diff --git a/core/main/command.rb b/core/main/command.rb
index 90a1dd2e3..2856f23fe 100644
--- a/core/main/command.rb
+++ b/core/main/command.rb
@@ -13,42 +13,38 @@
 #   See the License for the specific language governing permissions and
 #   limitations under the License.
 #
+
 module BeEF
 module Core
 
-
-  #
-  # This module contains a list of utils functions to use
-  # when writing commands.
-  #
+  # @note This module contains a list of utils functions to use when writing commands
   module CommandUtils
     
     # Format a string to support multiline in javascript.
+    # @param [String] text String to convert
+    # @return [String] Formatted string
     def format_multiline(text); text.gsub(/\n/, '\n'); end
     
   end
 
 
   
-  #
-  # The Command Module Context is being used when evaluating code in eruby.
-  # In other words, we use that code to add funky functions to the
-  # javascript templates of our commands.
-  #
+  # @note The Command Module Context is being used when evaluating code in eruby.
+  #   In other words, we use that code to add funky functions to the
+  #   javascript templates of our commands.
   class CommandContext < Erubis::Context
     include BeEF::Core::CommandUtils
     
+    # Constructor
+    # @param [Hash] hash
     def initialize(hash=nil); 
       super(hash); 
     end
     
   end
   
-  #
-  # This class is the base class for all command modules in the framework.
-  #
-  # Two instances of this object are created during the execution of command module.
-  #
+  # @note This class is the base class for all command modules in the framework.
+  #   Two instances of this object are created during the execution of command module.
   class Command
   
     attr_reader :datastore, :path, :default_command_url, :beefjs_components, :friendlyname
@@ -59,6 +55,7 @@ module Core
     include BeEF::Core::Constants::CommandModule
 
     # Super class controller
+    # @param [String] key command module key
     def initialize(key)
       get_extensions
       config = BeEF::Core::Configuration.instance
@@ -75,42 +72,32 @@ module Core
       @beefjs_components = {}
     end
     
-    #
-    # Uses the API to include all the code from extensions that need to add
-    # methods, constants etc to that class.
-    #
-    # See BeEF::API::Command for examples.
-    #
+    # Uses the API to include all the code from extensions that need to add methods, constants etc to that class.
+    # @todo Determine if this method is deprecated
     def get_extensions
       BeEF::API::Command.extended_in_modules.each do |mod|
         self.class.send(:include, mod)
       end
     end
     
-    #
-    # This function is called just before the intructions are sent to hooked browser.
-    # The derived class can use this function to update params used in the command module.
-    #
+    # This function is called just before the instructions are sent to hooked browser.
     def pre_send; end
     
-    #
     # Callback method. This function is called when the hooked browser sends results back.
-    #
     def callback; end
     
-    #
     # If the command requires some data to be sent back, this function will process them.
-    #
+    # @param [] head
+    # @param [Hash] params Hash of parameters
+    # @todo Determine argument "head" type
     def process_zombie_response(head, params); end
     
-    #
     # Returns true if the command needs configurations to work. False if not.
-    #
+    # @deprecated This command should not be used since the implementation of the new configuration system
     def needs_configuration?; !@datastore.nil?; end
     
-    #
     # Returns information about the command in a JSON format.
-    #
+    # @return [String] JSON formatted string
     def to_json
        {
         'Name'          => @friendlyname,
@@ -120,18 +107,16 @@ module Core
       }.to_json
     end
     
-    #
     # Builds the 'datastore' attribute of the command which is used to generate javascript code.
-    #
+    # @param [Hash] data Data to be inserted into the datastore
+    # @todo Confirm argument "data" type
     def build_datastore(data); 
       @datastore = JSON.parse(data)
     end
     
-    #
     # Sets the datastore for the callback function. This function is meant to be called by the CommandHandler
-    #
-    #  build_callback_datastore(http_params, http_header)
-    #
+    # @param [Hash] http_params HTTP parameters
+    # @param [Hash] http_header HTTP headers
     def build_callback_datastore(http_params, http_header)
       @datastore = {'http_headers' => {}} # init the datastore
       
@@ -152,9 +137,8 @@ module Core
       } 
     end
     
-    #
     # Returns the output of the command. These are the actual instructions sent to the browser.
-    #
+    # @return [String] The command output
     def output
         f = @path+'command.js'
         raise WEBrick::HTTPStatus::BadRequest, "#{f} file does not exist" if not File.exists? f
@@ -178,28 +162,25 @@ module Core
       @output
     end
     
-    #
-    # Saves the results received from the zombie.
-    #
+    # Saves the results received from the hooked browser
+    # @param [Hash] results Results from hooked browser
     def save(results); 
       @results = results; 
     end
 
-    # If nothing else than the file is specified, the function will map the file to a random path
-    # without any extension.
+    # If nothing else than the file is specified, the function will map the file to a random path without any extension.
+    # @param [String] file File to be mounted
+    # @param [String] path URL path to mounted file
+    # @param [String] extension URL extension
+    # @param [Integer] count The amount of times this file can be accessed before being automatically unmounted
+    # @deprecated This function is possibly deprecated in place of the API
     def map_file_to_url(file, path=nil, extension=nil, count=1)
            return  BeEF::Core::NetworkStack::Handlers::AssetHandler.instance.bind(file, path, extension, count)
     end
     
-    #
-    # Tells the framework to load a specific module of the BeEFJS library that
-    # the command will be using.
-    #
-    #  Example:
-    #
-    #   use 'beef.net.local'
-    #   use 'beef.encode.base64'
-    #
+    # Tells the framework to load a specific module of the BeEFJS library that the command will be using.
+    # @param [String] component String of BeEFJS component to load
+    # @note Example: use 'beef.net.local'
     def use(component)
       return if @beefjs_components.include? component
       
@@ -213,12 +194,14 @@ module Core
       @beefjs_components[component] = component_path
     end
 
+    # @todo Document
     def oc_value(name)
         option =  BeEF::Core::Models::OptionCache.first(:name => name)
 		return nil if not option
       	return option.value
 	end
 
