diff --git a/lib/jekyll.rb b/lib/jekyll.rb
index 65bdd7fe..6393d4eb 100644
--- a/lib/jekyll.rb
+++ b/lib/jekyll.rb
@@ -94,8 +94,8 @@ module Jekyll
     }
   }
 
-  # Generate a Jekyll configuration Hash by merging the default options
-  # with anything in _config.yml, and adding the given options on top.
+  # 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::DEFAULTS for a
diff --git a/lib/jekyll/generators/pagination.rb b/lib/jekyll/generators/pagination.rb
index 59d71093..a9571046 100644
--- a/lib/jekyll/generators/pagination.rb
+++ b/lib/jekyll/generators/pagination.rb
@@ -1,8 +1,14 @@
 module Jekyll
 
   class Pagination < Generator
+    # This generator is safe from arbitrary code execution.
     safe true
 
+    # Generate paginated pages if necessary.
+    #
+    # site - The Site.
+    #
+    # Returns nothing.
     def generate(site)
       site.pages.dup.each do |page|
         paginate(site, page) if Pager.pagination_enabled?(site.config, page.name)
@@ -10,9 +16,11 @@ module Jekyll
     end
 
     # Paginates the blog's posts. Renders the index.html file into paginated
-    # directories, ie: page2/index.html, page3/index.html, etc and adds more
+    # directories, e.g.: page2/index.html, page3/index.html, etc and adds more
     # site-wide data.
-    #   +page+ is the index.html Page that requires pagination
+    #
+    # site - The Site.
+    # page - The index.html Page that requires pagination.
     #
     # {"paginator" => { "page" => <Number>,
     #                   "per_page" => <Number>,
@@ -36,22 +44,40 @@ module Jekyll
         end
       end
     end
-
   end
 
   class Pager
     attr_reader :page, :per_page, :posts, :total_posts, :total_pages, :previous_page, :next_page
 
+    # Calculate the number of pages.
+    #
+    # all_posts - The Array of all Posts.
+    # per_page  - The Integer of entries per page.
+    #
+    # Returns the Integer number of pages.
     def self.calculate_pages(all_posts, per_page)
       num_pages = all_posts.size / per_page.to_i
       num_pages = num_pages + 1 if all_posts.size % per_page.to_i != 0
       num_pages
     end
 
+    # Determine if pagination is enabled for a given file.
+    #
+    # config - The configuration Hash.
+    # file   - The String filename of the file.
+    #
+    # Returns true if pagination is enabled, false otherwise.
     def self.pagination_enabled?(config, file)
       file == 'index.html' && !config['paginate'].nil?
     end
 
+    # Initialize a new Pager.
+    #
+    # config    - The Hash configuration of the site.
+    # page      - The Integer page number.
+    # all_posts - The Array of all the site's Posts.
+    # num_pages - The Integer number of pages or nil if you'd like the number
+    #             of pages calculated.
     def initialize(config, page, all_posts, num_pages = nil)
       @page = page
       @per_page = config['paginate'].to_i
@@ -70,6 +96,9 @@ module Jekyll
       @next_page = @page != @total_pages ? @page + 1 : nil
     end
 
+    # Convert this Pager's data to a Hash suitable for use by Liquid.
+    #
+    # Returns the Hash representation of this Pager.
     def to_liquid
       {
         'page' => page,
@@ -83,5 +112,4 @@ module Jekyll
     end
   end
 
-
 end
diff --git a/lib/jekyll/site.rb b/lib/jekyll/site.rb
index 1ee62a54..41905d65 100644
--- a/lib/jekyll/site.rb
+++ b/lib/jekyll/site.rb
@@ -9,10 +9,9 @@ module Jekyll
 
     attr_accessor :converters, :generators
 
-    # Initialize the site
-    #   +config+ is a Hash containing site configurations details
+    # Public: Initialize a new Site.
     #
-    # Returns <Site>
+    # config - A Hash containing site configuration details.
     def initialize(config)
       self.config          = config.clone
 
@@ -31,6 +30,21 @@ module Jekyll
       self.setup
     end
 
+    # Public: Read, process, and write this Site to output.
+    #
+    # Returns nothing.
+    def process
+      self.reset
+      self.read
+      self.generate
+      self.render
+      self.cleanup
+      self.write
+    end
+
+    # Reset Site details.
+    #
+    # Returns nothing
     def reset
       self.time            = if self.config['time']
                                Time.parse(self.config['time'].to_s)
@@ -44,13 +58,18 @@ module Jekyll
       self.categories      = Hash.new { |hash, key| hash[key] = [] }
       self.tags            = Hash.new { |hash, key| hash[key] = [] }
 
