diff --git a/lib/jekyll.rb b/lib/jekyll.rb
index eb55fb8e..a14a970f 100644
--- a/lib/jekyll.rb
+++ b/lib/jekyll.rb
@@ -68,66 +68,88 @@ module Jekyll
   require 'jekyll/command'
   require 'jekyll/liquid_extensions'
 
-  # Public: Tells you which Jekyll environment you are building in so you can skip tasks
-  # if you need to.  This is useful when doing expensive compression tasks on css and
-  # images and allows you to skip that when working in development.
+  class << self
+    # Public: Tells you which Jekyll environment you are building in so you can skip tasks
+    # if you need to.  This is useful when doing expensive compression tasks on css and
+    # images and allows you to skip that when working in development.
 
-  def self.env
-    ENV["JEKYLL_ENV"] || "development"
-  end
-
-  # Public: Generate a Jekyll configuration Hash by merging the default
-  # options with anything in _config.yml, and adding the given options on top.
-  #
-  # override - A Hash of config directives that override any options in both
-  #            the defaults and the config file. See Jekyll::Configuration::DEFAULTS for a
-  #            list of option names and their defaults.
-  #
-  # Returns the final configuration Hash.
-  def self.configuration(override)
-    config = Configuration[Configuration::DEFAULTS]
-    override = Configuration[override].stringify_keys
-    config = config.read_config_files(config.config_files(override))
-
-    # Merge DEFAULTS < _config.yml < override
-    config = Utils.deep_merge_hashes(config, override).stringify_keys
-    set_timezone(config['timezone']) if config['timezone']
-
-    config
-  end
-
-  # Static: Set the TZ environment variable to use the timezone specified
-  #
-  # timezone - the IANA Time Zone
-  #
-  # Returns nothing
-  def self.set_timezone(timezone)
-    ENV['TZ'] = timezone
-  end
-
-  def self.logger
-    @logger ||= LogAdapter.new(Stevenson.new)
-  end
-
-  def self.logger=(writer)
-    @logger = LogAdapter.new(writer)
-  end
-
-  # Public: File system root
-  #
-  # Returns the root of the filesystem as a Pathname
-  def self.fs_root
-    @fs_root ||= "/"
-  end
-
-  def self.sanitized_path(base_directory, questionable_path)
-    clean_path = File.expand_path(questionable_path, fs_root)
-    clean_path.gsub!(/\A\w\:\//, '/')
-    unless clean_path.start_with?(base_directory)
-      File.join(base_directory, clean_path)
-    else
-      clean_path
+    def env
+      ENV["JEKYLL_ENV"] || "development"
     end
+
+    # Public: Generate a Jekyll configuration Hash by merging the default
+    # options with anything in _config.yml, and adding the given options on top.
+    #
+    # override - A Hash of config directives that override any options in both
+    #            the defaults and the config file. See Jekyll::Configuration::DEFAULTS for a
+    #            list of option names and their defaults.
+    #
+    # Returns the final configuration Hash.
+    def configuration(override = Hash.new)
+      config = Configuration[Configuration::DEFAULTS]
+      override = Configuration[override].stringify_keys
+      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
+      set_timezone(config['timezone']) if config['timezone']
+
+      config
+    end
+
+    # Public: Set the TZ environment variable to use the timezone specified
+    #
+    # timezone - the IANA Time Zone
+    #
+    # Returns nothing
+    def set_timezone(timezone)
+      ENV['TZ'] = timezone
+    end
+
+    # Public: Fetch the logger instance for this Jekyll process.
+    #
+    # Returns the LogAdapter instance.
+    def logger
+      @logger ||= LogAdapter.new(Stevenson.new)
+    end
+
+    # Public: Set the log writer.
+    #         New log writer must respond to the same methods
+    #         as Ruby's interal Logger.
+    #
+    # writer - the new Logger-compatible log transport
+    #
+    # Returns the new logger.
+    def logger=(writer)
+      @logger = LogAdapter.new(writer)
+    end
+
+    # Public: An array of sites
+    #
+    # Returns the Jekyll sites created.
+    def sites
+      @sites ||= []
+    end
+
+    # Public: Ensures the questionable path is prefixed with the base directory
+    #         and prepends the questionable path with the base directory if false.
+    #
+    # base_directory - the directory with which to prefix the questionable path
+    # questionable_path - the path we're unsure about, and want prefixed
+    #
+    # Returns the sanitized path.
+    def sanitized_path(base_directory, questionable_path)
+      clean_path = File.expand_path(questionable_path, "/")
+      clean_path.gsub!(/\A\w\:\//, '/')
+      unless clean_path.start_with?(base_directory)
+        File.join(base_directory, clean_path)
+      else
+        clean_path
+      end
+    end
+
   end
 end
 
