diff --git a/lib/jekyll/cleaner.rb b/lib/jekyll/cleaner.rb
index e7ee44a0..00191db7 100644
--- a/lib/jekyll/cleaner.rb
+++ b/lib/jekyll/cleaner.rb
@@ -13,7 +13,7 @@ module Jekyll
       # Cleans up the site's destination directory
       def cleanup!
         FileUtils.rm_rf(obsolete_files)
-        FileUtils.rm_rf(metadata_file) if @site.config["clean"]
+        FileUtils.rm_rf(metadata_file) if @site.config["full_rebuild"]
       end
 
       private
diff --git a/lib/jekyll/command.rb b/lib/jekyll/command.rb
index d463d235..423c3202 100644
--- a/lib/jekyll/command.rb
+++ b/lib/jekyll/command.rb
@@ -58,7 +58,7 @@ module Jekyll
         c.option 'unpublished', '--unpublished', 'Render posts that were marked as unpublished'
         c.option 'quiet',   '-q', '--quiet', 'Silence output.'
         c.option 'verbose', '-V', '--verbose', 'Print verbose output.'
-        c.option 'clean', '-c', '--clean', 'Clean the site before rebuilding.'
+        c.option 'full_rebuild', '-f', '--full-rebuild', 'Clean the site before rebuilding.'
       end
 
     end
diff --git a/lib/jekyll/configuration.rb b/lib/jekyll/configuration.rb
index 24e96898..7f1148a6 100644
--- a/lib/jekyll/configuration.rb
+++ b/lib/jekyll/configuration.rb
@@ -17,7 +17,7 @@ module Jekyll
       # Handling Reading
       'safe'          => false,
       'include'       => ['.htaccess'],
-      'exclude'       => ['.jekyll-metadata'],
+      'exclude'       => [],
       'keep_files'    => ['.git','.svn'],
       'encoding'      => 'utf-8',
       'markdown_ext'  => 'markdown,mkdown,mkdn,mkd,md',
diff --git a/lib/jekyll/metadata.rb b/lib/jekyll/metadata.rb
index 275ee9da..2012afc6 100644
--- a/lib/jekyll/metadata.rb
+++ b/lib/jekyll/metadata.rb
@@ -7,9 +7,8 @@ module Jekyll
     def initialize(site)
       @site = site
 
-      # Initialize metadata store by reading YAML file,
-      # or an empty hash if file does not exist
-      @metadata = (File.file?(metadata_file) && !(site.config['clean'])) ? SafeYAML.load(File.read(metadata_file)) : {}
+      # Read metadata from file
+      read_metadata
 
       # Initialize cache to an empty hash
       @cache = {}
@@ -92,5 +91,15 @@ module Jekyll
     def metadata_file
       Jekyll.sanitized_path(site.source, '.jekyll-metadata')
     end
+
+    private
+
+    # Read metadata from the metadata file, if no file is found,
+    # initialize with an empty hash
+    #
+    # Returns the read metadata.
+    def read_metadata
+      @metadata = (File.file?(metadata_file) && !(site.config['full_rebuild'])) ? SafeYAML.load(File.read(metadata_file)) : {}
+    end
   end
 end
diff --git a/lib/jekyll/site.rb b/lib/jekyll/site.rb
index f00e24c9..738cae0e 100644
--- a/lib/jekyll/site.rb
+++ b/lib/jekyll/site.rb
@@ -294,7 +294,7 @@ module Jekyll
       collections.each do |label, collection|
         collection.docs.each do |document|
           document.output = Jekyll::Renderer.new(self, document).run if (
-            @metadata.regenerate?(document.path, document.write?) ||
+            metadata.regenerate?(document.path, document.write?) ||
             document.data['regenerate']
           )
         end
@@ -303,7 +303,7 @@ module Jekyll
       payload = site_payload
       [posts, pages].flatten.each do |page_or_post|
         page_or_post.render(layouts, payload) if (
-          @metadata.regenerate?(Jekyll.sanitized_path(source, page_or_post.relative_path)) ||
+          metadata.regenerate?(Jekyll.sanitized_path(source, page_or_post.relative_path)) ||
           page_or_post.data['regenerate']
         )
       end
@@ -324,11 +324,11 @@ module Jekyll
     def write
       each_site_file { |item|
         item.write(dest) if (
-          @metadata.regenerate?(Jekyll.sanitized_path(source, item.path)) ||
+          metadata.regenerate?(Jekyll.sanitized_path(source, item.path)) ||
           (item.respond_to?(:data) && item.data['regenerate'])
         )
       }
-      @metadata.write
+      metadata.write
     end
 
     # Construct a Hash of Posts indexed by the specified Post attribute.
diff --git a/test/test_document.rb b/test/test_document.rb
index cf6c2cbf..2ff688ba 100644
--- a/test/test_document.rb
+++ b/test/test_document.rb
@@ -247,7 +247,7 @@ class TestDocument < Test::Unit::TestCase
         },
         "source"      => source_dir,
         "destination" => dest_dir,
-        "clean"       => true
+        "full_rebuild"       => true
       }))
       @site.process
       @document = @site.collections["slides"].files.find { |doc| doc.relative_path == "_slides/octojekyll.png" }
diff --git a/test/test_site.rb b/test/test_site.rb
index 2fd6ad36..a6ef5af8 100644
--- a/test/test_site.rb
+++ b/test/test_site.rb
@@ -331,7 +331,7 @@ class TestSite < Test::Unit::TestCase
         end
 
         bad_processor = "Custom::Markdown"
-        s = Site.new(site_configuration('markdown' => bad_processor, 'clean' => true))
+        s = Site.new(site_configuration('markdown' => bad_processor, 'full_rebuild' => true))
         assert_raise Jekyll::Errors::FatalException do
           s.process
         end
@@ -351,7 +351,7 @@ class TestSite < Test::Unit::TestCase
 
       should 'throw FatalException at process time' do
         bad_processor = 'not a processor name'
-        s = Site.new(site_configuration('markdown' => bad_processor, 'clean' => true))
+        s = Site.new(site_configuration('markdown' => bad_processor, 'full_rebuild' => true))
         assert_raise Jekyll::Errors::FatalException do
           s.process
         end
@@ -422,7 +422,7 @@ class TestSite < Test::Unit::TestCase
     context "manipulating the Jekyll environment" do
       setup do
         @site = Site.new(site_configuration({
-          "clean" => true
+          'full_rebuild' => true
         }))
         @site.process
         @page = @site.pages.find { |p| p.name == "environment.html" }
@@ -436,7 +436,7 @@ class TestSite < Test::Unit::TestCase
         setup do
           ENV["JEKYLL_ENV"] = "production"
           @site = Site.new(site_configuration({
-            "clean" => true
+            'full_rebuild' => true
           }))
           @site.process
           @page = @site.pages.find { |p| p.name == "environment.html" }