-      raise ArgumentError, "Limit posts must be nil or >= 1" if !self.limit_posts.nil? && self.limit_posts < 1
+      if !self.limit_posts.nil? && self.limit_posts < 1
+        raise ArgumentError, "Limit posts must be nil or >= 1"
+      end
     end
 
+    # Load necessary libraries, plugins, converters, and generators.
+    #
+    # Returns nothing.
     def setup
       require 'classifier' if self.lsi
 
-      # If safe mode is off, load in any ruby files under the plugins
+      # If safe mode is off, load in any Ruby files under the plugins
       # directory.
       unless self.safe
         Dir[File.join(self.plugins, "**/*.rb")].each do |f|
@@ -71,29 +90,18 @@ module Jekyll
       end
     end
 
-    # Do the actual work of processing the site and generating the
-    # real deal.  5 phases; reset, read, generate, render, write.  This allows
-    # rendering to have full site payload available.
+    # Read Site data from disk and load it into internal data structures.
     #
-    # Returns nothing
-    def process
-      self.reset
-      self.read
-      self.generate
-      self.render
-      self.cleanup
-      self.write
-    end
-
+    # Returns nothing.
     def read
-      self.read_layouts # existing implementation did this at top level only so preserved that
+      self.read_layouts
       self.read_directories
     end
 
     # Read all the files in <source>/<dir>/_layouts and create a new Layout
     # object with each one.
     #
-    # Returns nothing
+    # Returns nothing.
     def read_layouts(dir = '')
       base = File.join(self.source, dir, "_layouts")
       return unless File.exists?(base)
@@ -106,10 +114,44 @@ module Jekyll
       end
     end
 
+    # Recursively traverse directories to find posts, pages and static files
+    # that will become part of the site according to the rules in
+    # filter_entries.
+    #
+    # dir - The String relative path of the directory to read.
+    #
+    # Returns nothing.
+    def read_directories(dir = '')
+      base = File.join(self.source, dir)
+      entries = Dir.chdir(base) { filter_entries(Dir['*']) }
+
+      self.read_posts(dir)
+
+      entries.each do |f|
+        f_abs = File.join(base, f)
+        f_rel = File.join(dir, f)
+        if File.directory?(f_abs)
+          next if self.dest.sub(/\/$/, '') == f_abs
+          read_directories(f_rel)
+        elsif !File.symlink?(f_abs)
+          first3 = File.open(f_abs) { |fd| fd.read(3) }
+          if first3 == "---"
+            # file appears to have a YAML header so process it as a page
+            pages << Page.new(self, self.source, dir, f)
+          else
+            # otherwise treat it as a static file
+            static_files << StaticFile.new(self, self.source, dir, f)
+          end
+        end
+      end
+    end
+
     # Read all the files in <source>/<dir>/_posts and create a new Post
     # object with each one.
     #
-    # Returns nothing
+    # dir - The String relative path of the directory to read.
+    #
+    # Returns nothing.
     def read_posts(dir)
       base = File.join(self.source, dir, '_posts')
       return unless File.exists?(base)
@@ -134,12 +176,18 @@ module Jekyll
       self.posts = self.posts[-limit_posts, limit_posts] if limit_posts
     end
 
+    # Run each of the Generators.
+    #
+    # Returns nothing.
     def generate
       self.generators.each do |generator|
         generator.generate(self)
       end
     end
 
+    # Render the site to the destination.
+    #
+    # Returns nothing.
     def render
       self.posts.each do |post|
         post.render(self.layouts, site_payload)
@@ -149,15 +197,15 @@ module Jekyll
         page.render(self.layouts, site_payload)
       end
 