diff --git a/lib/jekyll/cleaner.rb b/lib/jekyll/cleaner.rb
index 1786a317..6dd59ea0 100644
--- a/lib/jekyll/cleaner.rb
+++ b/lib/jekyll/cleaner.rb
@@ -29,7 +29,7 @@ module Jekyll
       # Returns a Set with the file paths
       def existing_files
         files = Set.new
-        Dir.glob(File.join(site.dest, "**", "*"), File::FNM_DOTMATCH) do |file|
+        Dir.glob(site.in_dest_dir("**", "*"), File::FNM_DOTMATCH) do |file|
           files << file unless file =~ /\/\.{1,2}$/ || file =~ keep_file_regex || keep_dirs.include?(file)
         end
         files
@@ -76,7 +76,7 @@ module Jekyll
       #
       # Returns a Set with the directory paths
       def keep_dirs
-        site.keep_files.map { |file| parent_dirs(File.join(site.dest, file)) }.flatten.to_set
+        site.keep_files.map { |file| parent_dirs(site.in_dest_dir(file)) }.flatten.to_set
       end
 
       # Private: Creates a regular expression from the config's keep_files array
diff --git a/lib/jekyll/collection.rb b/lib/jekyll/collection.rb
index 33654f45..73e480dd 100644
--- a/lib/jekyll/collection.rb
+++ b/lib/jekyll/collection.rb
@@ -35,7 +35,8 @@ module Jekyll
     # Returns the sorted array of docs.
     def read
       filtered_entries.each do |file_path|
-        full_path = Jekyll.sanitized_path(directory, 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
@@ -54,9 +55,10 @@ module Jekyll
     #   relative to the collection's directory
     def entries
       return Array.new unless exists?
-      Dir.glob(File.join(directory, "**", "*.*")).map do |entry|
-        entry[File.join(directory, "")] = ''; entry
-      end
+      @entries ||=
+        Dir.glob(collection_dir("**", "*.*")).map do |entry|
+          entry["#{collection_dir}/"] = ''; entry
+        end
     end
 
     # Filtered version of the entries in this collection.
@@ -65,9 +67,13 @@ module Jekyll
     # Returns a list of filtered entry paths.
     def filtered_entries
       return Array.new unless exists?
-      Dir.chdir(directory) do
-        entry_filter.filter(entries).reject { |f| File.directory?(f) }
-      end
+      @filtered_entries ||=
+        Dir.chdir(directory) do
+          entry_filter.filter(entries).reject do |f|
+            path = collection_dir(f)
+            File.directory?(path) || (File.symlink?(f) && site.safe)
+          end
+        end
     end
 
     # The directory for this Collection, relative to the site source.
@@ -78,12 +84,25 @@ module Jekyll
       @relative_directory ||= "_#{label}"
     end
 
-    # The full path to the directory containing the
+    # The full path to the directory containing the collection.
     #
     # Returns a String containing th directory name where the collection
     #   is stored on the filesystem.
     def directory
-      @directory ||= Jekyll.sanitized_path(site.source, relative_directory)
+      @directory ||= site.in_source_dir(relative_directory)
+    end
+
+    # 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
+    #
+    # Returns a String containing th directory name where the collection
+    #   is stored on the filesystem.
+    def collection_dir(*files)
+      return directory if files.empty?
+      site.in_source_dir(relative_directory, *files)
     end
 
     # Checks whether the directory "exists" for this collection.
diff --git a/lib/jekyll/convertible.rb b/lib/jekyll/convertible.rb
index 74c27117..2b52bca3 100644
--- a/lib/jekyll/convertible.rb
+++ b/lib/jekyll/convertible.rb
@@ -43,7 +43,7 @@ module Jekyll
     # Returns nothing.
     def read_yaml(base, name, opts = {})
       begin
-        self.content = File.read(Jekyll.sanitized_path(base, name),
+        self.content = File.read(site.in_source_dir(base, name),
                                  merged_file_read_opts(opts))
         if content =~ /\A(---\s*\n.*?\n?)^((---|\.\.\.)\s*$\n?)/m
           self.content = $POSTMATCH
diff --git a/lib/jekyll/document.rb b/lib/jekyll/document.rb
index 95a2bdcd..003c04eb 100644
--- a/lib/jekyll/document.rb
+++ b/lib/jekyll/document.rb
@@ -159,7 +159,8 @@ module Jekyll
     #
     # Returns the full path to the output file of this document.
     def destination(base_directory)
-      path = Jekyll.sanitized_path(base_directory, url)
+      dest = site.in_dest_dir(base_directory)
+      path = site.in_dest_dir(dest, url)
       path = File.join(path, "index.html") if url =~ /\/$/
       path
     end
diff --git a/lib/jekyll/draft.rb b/lib/jekyll/draft.rb
index 7b1d9aca..16daefdf 100644
--- a/lib/jekyll/draft.rb
+++ b/lib/jekyll/draft.rb
@@ -14,8 +14,8 @@ module Jekyll
     end
 