+    # @todo Document
 	def apply_defaults()
 	    @datastore.each { |opt|
 		    opt["value"] = oc_value(opt["name"]) || opt["value"]
diff --git a/core/main/configuration.rb b/core/main/configuration.rb
index be6b4c317..e4ae5e3b3 100644
--- a/core/main/configuration.rb
+++ b/core/main/configuration.rb
@@ -13,23 +13,16 @@
 #   See the License for the specific language governing permissions and
 #   limitations under the License.
 #
+
 module BeEF
 module Core
-  #
-  # Parses the user configuration file for beef.
-  #
-  # Example:
-  #
-  #   configuration = BeEF::Core::Configuration.instance
-  #   p configuration.get('beef.http.host) # => "0.0.0.0"
-  #
+
   class Configuration
     
     include Singleton
   
-    #
-    # Constructor
-    #
+    # Loads the default configuration system
+    # @param [String] configuration_file Configuration file to be loaded, by default loads $root_dir/config.yaml
     def initialize(configuration_file="#{$root_dir}/config.yaml")
       # argument type checking
       raise Exception::TypeError, '"configuration_file" needs to be a string' if not configuration_file.string?
@@ -41,18 +34,18 @@ module Core
       @config.default = nil
     end
 
-    #
     # Loads yaml file
-    #
+    # @param [String] file YAML file to be loaded
+    # @return [Hash] YAML formatted hash
     def load(file)
         return nil if not File.exists?(file)
         raw = File.read(file)
         return YAML.load(raw)
     end
 
-    #
     # Returns the value of a selected key in the configuration file.
-    #
+    # @param [String] key Key of configuration item
+    # @return [Hash|String] The resulting value stored against the 'key'
     def get(key)
         subkeys = key.split('.')
         lastkey = subkeys.pop
@@ -62,9 +55,10 @@ module Core
         return (subhash != nil and subhash.has_key?(lastkey)) ? subhash[lastkey] : nil 
     end
 
-    #
     # Sets the give key value pair to the config instance
-    #
+    # @param [String] key The configuration key
+    # @param value The value to be stored against the 'key'
+    # @return [Boolean] If the store procedure was successful
     def set(key, value)
         subkeys = key.split('.').reverse
         return false if subkeys.length == 0
@@ -76,9 +70,9 @@ module Core
         return true
     end
 
-    #
     # Clears the given key hash
-    #
+    # @param [String] key Configuration key to be cleared
+    # @return [Boolean] If the configuration key was cleared
     def clear(key)
         subkeys = key.split('.')
         return false if subkeys.length == 0
@@ -90,9 +84,7 @@ module Core
         return (hash.delete(lastkey) == nil) ? false : true    
     end
 
-    #
-    # load extensions configurations
-    #
+    # Load extensions configurations
     def load_extensions_config
         self.set('beef.extension', {})
         Dir.glob("#{$root_dir}/extensions/*/config.yaml") do | cf |
@@ -104,9 +96,7 @@ module Core
         end
     end
 
-    #
     # Load module configurations
-    #
     def load_modules_config
         self.set('beef.module', {})
         Dir.glob("#{$root_dir}/modules/**/*/config.yaml") do | cf |
diff --git a/core/main/constants/browsers.rb b/core/main/constants/browsers.rb
index 4b1a29411..4325e1a36 100644
--- a/core/main/constants/browsers.rb
+++ b/core/main/constants/browsers.rb
@@ -13,6 +13,7 @@
 #   See the License for the specific language governing permissions and
 #   limitations under the License.
 #
+
 module BeEF
 module Core
 module Constants
@@ -38,6 +39,9 @@ module Constants
     FRIENDLY_O_NAME   = 'Opera'
    	FRIENDLY_UN_NAME  = "UNKNOWN"
  
+    # Attempt to retrieve a browsers friendly name
+    # @param [String] browser_name Short browser name
+    # @return [String] Friendly browser name
    	def self.friendly_name(browser_name)
 	  
    	  case browser_name
@@ -53,6 +57,10 @@ module Constants
 	    
   	end
 
+    # Attempt to match the browserstring to a browser constant
+    # @param [String] browserstring Browser UA string
+    # @return [Array] An array of matching browser constants
+    # @todo Confirm this function returns an array if multiple constants are matched
   	def self.match_browser(browserstring)
   		matches = []
 			browserstring.split(" ").each do |chunk|
@@ -80,4 +88,4 @@ module Constants
   
 end
 end
-end
\ No newline at end of file
+end
diff --git a/core/main/constants/commandmodule.rb b/core/main/constants/commandmodule.rb
index 4aeed9791..e5c7e42bf 100644
--- a/core/main/constants/commandmodule.rb
+++ b/core/main/constants/commandmodule.rb
@@ -13,6 +13,7 @@
 #   See the License for the specific language governing permissions and
 #   limitations under the License.
 #
+
 module BeEF
 module Core
 module Constants
@@ -20,6 +21,7 @@ module Constants
   module CommandModule
 
 
+    # @note Constants to define the execution probability of a command module (this is browser dependant)
     VERIFIED_WORKING =      0
     VERIFIED_UNKNOWN =      1
     VERIFIED_USER_NOTIFY =  2
@@ -30,4 +32,4 @@ module Constants
   
 end
 end
-end
\ No newline at end of file
+end
diff --git a/core/main/constants/distributedengine.rb b/core/main/constants/distributedengine.rb
index 6faa4ea08..8a06f56a0 100644
--- a/core/main/constants/distributedengine.rb
+++ b/core/main/constants/distributedengine.rb
@@ -13,11 +13,12 @@
 #   See the License for the specific language governing permissions and
 #   limitations under the License.
 #
+
 module BeEF
 module Core
 module Constants
   
-  # The distributed engine codes
+  # @note The distributed engine codes
   module DistributedEngine
   
     REQUESTER     = 1
@@ -27,4 +28,4 @@ module Constants
   
 end
 end
-end
\ No newline at end of file
+end
diff --git a/core/main/constants/os.rb b/core/main/constants/os.rb
index 367f10d61..e3ad74c32 100644
--- a/core/main/constants/os.rb
+++ b/core/main/constants/os.rb
@@ -13,11 +13,12 @@
 #   See the License for the specific language governing permissions and
 #   limitations under the License.
 #
+
 module BeEF
 module Core
 module Constants
   
-  # The OS'es strings for os detection.
+  # @note The OS'es strings for os detection.
   module Os
   
     OS_UNKNOWN_IMG        = 'unknown.png'
@@ -47,6 +48,9 @@ module Constants
 	OS_ANDROID_IMG        = 'android.png'
     OS_ALL_UA_STR         = 'All'
 
