diff --git a/docs/Doxyfile b/docs/Doxyfile
index 4efd575..e9afc88 100644
--- a/docs/Doxyfile
+++ b/docs/Doxyfile
@@ -38,7 +38,7 @@
 # If a relative path is entered, it will be relative to the location
 # where doxygen was started. If left blank the current directory will be used.
 
-OUTPUT_DIRECTORY       = doxygen
+OUTPUT_DIRECTORY       = 
 
 # If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
 # 4096 sub-directories (in 2 levels) under the output directory of each output
@@ -569,7 +569,7 @@
 # with spaces.
 
 INPUT                  = ../model ../helper ../utils ../apps \
-						 introspected-doxygen.h
+						 introspected-doxygen.h doxygen.h
 
 # introspected-doxygen.h should be manually created:
 # For example:
@@ -773,7 +773,7 @@
 # If a relative path is entered the value of OUTPUT_DIRECTORY will be
 # put in front of it. If left blank `html' will be used as the default path.
 
-HTML_OUTPUT            = html
+HTML_OUTPUT            = build/html/doxygen
 
 # The HTML_FILE_EXTENSION tag can be used to specify the file extension for
 # each generated HTML page (for example: .htm,.php,.asp). If it is left blank
@@ -791,7 +791,7 @@
 # each generated HTML page. If it is left blank doxygen will generate a
 # standard footer.
 
-HTML_FOOTER            =
+HTML_FOOTER            = analytics.html
 
 # The HTML_STYLESHEET tag can be used to specify a user-defined cascading
 # style sheet that is used by each HTML page. It can be used to
@@ -800,7 +800,7 @@
 # the style sheet file to the HTML output directory, so don't put your own
 # stylesheet in the HTML output directory as well, or it will be erased!
 
-HTML_STYLESHEET        =
+HTML_STYLESHEET        = 
 
 # If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
 # files or namespaces will be aligned in HTML using tables. If set to
@@ -965,7 +965,7 @@
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
 
-TREEVIEW_WIDTH         = 250
+TREEVIEW_WIDTH         = 300
 
 # Use this tag to change the font size of Latex formulas included
 # as images in the HTML documentation. The default is 10. Note that
@@ -980,7 +980,7 @@
 # there is already a search function so this one should typically
 # be disabled.
 