     # Get the full path to the directory containing the draft files
-    def containing_dir(source, dir)
-      File.join(source, dir, '_drafts')
+    def containing_dir(dir)
+      site.in_source_dir(dir, '_drafts')
     end
 
     # The path to the draft source file, relative to the site source
diff --git a/lib/jekyll/excerpt.rb b/lib/jekyll/excerpt.rb
index 958e3f3c..41d4976c 100644
--- a/lib/jekyll/excerpt.rb
+++ b/lib/jekyll/excerpt.rb
@@ -106,7 +106,7 @@ module Jekyll
     # Returns excerpt String
     def extract_excerpt(post_content)
       separator     = site.config['excerpt_separator']
-      head, _, tail = post_content.partition(separator)
+      head, _, tail = post_content.to_s.partition(separator)
 
       "" << head << "\n\n" << tail.scan(/^\[[^\]]+\]:.+$/).join("\n")
     end
diff --git a/lib/jekyll/layout_reader.rb b/lib/jekyll/layout_reader.rb
index a9172c06..a8466beb 100644
--- a/lib/jekyll/layout_reader.rb
+++ b/lib/jekyll/layout_reader.rb
@@ -38,12 +38,12 @@ module Jekyll
     end
 
     def layout_directory_inside_source
-      Jekyll.sanitized_path(site.source, site.config['layouts'])
+      site.in_source_dir(site.config['layouts'])
     end
 
     def layout_directory_in_cwd
       dir = Jekyll.sanitized_path(Dir.pwd, site.config['layouts'])
-      if File.directory?(dir)
+      if File.directory?(dir) && !site.safe
         dir
       else
         nil
diff --git a/lib/jekyll/page.rb b/lib/jekyll/page.rb
index dcbd3ac5..98f730bf 100644
--- a/lib/jekyll/page.rb
+++ b/lib/jekyll/page.rb
@@ -140,7 +140,7 @@ module Jekyll
     #
     # Returns the destination file path String.
     def destination(dest)
-      path = Jekyll.sanitized_path(dest, URL.unescape_path(url))
+      path = site.in_dest_dir(dest, URL.unescape_path(url))
       path = File.join(path, "index.html") if url =~ /\/$/
       path
     end
diff --git a/lib/jekyll/plugin_manager.rb b/lib/jekyll/plugin_manager.rb
index 7b817e38..c52a5205 100644
--- a/lib/jekyll/plugin_manager.rb
+++ b/lib/jekyll/plugin_manager.rb
@@ -66,7 +66,7 @@ module Jekyll
     # Returns an Array of plugin search paths
     def plugins_path
       if (site.config['plugins'] == Jekyll::Configuration::DEFAULTS['plugins'])
-        [Jekyll.sanitized_path(site.source, site.config['plugins'])]
+        [site.in_source_dir(site.config['plugins'])]
       else
         Array(site.config['plugins']).map { |d| File.expand_path(d) }
       end
diff --git a/lib/jekyll/post.rb b/lib/jekyll/post.rb
index 68b85acb..c377e376 100644
--- a/lib/jekyll/post.rb
+++ b/lib/jekyll/post.rb
@@ -49,7 +49,7 @@ module Jekyll
     def initialize(site, source, dir, name)
       @site = site
       @dir = dir
-      @base = containing_dir(source, dir)
+      @base = containing_dir(dir)
       @name = name
 
       self.categories = dir.downcase.split('/').reject { |x| x.empty? }
@@ -88,8 +88,8 @@ module Jekyll
     end
 
     # Get the full path to the directory containing the post files
-    def containing_dir(source, dir)
-      return File.join(source, dir, '_posts')
+    def containing_dir(dir)
+      site.in_source_dir(dir, '_posts')
     end
 