+        # Attempt to match operating system string to constant
+        # @param [String] name Name of operating system
+        # @return [String] Constant name of matched operating system, returns 'ALL'  if nothing are matched
 		def self.match_os(name)
 			case name.downcase
 				when /win/
diff --git a/core/main/crypto.rb b/core/main/crypto.rb
index f6bf6b5de..e4c6840d7 100644
--- a/core/main/crypto.rb
+++ b/core/main/crypto.rb
@@ -13,21 +13,18 @@
 #   See the License for the specific language governing permissions and
 #   limitations under the License.
 #
+
 module BeEF
 module Core
-  #
-  # This module provides crypto functionality
-  #
+
   module Crypto
     
-    # the minimum length of the security token
+    # @note the minimum length of the security token
     TOKEN_MINIMUM_LENGTH = 15
     
-    #
     # Generate a secure random token
-    #
-    # @param: {Integer} the length of the secure token
-    #
+    # @param [Integer] len The length of the secure token
+    # @return [String] Security token
     def self.secure_token(len = nil)
       # get default length from config
       config = BeEF::Core::Configuration.instance
diff --git a/core/main/distributed_engine/models/rules.rb b/core/main/distributed_engine/models/rules.rb
index 8884a1cbb..986a91ae7 100644
--- a/core/main/distributed_engine/models/rules.rb
+++ b/core/main/distributed_engine/models/rules.rb
@@ -13,13 +13,13 @@
 #   See the License for the specific language governing permissions and
 #   limitations under the License.
 #
+
 module BeEF
 module Core
 module DistributedEngine
 module Models
-  #
-  # Table stores the rules for the Distributed Engine.
-  #
+
+  # @note Table stores the rules for the Distributed Engine.
   class Rules
   
     include DataMapper::Resource
@@ -35,4 +35,4 @@ module Models
 end
 end
 end
-end
\ No newline at end of file
+end
diff --git a/core/main/handlers/commands.rb b/core/main/handlers/commands.rb
index 42a97a33a..1ebbd62d2 100644
--- a/core/main/handlers/commands.rb
+++ b/core/main/handlers/commands.rb
@@ -25,6 +25,10 @@ module Handlers
     attr_reader :guard
     @data = {}
     
+    # Handles command data
+    # @param [Hash] data Data from command execution
+    # @param [Class] kclass Class of command
+    # @todo Confirm argument data variable type.
     def initialize(data, kclass)
       @guard = Mutex.new
       @kclass = BeEF::Core::Command.const_get(kclass.capitalize)
@@ -32,40 +36,45 @@ module Handlers
       setup()
     end
     
+    # Initial setup function, creates the command module and saves details to datastore
     def setup()
-      @http_params = @data['request'].query  # used to populate datastore
-      @http_header = @data['request'].header # used to populate datastore
-      @http_header['referer'] ||= '' # used to populate datastore
+      @http_params = @data['request'].query  
+      @http_header = @data['request'].header
+      @http_header['referer'] ||= '' 
       
-      # get and check command id from the request
+      # @note get and check command id from the request
       command_id  = get_param(@data, 'cid')
-      # ruby filter needs to be updated to detect fixnums not strings
+      # @todo ruby filter needs to be updated to detect fixnums not strings
       command_id = command_id.to_s()
       raise WEBrick::HTTPStatus::BadRequest, "command_id is invalid" if not BeEF::Filters.is_valid_command_id?(command_id.to_s())   
 
-      # get and check session id from the request
+      # @note get and check session id from the request
       beefhook = get_param(@data, 'beefhook')
       raise WEBrick::HTTPStatus::BadRequest, "beefhook is invalid" if not BeEF::Filters.is_valid_hook_session_id?(beefhook)   
 
-      # create the command module to handle the response
-      command = @kclass.new(BeEF::Module.get_key_by_class(@kclass)) # create the commamd module 
-      command.build_callback_datastore(@http_params, @http_header) # build datastore from the response
+      # @note create the command module to handle the response
+      command = @kclass.new(BeEF::Module.get_key_by_class(@kclass))  
+      command.build_callback_datastore(@http_params, @http_header) 
       command.session_id = beefhook 
       if command.respond_to?(:post_execute)
         command.post_execute
       end
 
-      # get/set details for datastore and log entry
+      # @note get/set details for datastore and log entry
       command_friendly_name = command.friendlyname
       raise WEBrick::HTTPStatus::BadRequest, "command friendly name empty" if command_friendly_name.empty?
       command_results = get_param(@data, 'results')
       raise WEBrick::HTTPStatus::BadRequest, "command results empty" if command_results.empty?
-      # save the command module results to the datastore and create a log entry
+      # @note save the command module results to the datastore and create a log entry
       command_results = {'data' => command_results}
       BeEF::Core::Models::Command.save_result(beefhook, command_id, command_friendly_name, command_results) 
 
     end
     
+    # Returns parameter from hash
+    # @param [Hash] query Hash of data to return data from
+    # @param [String] key Key to search for and return inside `query`
+    # @return Value referenced in hash at the supplied key
     def get_param(query, key)
         return (query.class == Hash and query.has_key?(key)) ? query[key] : nil
     end
diff --git a/core/main/handlers/hookedbrowsers.rb b/core/main/handlers/hookedbrowsers.rb
index 155525e6c..57f2e7b1d 100644
--- a/core/main/handlers/hookedbrowsers.rb
+++ b/core/main/handlers/hookedbrowsers.rb
@@ -17,9 +17,7 @@ module BeEF
 module Core
 module Handlers
   
-  #
-  # This class handles connections from zombies to the framework.
-  #
+  # @note This class handles connections from hooked browsers to the framework.
   class HookedBrowsers < WEBrick::HTTPServlet::AbstractServlet
     
     include BeEF::Core::Handlers::Modules::BeEFJS
@@ -31,11 +29,10 @@ module Handlers
       @guard = Mutex.new
     end
     
-    #
-    # This method processes the http requests sent by a zombie to the framework.
-    # It will update the database to add or update the current zombie and deploy
-    # some command modules or plugins.
-    #
+    # This method processes the http requests sent by a hooked browser to the framework. It will update the database to add or update the current zombie and deploy some command modules or plugins.
+    # @param [Hash] request HTTP request object
+    # @param [Hash] response HTTP response object
+    # @todo Confirm return type of this function
     def do_GET(request, response)
       @body = ''
       @params = request.query
@@ -43,7 +40,7 @@ module Handlers
       @response = response
       config = BeEF::Core::Configuration.instance
       
