diff --git a/lib/jekyll.rb b/lib/jekyll.rb
index a0a60242..3ea79215 100644
--- a/lib/jekyll.rb
+++ b/lib/jekyll.rb
@@ -88,7 +88,9 @@ module Jekyll
     def configuration(override)
       config = Configuration[Configuration::DEFAULTS]
       override = Configuration[override].stringify_keys
-      config = config.read_config_files(config.config_files(override))
+      unless override.delete('skip_config_files')
+        config = config.read_config_files(config.config_files(override))
+      end
 
       # Merge DEFAULTS < _config.yml < override
       config = Utils.deep_merge_hashes(config, override).stringify_keys
diff --git a/lib/jekyll/collection.rb b/lib/jekyll/collection.rb
index 84e207f8..76374d2f 100644
--- a/lib/jekyll/collection.rb
+++ b/lib/jekyll/collection.rb
@@ -36,6 +36,7 @@ module Jekyll
     def read
       filtered_entries.each do |file_path|
         full_path = collection_dir(file_path)
+        next if File.directory?(full_path)
         if Utils.has_yaml_header? full_path
           doc = Jekyll::Document.new(full_path, { site: site, collection: self })
           doc.read
@@ -86,7 +87,8 @@ module Jekyll
       @directory ||= site.in_source_dir(relative_directory)
     end
 
-    # The full path to the directory containing the collection.
+    # The full path to the directory containing the collection, with
+    #   optional subpaths.
     #
     # *files - (optional) any other path pieces relative to the
     #           directory to append to the path
diff --git a/lib/jekyll/document.rb b/lib/jekyll/document.rb
index 9cb4264e..0ab0cb72 100644
--- a/lib/jekyll/document.rb
+++ b/lib/jekyll/document.rb
@@ -159,7 +159,8 @@ module Jekyll
     #
     # Returns the full path to the output file of this document.
     def destination(base_directory)
-      path = site.in_dest_dir(base_directory, url)
+      dest = site.in_dest_dir(base_directory)
+      path = Jekyll.sanitized_path(dest, url)
       path = File.join(path, "index.html") if url =~ /\/$/
       path
     end
diff --git a/lib/jekyll/page.rb b/lib/jekyll/page.rb
index 98f730bf..0cd3cf0a 100644
--- a/lib/jekyll/page.rb
+++ b/lib/jekyll/page.rb
@@ -140,7 +140,8 @@ module Jekyll
     #
     # Returns the destination file path String.
     def destination(dest)
-      path = site.in_dest_dir(dest, URL.unescape_path(url))
+      dest = site.in_dest_dir(dest)
+      path = Jekyll.sanitized_path(dest, URL.unescape_path(url))
       path = File.join(path, "index.html") if url =~ /\/$/
       path
     end
diff --git a/lib/jekyll/post.rb b/lib/jekyll/post.rb
index d89034ce..36536173 100644
--- a/lib/jekyll/post.rb
+++ b/lib/jekyll/post.rb
@@ -268,7 +268,8 @@ module Jekyll
     # Returns destination file path String.
     def destination(dest)
       # The url needs to be unescaped in order to preserve the correct filename
-      path = site.in_dest_dir(dest, URL.unescape_path(url))
+      dest = site.in_dest_dir(dest)
+      path = Jekyll.sanitized_path(dest, URL.unescape_path(url))
       path = File.join(path, "index.html") if path[/\.html$/].nil?
       path
     end
diff --git a/lib/jekyll/site.rb b/lib/jekyll/site.rb
index 0fc5130c..42935638 100644
--- a/lib/jekyll/site.rb
+++ b/lib/jekyll/site.rb
@@ -3,12 +3,12 @@ require 'csv'
 
 module Jekyll
   class Site
-    attr_reader   :source, :dest
-    attr_accessor :config, :layouts, :posts, :pages, :static_files,
-                  :exclude, :include, :lsi, :highlighter,
-                  :permalink_style, :time, :future, :unpublished, :safe, :plugins, :limit_posts,
-                  :show_drafts, :keep_files, :baseurl, :data, :file_read_opts, :gems,
-                  :plugin_manager
+    attr_reader   :source, :dest, :config
+    attr_accessor :layouts, :posts, :pages, :static_files,
+                  :exclude, :include, :lsi, :highlighter, :permalink_style,
+                  :time, :future, :unpublished, :safe, :plugins, :limit_posts,
+                  :show_drafts, :keep_files, :baseurl, :data, :file_read_opts,
+                  :gems, :plugin_manager
 
     attr_accessor :converters, :generators
 
@@ -16,7 +16,7 @@ module Jekyll
     #
     # config - A Hash containing site configuration details.
     def initialize(config)
-      self.config = config.clone
+      @config = config.clone
 
       %w[safe lsi highlighter baseurl exclude include future unpublished
         show_drafts limit_posts keep_files gems].each do |opt|
diff --git a/test/test_document.rb b/test/test_document.rb
index 3464cd2b..412ab0ff 100644
--- a/test/test_document.rb
+++ b/test/test_document.rb
@@ -10,9 +10,14 @@ class TestDocument < Test::Unit::TestCase
         "destination" => dest_dir
       }))
       @site.process
+      p @site.collections["methods"]
       @document = @site.collections["methods"].docs.first
     end
 
+    should "exist" do
+      assert !@document.nil?
+    end
+
     should "know its relative path" do
       assert_equal "_methods/configuration.md", @document.relative_path
     end
@@ -220,6 +225,7 @@ class TestDocument < Test::Unit::TestCase
         "destination" => dest_dir
       }))
       @site.process
+      p @site.collections["slides"]
       @document = @site.collections["slides"].docs[3]
       @document_without_title = @site.collections["slides"].docs[4]
     end
diff --git a/test/test_post.rb b/test/test_post.rb
index 48e2eb03..206060d8 100644
--- a/test/test_post.rb
+++ b/test/test_post.rb
@@ -15,8 +15,11 @@ class TestPost < Test::Unit::TestCase
   context "A Post" do
     setup do
       clear_dest
-      stub(Jekyll).configuration { Jekyll::Configuration::DEFAULTS }
-      @site = Site.new(Jekyll.configuration)
+      @site = Site.new(Jekyll.configuration({
+        "skip_config_files" => true,
+        "source" => source_dir,
+        "destination" => dest_dir
+      }))
     end
 
     should "ensure valid posts are valid" do
@@ -145,7 +148,7 @@ class TestPost < Test::Unit::TestCase
         do_render(post)
         post.write(dest_dir)
 
-        assert !File.exist?(unexpected)
+        assert !File.exist?(unexpected), "../../../baddie.html should not exist."
         assert File.exist?(File.expand_path("baddie.html", dest_dir))
       end
 
@@ -606,7 +609,7 @@ class TestPost < Test::Unit::TestCase
 
         should "include templates" do
           post = setup_post("2008-12-13-include.markdown")
-          post.site.source = File.join(File.dirname(__FILE__), 'source')
+          post.site.instance_variable_set(:@source, File.join(File.dirname(__FILE__), 'source'))
           do_render(post)
 
           assert_equal "<<< <hr />\n<p>Tom Preston-Werner\ngithub.com/mojombo</p>\n\n<p>This <em>is</em> cool</p>\n >>>", post.output