     # Read the YAML frontmatter.
@@ -268,7 +268,7 @@ module Jekyll
     # Returns destination file path String.
     def destination(dest)
       # The url needs to be unescaped in order to preserve the correct filename
-      path = Jekyll.sanitized_path(dest, URL.unescape_path(url))
+      path = site.in_dest_dir(dest, URL.unescape_path(url))
       path = File.join(path, "index.html") if path[/\.html?$/].nil?
       path
     end
diff --git a/lib/jekyll/related_posts.rb b/lib/jekyll/related_posts.rb
index be0513fc..041ee551 100644
--- a/lib/jekyll/related_posts.rb
+++ b/lib/jekyll/related_posts.rb
@@ -46,8 +46,7 @@ module Jekyll
     end
 
     def most_recent_posts
-      recent_posts = site.posts.reverse - [post]
-      recent_posts.first(10)
+      @most_recent_posts ||= (site.posts.reverse - [post]).first(10)
     end
 
     def display(output)
diff --git a/lib/jekyll/site.rb b/lib/jekyll/site.rb
index 502e3ecb..115b4133 100644
--- a/lib/jekyll/site.rb
+++ b/lib/jekyll/site.rb
@@ -3,11 +3,12 @@ require 'csv'
 
 module Jekyll
   class Site
-    attr_accessor :config, :layouts, :posts, :pages, :static_files,
-                  :exclude, :include, :source, :dest, :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
 
@@ -15,16 +16,16 @@ 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|
         self.send("#{opt}=", config[opt])
       end
 
-      self.source          = File.expand_path(config['source'])
-      self.dest            = File.expand_path(config['destination'])
-      self.permalink_style = config['permalink'].to_sym
+      # Source and destination may not be changed after the site has been created.
+      @source              = File.expand_path(config['source']).freeze
+      @dest                = File.expand_path(config['destination']).freeze
 
       self.plugin_manager = Jekyll::PluginManager.new(self)
       self.plugins        = plugin_manager.plugins_path
@@ -32,6 +33,10 @@ module Jekyll
       self.file_read_opts = {}
       self.file_read_opts[:encoding] = config['encoding'] if config['encoding']
 
+      self.permalink_style = config['permalink'].to_sym
+
+      Jekyll.sites << self
+
       reset
       setup
     end
@@ -88,6 +93,30 @@ module Jekyll
       end
     end
 
+    # Public: Prefix a given path with the source directory.
+    #
+    # paths - (optional) path elements to a file or directory within the
+    #         source directory
+    #
+    # Returns a path which is prefixed with the source directory.
+    def in_source_dir(*paths)
+      paths.reduce(source) do |base, path|
+        Jekyll.sanitized_path(base, path)
+      end
+    end
+
+    # Public: Prefix a given path with the destination directory.
+    #
+    # paths - (optional) path elements to a file or directory within the
+    #         destination directory
+    #
+    # Returns a path which is prefixed with the destination directory.
+    def in_dest_dir(*paths)
+      paths.reduce(dest) do |base, path|
+        Jekyll.sanitized_path(base, path)
+      end
+    end
+
     # The list of collections and their corresponding Jekyll::Collection instances.
     # If config['collections'] is set, a new instance is created for each item in the collection.
     # If config['collections'] is not set, a new hash is returned.
@@ -132,7 +161,7 @@ module Jekyll
     #
     # Returns nothing.
     def read_directories(dir = '')
-      base = File.join(source, dir)
+      base = in_source_dir(dir)
       entries = Dir.chdir(base) { filter_entries(Dir.entries('.'), base) }
 
       read_posts(dir)
@@ -141,7 +170,7 @@ module Jekyll
       limit_posts! if limit_posts > 0 # limit the posts if :limit_posts option is set
 
       entries.each do |f|
-        f_abs = File.join(base, f)
+        f_abs = in_source_dir(base, f)
         if File.directory?(f_abs)
           f_rel = File.join(dir, f)
           read_directories(f_rel) unless dest.sub(/\/$/, '') == f_abs
@@ -198,7 +227,7 @@ module Jekyll
     #
     # Returns nothing
     def read_data(dir)
-      base = Jekyll.sanitized_path(source, dir)
+      base = in_source_dir(dir)
       read_data_to(base, self.data)
     end
 
@@ -217,7 +246,7 @@ module Jekyll
       end
 
       entries.each do |entry|
-        path = Jekyll.sanitized_path(dir, entry)
+        path = in_source_dir(dir, entry)
         next if File.symlink?(path) && safe
 
         key = sanitize_filename(File.basename(entry, '.*'))
@@ -407,10 +436,10 @@ module Jekyll
     #
     # Returns the list of entries to process
     def get_entries(dir, subfolder)
-      base = File.join(source, dir, subfolder)
+      base = in_source_dir(dir, subfolder)
       return [] unless File.exist?(base)
       entries = Dir.chdir(base) { filter_entries(Dir['**/*'], base) }
-      entries.delete_if { |e| File.directory?(File.join(base, e)) }
+      entries.delete_if { |e| File.directory?(in_source_dir(base, e)) }
     end
 
