diff --git a/lib/jekyll/cleaner.rb b/lib/jekyll/cleaner.rb
index 4c93411d..a8b269f4 100644
--- a/lib/jekyll/cleaner.rb
+++ b/lib/jekyll/cleaner.rb
@@ -36,7 +36,7 @@ module Jekyll
     # Returns a Set with the file paths
     def existing_files
       files = Set.new
-      Dir.glob(site.reader.in_dest_dir("**", "*"), 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
@@ -83,7 +83,7 @@ module Jekyll
     #
     # Returns a Set with the directory paths
     def keep_dirs
-      site.keep_files.map { |file| parent_dirs(site.reader.in_dest_dir(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 4b07b2af..b09a7ed9 100644
--- a/lib/jekyll/collection.rb
+++ b/lib/jekyll/collection.rb
@@ -89,7 +89,7 @@ module Jekyll
     # Returns a String containing th directory name where the collection
     #   is stored on the filesystem.
     def directory
-      @directory ||= site.reader.in_source_dir(relative_directory)
+      @directory ||= site.in_source_dir(relative_directory)
     end
 
     # The full path to the directory containing the collection, with
@@ -102,7 +102,7 @@ module Jekyll
     #   is stored on the filesystem.
     def collection_dir(*files)
       return directory if files.empty?
-      site.reader.in_source_dir(relative_directory, *files)
+      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 becc78ed..d587f8f3 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(site.reader.in_source_dir(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
@@ -209,8 +209,8 @@ module Jekyll
 
         # Add layout to dependency tree
         site.regenerator.add_dependency(
-          site.reader.in_source_dir(path),
-          site.reader.in_source_dir(layout.path)
+          site.in_source_dir(path),
+          site.in_source_dir(layout.path)
         )
 
         if layout = layouts[layout.data["layout"]]
diff --git a/lib/jekyll/document.rb b/lib/jekyll/document.rb
index 5419647c..cd407dfa 100644
--- a/lib/jekyll/document.rb
+++ b/lib/jekyll/document.rb
@@ -162,8 +162,8 @@ module Jekyll
     #
     # Returns the full path to the output file of this document.
     def destination(base_directory)
-      dest = site.reader.in_dest_dir(base_directory)
-      path = site.reader.in_dest_dir(dest, URL.unescape_path(url))
+      dest = site.in_dest_dir(base_directory)
+      path = site.in_dest_dir(dest, URL.unescape_path(url))
       path = File.join(path, "index.html") if url.end_with?("/")
       path << output_ext unless path.end_with?(output_ext)
       path
diff --git a/lib/jekyll/draft.rb b/lib/jekyll/draft.rb
index 4167f154..16daefdf 100644
--- a/lib/jekyll/draft.rb
+++ b/lib/jekyll/draft.rb
@@ -15,7 +15,7 @@ module Jekyll
 
     # Get the full path to the directory containing the draft files
     def containing_dir(dir)
-      site.reader.in_source_dir(dir, '_drafts')
+      site.in_source_dir(dir, '_drafts')
     end
 
     # The path to the draft source file, relative to the site source
diff --git a/lib/jekyll/layout.rb b/lib/jekyll/layout.rb
index 81ba7f81..c29f353f 100644
--- a/lib/jekyll/layout.rb
+++ b/lib/jekyll/layout.rb
@@ -29,7 +29,7 @@ module Jekyll
       @site = site
       @base = base
       @name = name
-      @path = site.reader.in_source_dir(base, name)
+      @path = site.in_source_dir(base, name)
 
       self.data = {}
 
diff --git a/lib/jekyll/layout_reader.rb b/lib/jekyll/layout_reader.rb
index 645d3cf8..a8466beb 100644
--- a/lib/jekyll/layout_reader.rb
+++ b/lib/jekyll/layout_reader.rb
@@ -38,7 +38,7 @@ module Jekyll
     end
 
     def layout_directory_inside_source
-      site.reader.in_source_dir(site.config['layouts'])
+      site.in_source_dir(site.config['layouts'])
     end
 