-      self.categories.values.map { |ps| ps.sort! { |a, b| b <=> a} }
-      self.tags.values.map { |ps| ps.sort! { |a, b| b <=> a} }
+      self.categories.values.map { |ps| ps.sort! { |a, b| b <=> a } }
+      self.tags.values.map { |ps| ps.sort! { |a, b| b <=> a } }
     rescue Errno::ENOENT => e
       # ignore missing layout dir
     end
-    
-    # Remove orphaned files and empty directories in destination
+
+    # Remove orphaned files and empty directories in destination.
     #
-    # Returns nothing
+    # Returns nothing.
     def cleanup
       # all files and directories in destination, including hidden ones
       dest_files = Set.new
@@ -176,20 +224,20 @@ module Jekyll
       self.static_files.each do |sf|
         files << sf.destination(self.dest)
       end
-      
+
       # adding files' parent directories
       dirs = Set.new
       files.each { |file| dirs << File.dirname(file) }
       files.merge(dirs)
-      
+
       obsolete_files = dest_files - files
-      
+
       FileUtils.rm_rf(obsolete_files.to_a)
     end
 
-    # Write static files, pages and posts
+    # Write static files, pages, and posts.
     #
-    # Returns nothing
+    # Returns nothing.
     def write
       self.posts.each do |post|
         post.write(self.dest)
@@ -202,59 +250,45 @@ module Jekyll
       end
     end
 
-    # Reads the directories and finds posts, pages and static files that will
-    # become part of the valid site according to the rules in +filter_entries+.
-    #   The +dir+ String is a relative path used to call this method
-    #            recursively as it descends through directories
+    # Constructs a Hash of Posts indexed by the specified Post attribute.
     #
-    # Returns nothing
-    def read_directories(dir = '')
-      base = File.join(self.source, dir)
-      entries = Dir.chdir(base){ filter_entries(Dir['*']) }
-
-      self.read_posts(dir)
-
-      entries.each do |f|
-        f_abs = File.join(base, f)
-        f_rel = File.join(dir, f)
-        if File.directory?(f_abs)
-          next if self.dest.sub(/\/$/, '') == f_abs
-          read_directories(f_rel)
-        elsif !File.symlink?(f_abs)
-          first3 = File.open(f_abs) { |fd| fd.read(3) }
-          if first3 == "---"
-            # file appears to have a YAML header so process it as a page
-            pages << Page.new(self, self.source, dir, f)
-          else
-            # otherwise treat it as a static file
-            static_files << StaticFile.new(self, self.source, dir, f)
-          end
-        end
-      end
-    end
-
-    # Constructs a hash map of Posts indexed by the specified Post attribute
+    # post_attr - The String name of the Post attribute.
     #
-    # Returns {post_attr => [<Post>]}
+    # Examples
+    #
+    #   post_attr_hash('categories')
+    #   # => { 'tech' => [<Post A>, <Post B>],
+    #   #      'ruby' => [<Post B>] }
+    #
+    # Returns the Hash: { attr => posts } where
+    #   attr  - One of the values for the requested attribute.
+    #   posts - The Array of Posts with the given attr value.
     def post_attr_hash(post_attr)
-      # Build a hash map based on the specified post attribute ( post attr => array of posts )
-      # then sort each array in reverse order
+      # Build a hash map based on the specified post attribute ( post attr =>
+      # array of posts ) then sort each array in reverse order.
       hash = Hash.new { |hash, key| hash[key] = Array.new }
       self.posts.each { |p| p.send(post_attr.to_sym).each { |t| hash[t] << p } }
-      hash.values.map { |sortme| sortme.sort! { |a, b| b <=> a} }
-      return hash
+      hash.values.map { |sortme| sortme.sort! { |a, b| b <=> a } }
+      hash
     end
 
-    # The Hash payload containing site-wide data
+    # The Hash payload containing site-wide data.
     #
-    # Returns {"site" => {"time" => <Time>,
-    #                     "posts" => [<Post>],
-    #                     "pages" => [<Page>],
-    #                     "categories" => [<Post>]}
+    # Returns the Hash: { "site" => data } where data is a Hash with keys:
+    #   "time"       - The Time as specified in the configuration or the
+    #                  current time if none was specified.
+    #   "posts"      - The Array of Posts, sorted chronologically by post date
+    #                  and then title.
+    #   "pages"      - The Array of all Pages.
+    #   "html_pages" - The Array of HTML Pages.
+    #   "categories" - The Hash of category values and Posts.
+    #                  See Site#post_attr_hash for type info.
+    #   "tags"       - The Hash of tag values and Posts.
+    #                  See Site#post_attr_hash for type info.
     def site_payload
       {"site" => self.config.merge({
           "time"       => self.time,
-          "posts"      => self.posts.sort { |a,b| b <=> a },
+          "posts"      => self.posts.sort { |a, b| b <=> a },
           "pages"      => self.pages,
           "html_pages" => self.pages.reject { |page| !page.html? },
           "categories" => post_attr_hash('categories'),
@@ -264,7 +298,11 @@ module Jekyll
     # 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
-    # files such as '.htaccess'
+    # files such as '.htaccess'.
+    #
+    # entries - The Array of file/directory entries to filter.
+    #
+    # Returns the Array of filtered entries.
     def filter_entries(entries)
       entries = entries.reject do |e|
         unless ['.htaccess'].include?(e)
diff --git a/lib/jekyll/static_file.rb b/lib/jekyll/static_file.rb
index 5509db75..318177c7 100644
--- a/lib/jekyll/static_file.rb
+++ b/lib/jekyll/static_file.rb
@@ -1,15 +1,15 @@
 module Jekyll
 