     # Aggregate post information
diff --git a/lib/jekyll/static_file.rb b/lib/jekyll/static_file.rb
index 02087e49..eae85b54 100644
--- a/lib/jekyll/static_file.rb
+++ b/lib/jekyll/static_file.rb
@@ -37,7 +37,7 @@ module Jekyll
     #
     # Returns destination file path.
     def destination(dest)
-      File.join(*[dest, destination_rel_dir, @name].compact)
+      @site.in_dest_dir(*[dest, destination_rel_dir, @name].compact)
     end
 
     def destination_rel_dir
diff --git a/lib/jekyll/tags/include.rb b/lib/jekyll/tags/include.rb
index c6b1ed9c..3eb4d7c0 100644
--- a/lib/jekyll/tags/include.rb
+++ b/lib/jekyll/tags/include.rb
@@ -161,7 +161,7 @@ eos
       end
 
       def resolved_includes_dir(context)
-        Jekyll.sanitized_path(context.registers[:site].source, page_path(context))
+        context.registers[:site].in_source_dir(page_path(context))
       end
     end
   end
diff --git a/test/helper.rb b/test/helper.rb
index 97be56ad..3103e117 100644
--- a/test/helper.rb
+++ b/test/helper.rb
@@ -30,10 +30,10 @@ class Test::Unit::TestCase
   end
 
   def site_configuration(overrides = {})
+    full_overrides = build_configs(overrides, build_configs({"destination" => dest_dir}))
     build_configs({
       "source"      => source_dir,
-      "destination" => dest_dir
-    }, build_configs(overrides))
+    }, full_overrides)
   end
 
   def dest_dir(*subdirs)
diff --git a/test/test_cleaner.rb b/test/test_cleaner.rb
index e9bcc0f5..304ce623 100644
--- a/test/test_cleaner.rb
+++ b/test/test_cleaner.rb
@@ -4,15 +4,16 @@ class TestCleaner < Test::Unit::TestCase
   context "directory in keep_files" do
     setup do
       clear_dest
-      stub(Jekyll).configuration do
-        Jekyll::Configuration::DEFAULTS.merge({'source' => source_dir, 'destination' => dest_dir})
-      end
 
       FileUtils.mkdir_p(dest_dir('to_keep/child_dir'))
       FileUtils.touch(File.join(dest_dir('to_keep'), 'index.html'))
       FileUtils.touch(File.join(dest_dir('to_keep/child_dir'), 'index.html'))
 
-      @site = Site.new(Jekyll.configuration)
+      @site = Site.new(Jekyll.configuration({
+        "skip_config_files" => true,
+        "source" => source_dir,
+        "destination" => dest_dir
+      }))
       @site.keep_files = ['to_keep/child_dir']
 
       @cleaner = Site::Cleaner.new(@site)
@@ -43,14 +44,15 @@ class TestCleaner < Test::Unit::TestCase
   context "directory containing no files and non-empty directories" do
     setup do
       clear_dest
-      stub(Jekyll).configuration do
-        Jekyll::Configuration::DEFAULTS.merge({'source' => source_dir, 'destination' => dest_dir})
-      end
 
       FileUtils.mkdir_p(source_dir('no_files_inside/child_dir'))
       FileUtils.touch(File.join(source_dir('no_files_inside/child_dir'), 'index.html'))
 
-      @site = Site.new(Jekyll.configuration)
+      @site = Site.new(Jekyll.configuration({
+        "skip_config_files" => true,
+        "source" => source_dir,
+        "destination" => dest_dir
+      }))
       @site.process
 