     def layout_directory_in_cwd
diff --git a/lib/jekyll/page.rb b/lib/jekyll/page.rb
index 75ca190c..ca824245 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 = site.reader.in_dest_dir(dest, URL.unescape_path(url))
+      path = site.in_dest_dir(dest, URL.unescape_path(url))
       path = File.join(path, "index.html") if url.end_with?("/")
       path << output_ext unless path.end_with?(output_ext)
       path
diff --git a/lib/jekyll/plugin_manager.rb b/lib/jekyll/plugin_manager.rb
index 5abfd47c..64dea860 100644
--- a/lib/jekyll/plugin_manager.rb
+++ b/lib/jekyll/plugin_manager.rb
@@ -82,7 +82,7 @@ module Jekyll
     # Returns an Array of plugin search paths
     def plugins_path
       if (site.config['plugins'] == Jekyll::Configuration::DEFAULTS['plugins'])
-        [site.reader.in_source_dir(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 c80a35e4..780f40f7 100644
--- a/lib/jekyll/post.rb
+++ b/lib/jekyll/post.rb
@@ -91,7 +91,7 @@ module Jekyll
 
     # Get the full path to the directory containing the post files
     def containing_dir(dir)
-      site.reader.in_source_dir(dir, '_posts')
+      site.in_source_dir(dir, '_posts')
     end
 
     # Read the YAML frontmatter.
@@ -278,7 +278,7 @@ module Jekyll
     # Returns destination file path String.
     def destination(dest)
       # The url needs to be unescaped in order to preserve the correct filename
-      path = site.reader.in_dest_dir(dest, URL.unescape_path(url))
+      path = site.in_dest_dir(dest, URL.unescape_path(url))
       path = File.join(path, "index.html") if self.url.end_with?("/")
       path << output_ext unless path.end_with?(output_ext)
       path
diff --git a/lib/jekyll/reader.rb b/lib/jekyll/reader.rb
index 731937ff..79464d46 100644
--- a/lib/jekyll/reader.rb
+++ b/lib/jekyll/reader.rb
@@ -19,30 +19,6 @@ module Jekyll
       read_collections
     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(site.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(site.dest) do |base, path|
-        Jekyll.sanitized_path(base, path)
-      end
-    end
-
     # Filter out any files/directories that are hidden or backup files (start
     # with "." or "#" or end with "~"), or contain site content (start with "_"),
     # or are excluded in the site configuration, unless they are web server
@@ -62,10 +38,10 @@ module Jekyll
     #
     # Returns the list of entries to process
     def get_entries(dir, subfolder)
-      base = in_source_dir(dir, subfolder)
+      base = site.in_source_dir(dir, subfolder)
       return [] unless File.exist?(base)
       entries = Dir.chdir(base) { filter_entries(Dir['**/*'], base) }
-      entries.delete_if { |e| File.directory?(in_source_dir(base, e)) }
+      entries.delete_if { |e| File.directory?(site.in_source_dir(base, e)) }
     end
 
 
@@ -92,7 +68,7 @@ module Jekyll
     #
     # Returns nothing.
     def read_directories(dir = '')
-      base = in_source_dir(dir)
+      base = site.in_source_dir(dir)
       entries = Dir.chdir(base) { filter_entries(Dir.entries('.'), base) }
 
       read_posts(dir)
@@ -101,7 +77,7 @@ module Jekyll
       limit_posts if site.limit_posts > 0 # limit the posts if :limit_posts option is set
 
       entries.each do |f|
-        f_abs = in_source_dir(base, f)
+        f_abs = site.in_source_dir(base, f)
         if File.directory?(f_abs)
           f_rel = File.join(dir, f)
           read_directories(f_rel) unless site.dest.sub(/\/$/, '') == f_abs
@@ -168,7 +144,7 @@ module Jekyll
     #
     # Returns nothing
     def read_data(dir)
-      base = in_source_dir(dir)
+      base = site.in_source_dir(dir)
       read_data_to(base, site.data)
     end
 