-      # check source ip address of browser
+      # @note check source ip address of browser
       permitted_hooking_subnet = config.get('beef.restrictions.permitted_hooking_subnet')
       target_network = IPAddr.new(permitted_hooking_subnet)
       if not target_network.include?(request.peeraddr[3].to_s)
@@ -52,23 +49,24 @@ module Handlers
         return
       end
 
-      # get zombie if already hooked the framework
+      # @note get zombie if already hooked the framework
       hook_session_id = request.get_hook_session_id()
       hooked_browser = BeEF::Core::Models::HookedBrowser.first(:session => hook_session_id) if not hook_session_id.nil?
-      
-      if not hooked_browser # is a new browser so return instructions to set up the hook
+
+      # @note is a new browser so return instructions to set up the hook
+      if not hooked_browser 
         
-        # generate the instructions to hook the browser
-        host_name = @request.host # get the host from the HOST attribute in the HTTP header
+        # @note generate the instructions to hook the browser
+        host_name = @request.host 
         raise WEBrick::HTTPStatus::BadRequest, "Invalid host name" if not BeEF::Filters.is_valid_hostname?(host_name)
         build_beefjs!(host_name)
-      
-      else # is a known browseer so send instructions 
-      
-        # record the last poll from the browser
+
+      # @note is a known browser so send instructions 
+      else       
+        # @note record the last poll from the browser
         hooked_browser.lastseen = Time.new.to_i
         
-        # Check for a change in zombie IP and log an event
+        # @note Check for a change in zombie IP and log an event
         if hooked_browser.ip != @request.peeraddr[3].to_s
           BeEF::Core::Logger.instance.register('Zombie',"IP address has changed from #{hooked_browser.ip} to #{@request.peeraddr[3].to_s}","#{hooked_browser.id}")
           hooked_browser.ip = @request.peeraddr[3].to_s
@@ -77,17 +75,15 @@ module Handlers
         hooked_browser.count!
         hooked_browser.save
         
-        # add all availible command module instructions to the response
+        # @note add all available command module instructions to the response
         zombie_commands = BeEF::Core::Models::Command.all(:hooked_browser_id => hooked_browser.id, :instructions_sent => false)
         zombie_commands.each{|command| add_command_instructions(command, hooked_browser)}
 
-        #
-        # We dynamically get the list of all browser hook handler using the API and register them
-        #
+        # @note We dynamically get the list of all browser hook handler using the API and register them
         BeEF::API::Registrar.instance.fire(BeEF::API::Server::Hook, 'pre_hook_send', hooked_browser, @body, @params, @request, @response)
       end
 
-      # set response headers and body
+      # @note set response headers and body
       response.set_no_cache
       response.header['Content-Type'] = 'text/javascript' 
       response.header['Access-Control-Allow-Origin'] = '*'
@@ -96,17 +92,19 @@ module Handlers
       
     end
       
+    # @note alias do_POST function to do_GET
     alias do_POST do_GET
     
     private
     
-    # Object representing the HTTP request
+    # @note Object representing the HTTP request
     @request
     
-    # Object representing the HTTP response
+    # @note Object representing the HTTP response
     @response
     
-    # A string containing the list of BeEF components active in the hooked browser
+    # @note A string containing the list of BeEF components active in the hooked browser
+    # @todo Confirm this variable is still used
     @beef_js_cmps
     
   end
diff --git a/core/main/handlers/modules/beefjs.rb b/core/main/handlers/modules/beefjs.rb
index a1b78f1dd..8eb8607f2 100644
--- a/core/main/handlers/modules/beefjs.rb
+++ b/core/main/handlers/modules/beefjs.rb
@@ -18,50 +18,45 @@ module Core
 module Handlers
 module Modules
   
-  #
-  # Purpose: avoid rewriting several times the same code.
-  #
+  # @note Purpose: avoid rewriting several times the same code.
   module BeEFJS
     
-    #
     # Builds the default beefjs library (all default components of the library).
-    #
-    # @param: {Object} the hook session id
-    # @param: {Boolean} if the framework is already loaded in the hooked browser
-    #
+    # @param [Object] req_host The request object
     def build_beefjs!(req_host)
 
-      # set up values required to construct beefjs
-      beefjs = '' #  init the beefjs string (to be sent as the beefjs file)
-      beefjs_path = "#{$root_dir}/core/main/client/" # location of sub files      
+      # @note set up values required to construct beefjs
+      beefjs = '' 
+      # @note location of sub files      
+      beefjs_path = "#{$root_dir}/core/main/client/"
       js_sub_files = %w(lib/jquery-1.5.2.min.js lib/evercookie.js lib/json2.js beef.js browser.js browser/cookie.js session.js os.js dom.js logger.js net.js updater.js encode/base64.js encode/json.js net/local.js init.js)
 
-      # construct the beefjs string from file(s)
+      # @note construct the beefjs string from file(s)
       js_sub_files.each {|js_sub_file_name|
-        js_sub_file_abs_path = beefjs_path + js_sub_file_name # construct absolute path
-        beefjs << (File.read(js_sub_file_abs_path) + "\n\n") # concat each js sub file
+        js_sub_file_abs_path = beefjs_path + js_sub_file_name 
+        beefjs << (File.read(js_sub_file_abs_path) + "\n\n") 
       }
       
-      # create the config for the hooked browser session
+      # @note create the config for the hooked browser session
       config = BeEF::Core::Configuration.instance
       hook_session_name = config.get('beef.http.hook_session_name')
       hook_session_config = BeEF::Core::Server.instance.to_h
 
-      # if http_host="0.0.0.0" in config ini, use the host requested by client
+      # @note if http_host="0.0.0.0" in config ini, use the host requested by client
       if hook_session_config['beef_host'].eql? "0.0.0.0" 
         hook_session_config['beef_host'] = req_host 
         hook_session_config['beef_url'].sub!(/0\.0\.0\.0/, req_host)  
       end
       