       @cleaner = Site::Cleaner.new(@site)
diff --git a/test/test_collections.rb b/test/test_collections.rb
index 97b891ef..1975e402 100644
--- a/test/test_collections.rb
+++ b/test/test_collections.rb
@@ -187,6 +187,7 @@ class TestCollections < Test::Unit::TestCase
 
     should "not allow symlinks" do
       assert_not_include @collection.filtered_entries, "um_hi.md"
+      assert_not_include @collection.filtered_entries, "/um_hi.md"
     end
 
     should "not include the symlinked file in the list of docs" do
diff --git a/test/test_convertible.rb b/test/test_convertible.rb
index 28f99952..6482ad90 100644
--- a/test/test_convertible.rb
+++ b/test/test_convertible.rb
@@ -4,7 +4,11 @@ require 'ostruct'
 class TestConvertible < Test::Unit::TestCase
   context "yaml front-matter" do
     setup do
-      @convertible = OpenStruct.new
+      @convertible = OpenStruct.new(
+        "site" => Site.new(Jekyll.configuration(
+          "source" => File.expand_path('../fixtures', __FILE__)
+        ))
+      )
       @convertible.extend Jekyll::Convertible
       @base = File.expand_path('../fixtures', __FILE__)
     end
diff --git a/test/test_document.rb b/test/test_document.rb
index 3464cd2b..90c16b82 100644
--- a/test/test_document.rb
+++ b/test/test_document.rb
@@ -13,6 +13,10 @@ class TestDocument < Test::Unit::TestCase
       @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
diff --git a/test/test_draft.rb b/test/test_draft.rb
index b1b3d08d..5843665b 100644
--- a/test/test_draft.rb
+++ b/test/test_draft.rb
@@ -8,8 +8,7 @@ class TestDraft < Test::Unit::TestCase
   context "A Draft" do
     setup do
       clear_dest
-      stub(Jekyll).configuration { Jekyll::Configuration::DEFAULTS }
-      @site = Site.new(Jekyll.configuration)
+      @site = Site.new(site_configuration)
     end
 
     should "ensure valid drafts are valid" do
diff --git a/test/test_entry_filter.rb b/test/test_entry_filter.rb
index e562277e..5c5711cb 100644
--- a/test/test_entry_filter.rb
+++ b/test/test_entry_filter.rb
@@ -3,10 +3,7 @@ require 'helper'
 class TestEntryFilter < Test::Unit::TestCase
   context "Filtering entries" do
     setup do
-      stub(Jekyll).configuration do
-        Jekyll::Configuration::DEFAULTS.merge({'source' => source_dir, 'destination' => dest_dir})
-      end
-      @site = Site.new(Jekyll.configuration)
+      @site = Site.new(site_configuration)
     end
 
     should "filter entries" do
@@ -50,10 +47,7 @@ class TestEntryFilter < Test::Unit::TestCase
     end
 
     should "filter symlink entries when safe mode enabled" do
-      stub(Jekyll).configuration do
-        Jekyll::Configuration::DEFAULTS.merge({'source' => source_dir, 'destination' => dest_dir, 'safe' => true})
-      end
-      site = Site.new(Jekyll.configuration)
+      site = Site.new(site_configuration('safe' => true))
       stub(File).symlink?('symlink.js') {true}
       files = %w[symlink.js]
       assert_equal [], site.filter_entries(files)
@@ -66,10 +60,7 @@ class TestEntryFilter < Test::Unit::TestCase
     end
 
     should "not include symlinks in safe mode" do
-      stub(Jekyll).configuration do
-        Jekyll::Configuration::DEFAULTS.merge({'source' => source_dir, 'destination' => dest_dir, 'safe' => true})
-      end
-      site = Site.new(Jekyll.configuration)
+      site = Site.new(site_configuration('safe' => true))
 
       site.read_directories("symlink-test")
       assert_equal [], site.pages
@@ -77,10 +68,7 @@ class TestEntryFilter < Test::Unit::TestCase
     end
 
     should "include symlinks in unsafe mode" do
-      stub(Jekyll).configuration do
-        Jekyll::Configuration::DEFAULTS.merge({'source' => source_dir, 'destination' => dest_dir, 'safe' => false})
-      end
-      site = Site.new(Jekyll.configuration)
+      site = Site.new(site_configuration)
 
       site.read_directories("symlink-test")
       assert_not_equal [], site.pages
@@ -90,10 +78,7 @@ class TestEntryFilter < Test::Unit::TestCase
 
   context "#glob_include?" do
     setup do
-      stub(Jekyll).configuration do
-        Jekyll::Configuration::DEFAULTS.merge({'source' => source_dir, 'destination' => dest_dir})
-      end
-      @site = Site.new(Jekyll.configuration)
+      @site = Site.new(site_configuration)
       @filter = EntryFilter.new(@site)
     end
 
diff --git a/test/test_excerpt.rb b/test/test_excerpt.rb
index b6300fde..200a46be 100644
--- a/test/test_excerpt.rb
+++ b/test/test_excerpt.rb
@@ -13,10 +13,7 @@ class TestExcerpt < Test::Unit::TestCase
   context "With extraction disabled" do
     setup do
       clear_dest
-      stub(Jekyll).configuration do
-        Jekyll::Configuration::DEFAULTS.merge({'excerpt_separator' => ''})
-      end
-      @site = Site.new(Jekyll.configuration)
+      @site = Site.new(site_configuration('excerpt_separator' => ''))
       @post = setup_post("2013-07-22-post-excerpt-with-layout.markdown")
     end
 