@@ -187,7 +163,7 @@ module Jekyll
       end
 
       entries.each do |entry|
-        path = in_source_dir(dir, entry)
+        path = site.in_source_dir(dir, entry)
         next if File.symlink?(path) && site.safe
 
         key = sanitize_filename(File.basename(entry, '.*'))
diff --git a/lib/jekyll/regenerator.rb b/lib/jekyll/regenerator.rb
index 07273db6..0616fdd9 100644
--- a/lib/jekyll/regenerator.rb
+++ b/lib/jekyll/regenerator.rb
@@ -19,7 +19,7 @@ module Jekyll
       case document
       when Post, Page
         document.asset_file? || document.data['regenerate'] ||
-          modified?(site.reader.in_source_dir(document.relative_path))
+          modified?(site.in_source_dir(document.relative_path))
       when Document
         !document.write? || document.data['regenerate'] || modified?(document.path)
       else
@@ -113,7 +113,7 @@ module Jekyll
     #
     # Returns the String path of the file.
     def metadata_file
-      site.reader.in_source_dir('.jekyll-metadata')
+      site.in_source_dir('.jekyll-metadata')
     end
 
     # Check if metadata has been disabled
diff --git a/lib/jekyll/renderer.rb b/lib/jekyll/renderer.rb
index fd58bff9..f25ca343 100644
--- a/lib/jekyll/renderer.rb
+++ b/lib/jekyll/renderer.rb
@@ -141,8 +141,8 @@ module Jekyll
 
         # Add layout to dependency tree
         site.regenerator.add_dependency(
-          site.reader.in_source_dir(document.path),
-          site.reader.in_source_dir(layout.path)
+          site.in_source_dir(document.path),
+          site.in_source_dir(layout.path)
         ) if document.write?
 
         if layout = site.layouts[layout.data["layout"]]
diff --git a/lib/jekyll/site.rb b/lib/jekyll/site.rb
index fd1b2661..1e902e2d 100644
--- a/lib/jekyll/site.rb
+++ b/lib/jekyll/site.rb
@@ -342,6 +342,30 @@ module Jekyll
       @publisher ||= Publisher.new(self)
     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
+
     private
 
     # Checks if the site has any pages containing relative links
diff --git a/lib/jekyll/static_file.rb b/lib/jekyll/static_file.rb
index cb1b3079..b83f4fae 100644
--- a/lib/jekyll/static_file.rb
+++ b/lib/jekyll/static_file.rb
@@ -35,7 +35,7 @@ module Jekyll
     #
     # Returns destination file path.
     def destination(dest)
-      @site.reader.in_dest_dir(*[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 fcac41b2..b809ffe7 100644
--- a/lib/jekyll/tags/include.rb
+++ b/lib/jekyll/tags/include.rb
@@ -117,7 +117,7 @@ eos
         # Add include to dependency tree
         if context.registers[:page] and context.registers[:page].has_key? "path"
           site.regenerator.add_dependency(
-            site.reader.in_source_dir(context.registers[:page]["path"]),
+            site.in_source_dir(context.registers[:page]["path"]),
             path
           )
         end
@@ -135,7 +135,7 @@ eos
       end
 
       def resolved_includes_dir(context)
-        context.registers[:site].reader.in_source_dir(@includes_dir)
+        context.registers[:site].in_source_dir(@includes_dir)
       end
 
       def validate_path(path, dir, safe)
@@ -170,7 +170,7 @@ eos
       end
 
       def resolved_includes_dir(context)
-        context.registers[:site].reader.in_source_dir(page_path(context))
+        context.registers[:site].in_source_dir(page_path(context))
       end
     end
   end
diff --git a/test/test_regenerator.rb b/test/test_regenerator.rb
index cc505e39..15819487 100644
--- a/test/test_regenerator.rb
+++ b/test/test_regenerator.rb
@@ -63,7 +63,7 @@ class TestRegenerator < JekyllUnitTest
       }))
 
       @site.process
-      @path = @site.reader.in_source_dir(@site.pages.first.path)
+      @path = @site.in_source_dir(@site.pages.first.path)
       @regenerator = @site.regenerator
     end