   class StaticFile
-    @@mtimes = Hash.new # the cache of last modification times [path] -> mtime
+    # The cache of last modification times [path] -> mtime.
+    @@mtimes = Hash.new
 
     # Initialize a new StaticFile.
-    #   +site+ is the Site
-    #   +base+ is the String path to the <source>
-    #   +dir+ is the String path between <source> and the file
-    #   +name+ is the String filename of the file
     #
-    # Returns <StaticFile>
+    # site - The Site.
+    # base - The String path to the <source>.
+    # dir  - The String path between <source> and the file.
+    # name - The String filename of the file.
     def initialize(site, base, dir, name)
       @site = site
       @base = base
@@ -17,24 +17,21 @@ module Jekyll
       @name = name
     end
 
-    # Obtains source file path.
-    #
     # Returns source file path.
     def path
       File.join(@base, @dir, @name)
     end
 
     # Obtain destination path.
-    #   +dest+ is the String path to the destination dir
+    #
+    # dest - The String path to the destination dir.
     #
     # Returns destination file path.
     def destination(dest)
       File.join(dest, @dir, @name)
     end
 
-    # Obtain mtime of the source path.
-    #
-    # Returns last modifiaction time for this file.
+    # Returns last modification time for this file.
     def mtime
       File.stat(path).mtime.to_i
     end
@@ -47,13 +44,14 @@ module Jekyll
     end
 
     # Write the static file to the destination directory (if modified).
-    #   +dest+ is the String path to the destination dir
+    #
+    # dest - The String path to the destination dir.
     #
     # Returns false if the file was not modified since last time (no-op).
     def write(dest)
       dest_path = destination(dest)
 
-      return false if File.exist? dest_path and !modified?
+      return false if File.exist?(dest_path) and !modified?
       @@mtimes[path] = mtime
 
       FileUtils.mkdir_p(File.dirname(dest_path))
@@ -67,7 +65,6 @@ module Jekyll
     # Returns nothing.
     def self.reset_cache
       @@mtimes = Hash.new
-
       nil
     end
   end
diff --git a/lib/jekyll/tags/highlight.rb b/lib/jekyll/tags/highlight.rb
index 5d73c572..aeddfb2d 100644
--- a/lib/jekyll/tags/highlight.rb
+++ b/lib/jekyll/tags/highlight.rb
@@ -3,7 +3,7 @@ module Jekyll
   class HighlightBlock < Liquid::Block
     include Liquid::StandardFilters
 
-    # we need a language, but the linenos argument is optional.
+    # We need a language, but the linenos argument is optional.
     SYNTAX = /(\w+)\s?([\w\s=]+)*/
 
     def initialize(tag_name, markup, tokens)
@@ -24,7 +24,7 @@ module Jekyll
             tmp_options[key] = value
           end
           tmp_options = tmp_options.to_a.collect { |opt| opt.join('=') }
-          # additional options to pass to Albino.
+          # additional options to pass to Albino
           @options = { 'O' => tmp_options.join(',') }
         else
           @options = {}
@@ -50,7 +50,7 @@ module Jekyll
     end
 
     def render_codehighlighter(context, code)
-    #The div is required because RDiscount blows ass
+      #The div is required because RDiscount blows ass
       <<-HTML
 <div>
   <pre>
@@ -59,13 +59,13 @@ module Jekyll
 </div>
       HTML
     end
-    
+
     def add_code_tags(code, lang)
       # Add nested <code> tags to code blocks
       code = code.sub(/<pre>/,'<pre><code class="' + lang + '">')
       code = code.sub(/<\/pre>/,"</code></pre>")
     end
-    
+
   end
 
 end