-      # populate place holders in the beefjs string and set the response body
+      # @note populate place holders in the beefjs string and set the response body
       eruby = Erubis::FastEruby.new(beefjs)
       @body << eruby.evaluate(hook_session_config)
   
     end
     
-    #
     # Finds the path to js components
-    #
+    # @param [String] component Name of component
+    # @return [String|Boolean] Returns false if path was not found, otherwise returns component path
     def find_beefjs_component_path(component)
       component_path = component
       component_path.gsub!(/beef./, '')
@@ -73,13 +68,10 @@ module Modules
       component_path
     end
     
-    #
     # Builds missing beefjs components.
-    #
-    # Ex: build_missing_beefjs_components(['beef.net.local', 'beef.net.requester'])
-    #
+    # @param [Array] beefjs_components An array of component names
     def build_missing_beefjs_components(beefjs_components)
-      # verifies that @beef_js_cmps is not nil to avoid bugs
+      # @note verifies that @beef_js_cmps is not nil to avoid bugs
       @beef_js_cmps = '' if @beef_js_cmps.nil?
       
       if beefjs_components.is_a? String
@@ -91,14 +83,13 @@ module Modules
       beefjs_components.keys.each {|k|
         next if @beef_js_cmps.include? beefjs_components[k]
         
-        # path to the component
+        # @note path to the component
         component_path = beefjs_components[k]
         
-        # we output the component to the hooked browser
+        # @note we output the component to the hooked browser
         @body << File.read(component_path)+"\n\n"
         
-        # finally we add the component to the list of components already generated so it does not
-        # get generated numerous times.
+        # @note finally we add the component to the list of components already generated so it does not get generated numerous times.
         if @beef_js_cmps.eql? ''
           @beef_js_cmps = component_path
         else
diff --git a/core/main/handlers/modules/command.rb b/core/main/handlers/modules/command.rb
index 11979e071..78a78e251 100644
--- a/core/main/handlers/modules/command.rb
+++ b/core/main/handlers/modules/command.rb
@@ -20,9 +20,9 @@ module Modules
 
   module Command
 
-    #
     # Adds the command module instructions to a hooked browser's http response. 
-    #
+    # @param [Object] command Command object
+    # @param [Object] hooked_browser Hooked Browser object
     def add_command_instructions(command, hooked_browser)
 
       raise WEBrick::HTTPStatus::BadRequest, "hooked_browser is nil" if hooked_browser.nil?
@@ -30,7 +30,7 @@ module Modules
       raise WEBrick::HTTPStatus::BadRequest, "hooked_browser is nil" if command.nil?
       raise WEBrick::HTTPStatus::BadRequest, "hooked_browser.command_module_id is nil" if command.command_module_id.nil?
 
-      # get the command module
+      # @note get the command module
       command_module = BeEF::Core::Models::CommandModule.first(:id => command.command_module_id)      
       raise WEBrick::HTTPStatus::BadRequest, "command_module is nil" if command_module.nil?
       raise WEBrick::HTTPStatus::BadRequest, "command_module.path is nil" if command_module.path.nil?
@@ -51,13 +51,13 @@ module Modules
 
       @body << command_module.output + "\n\n"
       
-      # prints the event to the console
+      # @note prints the event to the console
       if BeEF::Settings.console?
       name = command_module.friendlyname || kclass
       print_info "Hooked browser #{hooked_browser.ip} has been sent instructions from command module '#{name}'"
       end
 
-      # flag that the command has been sent to the hooked browser
+      # @note flag that the command has been sent to the hooked browser
       command.instructions_sent = true 
       command.save
     end
diff --git a/core/main/logger.rb b/core/main/logger.rb
index 604d3428c..bb3d92cbf 100644
--- a/core/main/logger.rb
+++ b/core/main/logger.rb
@@ -13,48 +13,35 @@
 #   See the License for the specific language governing permissions and
 #   limitations under the License.
 #
+
 module BeEF
 module Core
-  #
-  # This class takes care of logging events in the db.
-  #
-  #   Example:
-  #
-  #     logger = BeEF::Core::Logger.instance
-  #     logger.register('Authentication', 'User with ip 127.0.0.1 has successfully authenticated into the application') # => true
-  #
-  #     zombie_id = 1
-  #     logger.register('Zombie', '123.456.789.123 just joined the horde', zombie_id) # => true
-  #
+
   class Logger
     
     include Singleton
     
-    #
     # Constructor
-    #
     def initialize
       @logs = BeEF::Core::Models::Log
     end
   
-    #
     # Registers a new event in the logs
-    #
-    # @param: {String} the origine of the event (i.e. Authentication, Zombie)
-    # @param: {String} the event description
-    # @param: {Integer} the id of the hooked browser affected (default = 0 if no HB)
-    #
-    def register(from, event, zombie = 0)
+    # @param [String] from The origin of the event (i.e. Authentication, Hooked Browser)
+    # @param [String] event The event description
+    # @param [Integer] hb The id of the hooked browser affected (default = 0 if no HB)
+    # @return [Boolean] True if the register was successful
+    def register(from, event, hb = 0)
       # type conversion to enforce standards
-      zombie = zombie.to_i
+      hb = hb.to_i
       
       # arguments type checking
       raise Exception::TypeError, '"from" needs to be a string' if not from.string?
       raise Exception::TypeError, '"event" needs to be a string' if not event.string?
-      raise Exception::TypeError, '"zombie" needs to be an integer' if not zombie.integer?
+      raise Exception::TypeError, '"Hooked Browser ID" needs to be an integer' if not hb.integer?
       
       # logging the new event into the database
-      @logs.new(:type => "#{from}", :event => "#{event}", :date => Time.now, :hooked_browser_id => zombie).save
+      @logs.new(:type => "#{from}", :event => "#{event}", :date => Time.now, :hooked_browser_id => hb).save
       
       # return
       true
diff --git a/core/main/migration.rb b/core/main/migration.rb
index e48c7e75f..bafc94720 100644
--- a/core/main/migration.rb
+++ b/core/main/migration.rb
@@ -13,27 +13,23 @@
 #   See the License for the specific language governing permissions and
 #   limitations under the License.
 #
+
 module BeEF
 module Core
-  #
-  # This class migrates and updates values in the database each time you restart BeEF.
-  # So for example, when you want to add a new command module, you stop BeEF, copy your command module into the framework
-  # and then restart BeEF. That class will take care of installing automatically the new command module in the db.
-  #
+
+  # @note This class migrates and updates values in the database each time you restart BeEF.
+  #   So for example, when you want to add a new command module, you stop BeEF, copy your command module into the framework
+  #   and then restart BeEF. That class will take care of installing automatically the new command module in the db.
   class Migration
   
     include Singleton
   
-    #
     # Updates the database.
-    #
     def update_db!
       update_commands!
     end
   