@@ -29,8 +26,7 @@ class TestExcerpt < Test::Unit::TestCase
   context "An extracted excerpt" do
     setup do
       clear_dest
-      stub(Jekyll).configuration { Jekyll::Configuration::DEFAULTS }
-      @site = Site.new(Jekyll.configuration)
+      @site = Site.new(site_configuration)
       @post = setup_post("2013-07-22-post-excerpt-with-layout.markdown")
       @excerpt = @post.send :extract_excerpt
     end
diff --git a/test/test_page.rb b/test/test_page.rb
index b34b511c..20ed3198 100644
--- a/test/test_page.rb
+++ b/test/test_page.rb
@@ -15,8 +15,11 @@ class TestPage < Test::Unit::TestCase
   context "A Page" do
     setup do
       clear_dest
-      stub(Jekyll).configuration { Jekyll::Configuration::DEFAULTS }
-      @site = Site.new(Jekyll.configuration)
+      @site = Site.new(Jekyll.configuration({
+        "source" => source_dir,
+        "destination" => dest_dir,
+        "skip_config_files" => true
+      }))
     end
 
     context "processing pages" do
diff --git a/test/test_post.rb b/test/test_post.rb
index 48e2eb03..582d100a 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
@@ -685,7 +688,7 @@ class TestPost < Test::Unit::TestCase
 
   context "site config with category" do
     setup do
-      config = Jekyll::Configuration::DEFAULTS.merge({
+      config = site_configuration({
         'defaults' => [
           'scope' => {
             'path' => ''
@@ -712,7 +715,7 @@ class TestPost < Test::Unit::TestCase
 
   context "site config with categories" do
     setup do
-      config = Jekyll::Configuration::DEFAULTS.merge({
+      config = site_configuration({
         'defaults' => [
           'scope' => {
             'path' => ''
diff --git a/test/test_site.rb b/test/test_site.rb
index 7c42862a..4b8409e7 100644
--- a/test/test_site.rb
+++ b/test/test_site.rb
@@ -8,7 +8,7 @@ class TestSite < Test::Unit::TestCase
     end
 
     should "look for plugins under the site directory by default" do
-      site = Site.new(Jekyll::Configuration::DEFAULTS.merge({'source' => File.expand_path(source_dir)}))
+      site = Site.new(site_configuration)
       assert_equal [File.join(source_dir, '_plugins')], site.plugins
     end
 
@@ -44,30 +44,35 @@ class TestSite < Test::Unit::TestCase
   end
   context "creating sites" do
     setup do
-      stub(Jekyll).configuration do
-        Jekyll::Configuration::DEFAULTS.merge({'source' => source_dir, 'destination' => dest_dir})
-      end
-      @site = Site.new(Jekyll.configuration)
+      @site = Site.new(site_configuration)
       @num_invalid_posts = 4
     end
 
+    teardown do
+      if defined?(MyGenerator)
+        self.class.send(:remove_const, :MyGenerator)
+      end
+    end
+
     should "have an empty tag hash by default" do
       assert_equal Hash.new, @site.tags
     end
 
     should "give site with parsed pages and posts to generators" do
-      @site.reset
-      @site.read
       class MyGenerator < Generator
         def generate(site)
           site.pages.dup.each do |page|
             raise "#{page} isn't a page" unless page.is_a?(Page)
             raise "#{page} doesn't respond to :name" unless page.respond_to?(:name)
           end
+          site.file_read_opts[:secret_message] = 'hi'
         end
       end
+      @site = Site.new(site_configuration)
+      @site.read
       @site.generate
       assert_not_equal 0, @site.pages.size
+      assert_equal 'hi', @site.file_read_opts[:secret_message]
     end
 
     should "reset data before processing" do
@@ -221,22 +226,14 @@ class TestSite < Test::Unit::TestCase
 
     context 'error handling' do
       should "raise if destination is included in source" do
-        stub(Jekyll).configuration do
-          Jekyll::Configuration::DEFAULTS.merge({'source' => source_dir, 'destination' => source_dir})
-        end
-
         assert_raise Jekyll::Errors::FatalException do
-          site = Site.new(Jekyll.configuration)
+          site = Site.new(site_configuration('destination' => source_dir))
         end
       end
 
