      @site = Site.new(Jekyll.configuration)
     end
 
     #should "read layouts" do
@@ -37,8 +37,8 @@ class TestSite < Test::Unit::TestCase
               .baz.markdow foo.markdown~]
       ent2 = %w[.htaccess _posts bla.bla]
 
-      assert_equal %w[foo.markdown bar.markdown baz.markdown], @s.filter_entries(ent1)
-      assert_equal ent2, @s.filter_entries(ent2)
+      assert_equal %w[foo.markdown bar.markdown baz.markdown], @site.filter_entries(ent1)
+      assert_equal ent2, @site.filter_entries(ent2)
     end
   end
 end