-    #
     # Checks for new command modules and updates the database.
-    #
     def update_commands!
       config = BeEF::Core::Configuration.instance
 
diff --git a/core/main/models/command.rb b/core/main/models/command.rb
index 1acd63871..069f51d61 100644
--- a/core/main/models/command.rb
+++ b/core/main/models/command.rb
@@ -13,22 +13,12 @@
 #   See the License for the specific language governing permissions and
 #   limitations under the License.
 #
+
 module BeEF
 module Core
 module Models
-  #
-  # Table stores the commands that have been sent to the Hooked Browsers.
-  #
-  #  Attributes:
-  #
-  #     - id
-  #     - data
-  #     - creationdate
-  #     - label
-  #     - instructions_sent
-  #     - command_module_id
-  #     - hooked_browser_id
-  #
+
+  # @note Table stores the commands that have been sent to the Hooked Browsers.
   class Command
 
     include DataMapper::Resource
@@ -43,25 +33,22 @@ module Models
 
     has n, :results
 
-    #
     # Save results and flag that the command has been run on the hooked browser
-    #
-    # @param: {String} the session_id.
-    # @param: {String} the command_id.
-    # @param: {String} the command friendly name.
-    # @param: {String} the result of the command module.
-    #
+    # @param [String] hook_session_id The session_id.
+    # @param [String] command_id The command_id.
+    # @param [String] command_friendly_name The command friendly name.
+    # @param [String] result The result of the command module.
     def self.save_result(hook_session_id, command_id, command_friendly_name, result)
-      # enforcing arguments types
+      # @note enforcing arguments types
       command_id = command_id.to_i
 
-      # argument type checking
+      # @note argument type checking
       raise Exception::TypeError, '"hook_session_id" needs to be a string' if not hook_session_id.string?
       raise Exception::TypeError, '"command_id" needs to be an integer' if not command_id.integer?
       raise Exception::TypeError, '"command_friendly_name" needs to be a string' if not command_friendly_name.string?
       raise Exception::TypeError, '"result" needs to be a hash' if not result.hash?
 
-      # get the hooked browser structure and id from the database
+      # @note get the hooked browser structure and id from the database
       hooked_browser = BeEF::Core::Models::HookedBrowser.first(:session => hook_session_id) || nil
       raise Exception::TypeError, "hooked_browser is nil" if hooked_browser.nil?
       raise Exception::TypeError, "hooked_browser.id is nil" if hooked_browser.id.nil?
@@ -69,18 +56,18 @@ module Models
       raise Exception::TypeError, "hooked_browser.ip is nil" if hooked_browser.ip.nil?
       hooked_browser_ip = hooked_browser.ip
 
-      # get the command module data structure from the database
+      # @note get the command module data structure from the database
       command = first(:id => command_id.to_i, :hooked_browser_id => hooked_browser_id) || nil
       raise Exception::TypeError, "command is nil" if command.nil?
 
-      # create the entry for the results 
+      # @note create the entry for the results 
       command.results.new(:hooked_browser_id => hooked_browser_id, :data => result.to_json, :date => Time.now.to_i)
       command.save
 
-      # log that the result was returned
+      # @note log that the result was returned
       BeEF::Core::Logger.instance.register('Command', "Hooked browser #{hooked_browser.ip} has executed instructions from command module '#{command_friendly_name}'", hooked_browser_id)
 
-      # prints the event into the console
+      # @note prints the event into the console
       if BeEF::Settings.console?
         print_info "Hooked browser #{hooked_browser.ip} has executed instructions from command module '#{command_friendly_name}'"
       end
@@ -90,4 +77,4 @@ module Models
 
 end
 end
-end
\ No newline at end of file
+end
diff --git a/core/main/models/hookedbrowser.rb b/core/main/models/hookedbrowser.rb
index 7539d382d..96519f340 100644
--- a/core/main/models/hookedbrowser.rb
+++ b/core/main/models/hookedbrowser.rb
@@ -31,27 +31,25 @@ module Models
     property :firstseen, String, :length => 15
     property :lastseen, String, :length => 15
     property :httpheaders, Text, :lazy => false
-    property :domain, Text, :lazy => false # the domain originating the hook request
+    # @note the domain originating the hook request
+    property :domain, Text, :lazy => false
     property :count, Integer, :lazy => false
     property :has_init, Boolean, :default => false
-    property :is_proxy, Boolean, :default => false # if true the HB is used as a tunneling proxy
-    
+    property :is_proxy, Boolean, :default => false     
+    # @note if true the HB is used as a tunneling proxy
+
     has n, :commands
     has n, :results
     has n, :logs
     #has n, :https
   
-    #
     # Increases the count of a zombie
-    #
     def count!
       if not self.count.nil? then self.count += 1; else self.count = 1; end
     end
   
-    #
-    # Returns the icon representing the browser type the
-    # zombie is using (i.e. Firefox, Internet Explorer)
-    #
+    # Returns the icon representing the browser type the hooked browser is using (i.e. Firefox, Internet Explorer)
+    # @return [String] String constant containing browser icon path
     def browser_icon
       agent = JSON.parse(self.httpheaders)['user-agent'].to_s || nil
     
@@ -67,10 +65,8 @@ module Models
       BeEF::Extension::AdminUI::Constants::Agents::AGENT_UNKNOWN_IMG
     end
   
-    #
-    # Returns the icon representing the os type the
-    # hooked browser is running (i.e. Windows, Linux)
-    #
+    # Returns the icon representing the os type the hooked browser is running (i.e. Windows, Linux)
+    # @return [String] String constant containing operating system icon path
     def os_icon
       agent = JSON.parse(self.httpheaders)['user-agent'].to_s || nil
     