       should "raise if destination is source" do
-        stub(Jekyll).configuration do
-          Jekyll::Configuration::DEFAULTS.merge({'source' => source_dir, 'destination' => File.join(source_dir, "..")})
-        end
-
         assert_raise Jekyll::Errors::FatalException do
-          site = Site.new(Jekyll.configuration)
+          site = Site.new(site_configuration('destination' => File.join(source_dir, "..")))
         end
       end
     end
@@ -281,7 +278,7 @@ class TestSite < Test::Unit::TestCase
       end
 
       should 'remove orphaned files in destination - keep_files .svn' do
-        config = Jekyll::Configuration::DEFAULTS.merge({'source' => source_dir, 'destination' => dest_dir, 'keep_files' => ['.svn']})
+        config = site_configuration('keep_files' => %w{.svn})
         @site = Site.new(config)
         @site.process
         assert !File.exist?(dest_dir('.htpasswd'))
@@ -308,7 +305,7 @@ class TestSite < Test::Unit::TestCase
         end
 
         custom_processor = "CustomMarkdown"
-        s = Site.new(Jekyll.configuration.merge({ 'markdown' => custom_processor }))
+        s = Site.new(site_configuration('markdown' => custom_processor))
         assert_nothing_raised do
           s.process
         end
@@ -331,7 +328,7 @@ class TestSite < Test::Unit::TestCase
         end
 
         bad_processor = "Custom::Markdown"
-        s = Site.new(Jekyll.configuration.merge({ 'markdown' => bad_processor }))
+        s = Site.new(site_configuration('markdown' => bad_processor))
         assert_raise Jekyll::Errors::FatalException do
           s.process
         end
@@ -345,13 +342,13 @@ class TestSite < Test::Unit::TestCase
       should 'not throw an error at initialization time' do
         bad_processor = 'not a processor name'
         assert_nothing_raised do
-          Site.new(Jekyll.configuration.merge({ 'markdown' => bad_processor }))
+          Site.new(site_configuration('markdown' => bad_processor))
         end
       end
 
       should 'throw FatalException at process time' do
         bad_processor = 'not a processor name'
-        s = Site.new(Jekyll.configuration.merge({ 'markdown' => bad_processor }))
+        s = Site.new(site_configuration('markdown' => bad_processor))
         assert_raise Jekyll::Errors::FatalException do
           s.process
         end
@@ -360,7 +357,7 @@ class TestSite < Test::Unit::TestCase
 
     context 'data directory' do
       should 'auto load yaml files' do
-        site = Site.new(Jekyll.configuration)
+        site = Site.new(site_configuration)
         site.process
 
         file_content = SafeYAML.load_file(File.join(source_dir, '_data', 'members.yaml'))
@@ -370,7 +367,7 @@ class TestSite < Test::Unit::TestCase
       end
 
       should 'auto load yml files' do
-        site = Site.new(Jekyll.configuration)
+        site = Site.new(site_configuration)
         site.process
 
         file_content = SafeYAML.load_file(File.join(source_dir, '_data', 'languages.yml'))
@@ -380,7 +377,7 @@ class TestSite < Test::Unit::TestCase
       end
 
       should 'auto load json files' do
-        site = Site.new(Jekyll.configuration)
+        site = Site.new(site_configuration)
         site.process
 
         file_content = SafeYAML.load_file(File.join(source_dir, '_data', 'members.json'))
@@ -390,7 +387,7 @@ class TestSite < Test::Unit::TestCase
       end
 
       should 'auto load yaml files in subdirectory' do
-        site = Site.new(Jekyll.configuration)
+        site = Site.new(site_configuration)
         site.process
 
         file_content = SafeYAML.load_file(File.join(source_dir, '_data', 'categories', 'dairy.yaml'))
@@ -400,7 +397,7 @@ class TestSite < Test::Unit::TestCase
       end
 
       should "load symlink files in unsafe mode" do
-        site = Site.new(Jekyll.configuration.merge({'safe' => false}))
+        site = Site.new(site_configuration('safe' => false))
         site.process
 
         file_content = SafeYAML.load_file(File.join(source_dir, '_data', 'products.yml'))
@@ -410,7 +407,7 @@ class TestSite < Test::Unit::TestCase
       end
 
       should "not load symlink files in safe mode" do
-        site = Site.new(Jekyll.configuration.merge({'safe' => true}))
+        site = Site.new(site_configuration('safe' => true))
         site.process
 
         assert_nil site.data['products']