@@ -86,4 +82,4 @@ module Models
 
 end
 end
-end
\ No newline at end of file
+end
diff --git a/core/main/models/log.rb b/core/main/models/log.rb
index d2674c0db..7bd992fce 100644
--- a/core/main/models/log.rb
+++ b/core/main/models/log.rb
@@ -16,11 +16,7 @@
 module BeEF
 module Core
 module Models
-  #
-  # This table stores the logs from the framework.
-  #
-  # See BeEF::Core::Logger for how to log events.
-  #
+
   class Log
   
     include DataMapper::Resource
@@ -36,4 +32,4 @@ module Models
   end
 end
 end
-end
\ No newline at end of file
+end
diff --git a/core/main/models/result.rb b/core/main/models/result.rb
index 70d86ffd0..9cc40653b 100644
--- a/core/main/models/result.rb
+++ b/core/main/models/result.rb
@@ -16,9 +16,7 @@
 module BeEF
 module Core
 module Models
-  #
-  # Table stores the results from commands.
-  #
+
   class Result
   
     include DataMapper::Resource
@@ -33,4 +31,4 @@ module Models
   
 end
 end
-end
\ No newline at end of file
+end
diff --git a/core/main/models/user.rb b/core/main/models/user.rb
index 551f684a5..b7cd05762 100644
--- a/core/main/models/user.rb
+++ b/core/main/models/user.rb
@@ -16,11 +16,8 @@
 module BeEF
 module Core
 module Models
-  #
-  # Table stores the list of users that have authenticated into beef.
-  #
-  # TODO: move this table into the AdminUI extension folder.
-  #
+
+  # @todo move this table into the AdminUI extension folder.
   class User
   
     include DataMapper::Resource
@@ -31,9 +28,8 @@ module Models
     property :session_id, String, :length => 255
     property :ip, Text
   
-    #
     # Checks if the user has been authenticated
-    #
+    # @return [Boolean] If the user is authenticated
     def authenticated?
       true || false if not @ip.nil?
     end
@@ -42,4 +38,4 @@ module Models
 
 end
 end
-end
\ No newline at end of file
+end
diff --git a/core/main/network_stack/api.rb b/core/main/network_stack/api.rb
index a6c023dbd..0f8a25392 100644
--- a/core/main/network_stack/api.rb
+++ b/core/main/network_stack/api.rb
@@ -18,17 +18,16 @@ module Core
 module NetworkStack
   
   module RegisterHttpHandler
-    #
+
     # Register the http handler for the network stack
-    #
+    # @param [Object] server HTTP server instance
     def self.mount_handler(server)
-      #dynamic handler
+      # @note this mounts the dynamic handler
       server.mount('/dh', true, BeEF::Core::NetworkStack::Handlers::DynamicReconstruction)
     end
     
   end
   
-    # Register core API calls
     BeEF::API::Registrar.instance.register(BeEF::Core::NetworkStack::RegisterHttpHandler, BeEF::API::Server, 'mount_handler')
 
 end
diff --git a/core/main/network_stack/assethandler.rb b/core/main/network_stack/assethandler.rb
index 89c9beb63..b80624a94 100644
--- a/core/main/network_stack/assethandler.rb
+++ b/core/main/network_stack/assethandler.rb
@@ -18,25 +18,28 @@ module Core
 module NetworkStack
 module Handlers
     
-  #
-  # Class defining BeEF assets 
-  #
+  # @note Class defining BeEF assets 
   class AssetHandler 
     
-    # call BeEF::Core::NetworkStack::Handlers::AssetHandler.instance
+    # @note call BeEF::Core::NetworkStack::Handlers::AssetHandler.instance
     include Singleton
     
     attr_reader :allocations, :root_dir
     
+    # Starts the AssetHandler instance
     def initialize
       @allocations = {}
       @http_server = BeEF::Core::Server.instance
       @root_dir = File.expand_path('../../../../', __FILE__)
     end
 
-    #
     # Binds a file to a mount point
-    #
+    # @param [String] file File path to asset
+    # @param [String] path URL path to mount the asset to (can be nil for random path)
+    # @param [String] extension Extension to append to the URL path (can be nil for none)
+    # @param [Integer] count The amount of times the asset can be accessed before being automatically unbinded (-1 = unlimited)
+    # @return [String] URL Path of mounted asset
+    # @todo This function should accept a hooked browser session to limit the mounted file to a certain session
     def bind(file, path=nil, extension=nil, count=-1)
         url = buildURL(path, extension) 
         @allocations[url] = {'file' => "#{root_dir}"+file, 'path' => path, 'extension' => extension, 'count' => count} 
@@ -45,26 +48,27 @@ module Handlers
         return url
     end
     
-    #
     # Unbinds a file from a mount point
-    #
+    # @param [String] url URL path of asset to be unbinded
     def unbind(url)
         @allocations.delete(url)
         @http_server.unmount(url, true)
     end
 
-    #
-    # Builds a URL based on the path and extention, if neither are passed a random URL will be generated
-    #
+    # Builds a URL based on the path and extension, if neither are passed a random URL will be generated
+    # @param [String] path URL Path defined by bind()
+    # @param [String] extension Extension defined by bind()
+    # @param [Integer] length The amount of characters to be used when generating a random URL
+    # @return [String] Generated URL
     def buildURL(path, extension, length=20)
         url = (path == nil) ? '/'+rand(36**length).to_s(36) : path;
         url += (extension == nil) ? '' : '.'+extension;
         return url
     end
 
-    #
     # Checks if the file is allocated, if the file isn't return true to pass onto FileHandler.
-    #
+    # @param [String] url URL Path of mounted file
+    # @return [Boolean] Returns true if the file is mounted
     def check(url)
         if @allocations.has_key?(url)
             count = @allocations[url]['count']
diff --git a/core/main/network_stack/handlers/dynamicreconstruction.rb b/core/main/network_stack/handlers/dynamicreconstruction.rb
index 955345e05..051e91c82 100644
--- a/core/main/network_stack/handlers/dynamicreconstruction.rb
+++ b/core/main/network_stack/handlers/dynamicreconstruction.rb
@@ -18,19 +18,20 @@ module Core
 module NetworkStack
 module Handlers
   
-  #DynamicHanlder is used reconstruct segmented traffic from the zombies
-
+  # @note DynamicHanlder is used reconstruct segmented traffic from the hooked browser
   class DynamicReconstruction < WEBrick::HTTPServlet::AbstractServlet
     
     attr_reader :guard
 
-    #holds packet queue
+    # @note holds packet queue
     PQ = Array.new() 
    
-    #obtain dynamic mount points from HttpHookServer
+    # @note obtain dynamic mount points from HttpHookServer
     MOUNTS = BeEF::Core::Server.instance.mounts
 
-    #Combines packet information and pushes to PQ, then checks packets
+    # Combines packet information and pushes to PQ, then checks packets
+    # @param [Object] request Request object
+    # @param [Object] response Response object
     def do_POST(request, response)
         @request = request
         response.set_no_cache
@@ -48,9 +49,10 @@ module Handlers
         check_packets()
     end
     
+    # @note Alias do_GET function to do_POST
     alias do_GET do_POST
 
-    #check packets goes through the PQ array and attempts to reconstruct the stream from multiple packets
+    # Check packets goes through the PQ array and attempts to reconstruct the stream from multiple packets
     def check_packets()
         checked = Array.new()
         PQ.each do |packet| 
@@ -88,14 +90,17 @@ module Handlers
        end
     end
 
-    #delete packets that have been reconstructed, return deleted packets
+    # Delete packets that have been reconstructed, return deleted packets
+    # @param [String] beefhook Beefhook of hooked browser
+    # @param [Integer] stream_id The stream ID
     def expunge(beefhook, stream_id)
         packets = PQ.select{ |p| p[:beefhook] == beefhook and p[:stream_id] == stream_id }
         PQ.delete_if { |p| p[:beefhook] == beefhook and p[:stream_id] == stream_id }
         return packets.sort_by { |p| p[:packet_id] }
     end
 
-    #execute is called once a stream has been rebuilt. it searches the mounts and passes the data to the correct handler
+    # Execute is called once a stream has been rebuilt. it searches the mounts and passes the data to the correct handler
+    # @param [Hash] data Hash of data that has been rebuilt by the dynamic reconstruction
     def execute(data)
         handler = get_param(data, 'handler')
         if (MOUNTS.has_key?(handler))
@@ -107,7 +112,10 @@ module Handlers
         end
     end
     
-    #assist function for getting parameter from hash
+    # Assist function for getting parameter from hash
+    # @param [Hash] query Hash to pull key from
+    # @param [String] key The key association to return from `query`
+    # @return Value associated with `key`
     def get_param(query, key)
       return nil if query[key].nil?
       query[key]
diff --git a/core/main/server.rb b/core/main/server.rb
index 4d26f05fc..3be3fae16 100644
--- a/core/main/server.rb
+++ b/core/main/server.rb
@@ -13,30 +13,20 @@
 #   See the License for the specific language governing permissions and
 #   limitations under the License.
 #
+
 module BeEF
 module Core
-  #
-  # Class defining the BeEF http server.
-  #
-  #   Example:
-  #
-  #     server = BeEF::Core::Server.instance
-  #     server.prepare
-  #     server.start
-  #     ...
-  #     server.stop
-  #
+
   class Server
 
     include Singleton
     
-    # Grabs the version of beef the framework is deployed on
+    # @note Grabs the version of beef the framework is deployed on
     VERSION = BeEF::Core::Configuration.instance.get('beef.version')
 
     attr_reader :root_dir, :url, :configuration, :command_urls, :mounts
-    #
-    # Constructor
-    #
+     
+    # Constructor starts the BeEF server including the configuration system
     def initialize
       @configuration = BeEF::Core::Configuration.instance
       beef_host = @configuration.get("beef.http.public") || @configuration.get("beef.http.host")
@@ -46,10 +36,8 @@ module Core
       @mounts = {}
     end
     
-    #
-    # Returns all server variables in a hash. Useful for Erubis when
-    # generating the javascript for the command modules and hooking.
-    #
+    # Returns all server variables in a hash. Useful for Erubis when generating the javascript for the command modules and hooking.
+    # @return [Hash] BeEF info hash
     def to_h
       {
         'beef_version' => VERSION,
@@ -62,9 +50,11 @@ module Core
       }
     end
     
-    #
-    #
-    #
+    # Returns command URL
+    # @param [String] command_path Command path
+    # @return [String] URL of command
+    # @todo Unsure how @command_urls is populated, this command is possibly deprecated
+    # @deprecated See note
     def get_command_url(command_path)
       # argument type checking
       raise Exception::TypeError, '"command_path" needs to be a string' if not command_path.string?
@@ -76,9 +66,7 @@ module Core
       end
     end
     
-    #
     # Starts the BeEF http server.
-    #
     def prepare
       if not @http_server
         config = {}
@@ -93,16 +81,12 @@ module Core
         # Create http handler for the javascript hook file
         mount("#{@configuration.get("beef.http.hook_file")}", true, BeEF::Core::Handlers::HookedBrowsers)
         
-        #
         # We dynamically get the list of all http handler using the API and register them
-        #
         BeEF::API::Registrar.instance.fire(BeEF::API::Server, 'mount_handler', self)
       end
     end
     
-    #
     # Starts the BeEF http server
-    #
     def start
       # we trap CTRL+C in the console and kill the server
       trap("INT") { BeEF::Core::Server.instance.stop }
@@ -111,9 +95,7 @@ module Core
       @http_server.start
     end
     
-    #
     # Stops the BeEF http server.
-    #
     def stop
       if @http_server
         # shuts down the server
@@ -125,19 +107,14 @@ module Core
       end
     end
     
-    #
     # Restarts the BeEF http server.
-    #
     def restart; stop; start; end
    
-    # 
     # Mounts a handler, can either be a hard or soft mount
-    #
-    # @param: {String} the url to mount
-    # @param: {Boolean} set to true for a hard mount, false for a soft mount.
-    # @param: {Class} class to call once mount is triggered
-    # @param: {Various} arguments to pass to the http handler class
-    #
+    # @param [String] url The url to mount
+    # @param [Boolean] hard Set to true for a hard mount, false for a soft mount.
+    # @param [Class] http_handler_class Class to call once mount is triggered
+    # @param args Arguments to pass to the http handler class
     def mount(url, hard, http_handler_class, args = nil)
       # argument type checking
       raise Exception::TypeError, '"url" needs to be a string' if not url.string?
@@ -161,12 +138,9 @@ module Core
       end
     end
     
-    #
     # Unmounts handler
-    #
-    # @param: {String} url to mount.
-    # @param: {Boolean} set to true for a hard mount, false for a soft mount.
-    #
+    # @param [String] url URL to unmount.
+    # @param [Boolean] hard Set to true for a hard mount, false for a soft mount.
     def unmount(url, hard)
       # argument type checking
       raise Exception::TypeError, '"url" needs to be a string' if not url.string?