-SEARCHENGINE           = NO
+SEARCHENGINE           = YES
 
 #---------------------------------------------------------------------------
 # configuration options related to the LaTeX output
diff --git a/docs/DoxygenLayout.xml b/docs/DoxygenLayout.xml
new file mode 100644
index 0000000..8ad1934
--- /dev/null
+++ b/docs/DoxygenLayout.xml
@@ -0,0 +1,172 @@
+<doxygenlayout version="1.0">
+  <!-- Navigation index tabs for HTML output -->
+  <navindex>
+    <tab type="mainpage" visible="no" title=""/>
+      <tab type="classlist" visible="yes" title="" intro=""/>
+      <tab type="classindex" visible="$ALPHABETICAL_INDEX" title=""/> 
+  </navindex>
+
+  <!-- Layout definition for a class page -->
+  <class>
+    <briefdescription visible="yes"/>
+    <includes visible="$SHOW_INCLUDE_FILES"/>
+    <inheritancegraph visible="$CLASS_GRAPH"/>
+    <collaborationgraph visible="$COLLABORATION_GRAPH"/>
+    <allmemberslink visible="yes"/>
+    <memberdecl>
+      <nestedclasses visible="yes" title=""/>
+      <publictypes title=""/>
+      <publicslots title=""/>
+      <signals title=""/>
+      <publicmethods title=""/>
+      <publicstaticmethods title=""/>
+      <publicattributes title=""/>
+      <publicstaticattributes title=""/>
+      <protectedtypes title=""/>
+      <protectedslots title=""/>
+      <protectedmethods title=""/>
+      <protectedstaticmethods title=""/>
+      <protectedattributes title=""/>
+      <protectedstaticattributes title=""/>
+      <packagetypes title=""/>
+      <packagemethods title=""/>
+      <packagestaticmethods title=""/>
+      <packageattributes title=""/>
+      <packagestaticattributes title=""/>
+      <properties title=""/>
+      <events title=""/>
+      <privatetypes title=""/>
+      <privateslots title=""/>
+      <privatemethods title=""/>
+      <privatestaticmethods title=""/>
+      <privateattributes title=""/>
+      <privatestaticattributes title=""/>
+      <friends title=""/>
+      <related title="" subtitle=""/>
+      <membergroups visible="yes"/>
+    </memberdecl>
+    <detaileddescription title=""/>
+    <memberdef>
+      <inlineclasses title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <constructors title=""/>
+      <functions title=""/>
+      <related title=""/>
+      <variables title=""/>
+      <properties title=""/>
+      <events title=""/>
+    </memberdef>
+    <usedfiles visible="$SHOW_USED_FILES"/>
+    <authorsection visible="yes"/>
+  </class>
+
+  <!-- Layout definition for a namespace page -->
+  <namespace>
+    <briefdescription visible="yes"/>
+    <memberdecl>
+      <nestednamespaces visible="yes" title=""/>
+      <classes visible="yes" title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <functions title=""/>
+      <variables title=""/>
+      <membergroups visible="yes"/>
+    </memberdecl>
+    <detaileddescription title=""/>
+    <memberdef>
+      <inlineclasses title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <functions title=""/>
+      <variables title=""/>
+    </memberdef>
+    <authorsection visible="yes"/>
+  </namespace>
+
+  <!-- Layout definition for a file page -->
+  <file>
+    <briefdescription visible="yes"/>
+    <includes visible="$SHOW_INCLUDE_FILES"/>
+    <includegraph visible="$INCLUDE_GRAPH"/>
+    <includedbygraph visible="$INCLUDED_BY_GRAPH"/>
+    <sourcelink visible="yes"/>
+    <memberdecl>
+      <classes visible="yes" title=""/>
+      <namespaces visible="yes" title=""/>
+      <defines title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <functions title=""/>
+      <variables title=""/>
+      <membergroups visible="yes"/>
+    </memberdecl>
+    <detaileddescription title=""/>
+    <memberdef>
+      <inlineclasses title=""/>
+      <defines title=""/>
+      <typedefs title=""/>
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+      <functions title=""/>
+      <variables title=""/>
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+    <authorsection/>
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+
+  <!-- Layout definition for a group page -->
+  <group>
+    <briefdescription visible="yes"/>
+    <groupgraph visible="$GROUP_GRAPHS"/>
+    <memberdecl>
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+      <dirs visible="yes" title=""/>
+      <files visible="yes" title=""/>
+      <namespaces visible="yes" title=""/>
+      <classes visible="yes" title=""/>
+      <defines title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <enumvalues title=""/>
+      <functions title=""/>
+      <variables title=""/>
+      <signals title=""/>
+      <publicslots title=""/>
+      <protectedslots title=""/>
+      <privateslots title=""/>
+      <events title=""/>
+      <properties title=""/>
+      <friends title=""/>
+      <membergroups visible="yes"/>
+    </memberdecl>
+    <detaileddescription title=""/>
+    <memberdef>
+      <pagedocs/>
+      <inlineclasses title=""/>
+      <defines title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <enumvalues title=""/>
+      <functions title=""/>
+      <variables title=""/>
+      <signals title=""/>
+      <publicslots title=""/>
+      <protectedslots title=""/>
+      <privateslots title=""/>
+      <events title=""/>
+      <properties title=""/>
+      <friends title=""/>
+    </memberdef>
+    <authorsection visible="yes"/>
+  </group>
+
+  <!-- Layout definition for a directory page -->
+  <directory>
+    <briefdescription visible="yes"/>
+    <directorygraph visible="yes"/>
+    <memberdecl>
+      <dirs visible="yes"/>
+      <files visible="yes"/>
+    </memberdecl>
+    <detaileddescription title=""/>
+  </directory>
+</doxygenlayout>
diff --git a/docs/analytics.html b/docs/analytics.html
new file mode 100644
index 0000000..f3bfda5
--- /dev/null
+++ b/docs/analytics.html
@@ -0,0 +1,20 @@
+<address style="text-align: right;"><small> 
+		<a href="http://irl.cs.ucla.edu/ndnSIM/">ndnSIM: NS-3 based NDN simulator</a> API Reference - Generated using <a href="http://www.doxygen.org">Doxygen $doxygenversion</a>
+</small></address>
+
+<script type="text/javascript">
+
+  var _gaq = _gaq || [];
+  _gaq.push(['_setAccount', 'UA-21372502-8']);
+  _gaq.push(['_trackPageview']);
+
+  (function() {
+    var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+    ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+    var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+  })();
+
+</script>
+
+</body> 
+</html>
diff --git a/docs/default.css b/docs/default.css
new file mode 100644
index 0000000..21f3f50
--- /dev/null
+++ b/docs/default.css
@@ -0,0 +1,256 @@
+/*
+ * default.css_t
+ * ~~~~~~~~~~~~~
+ *
+ * Sphinx stylesheet -- default theme.
+ *
+ * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+@import url("basic.css");
+
+/* -- page layout ----------------------------------------------------------- */
+
+body {
+    font-family: sans-serif;
+    font-size: 100%;
+    background-color: #11303d;
+    color: #000;
+    margin: 0;
+    padding: 0;
+}
+
+div.document {
+    background-color: #1c4e63;
+}
+
+div.documentwrapper {
+    float: left;
+    width: 100%;
+}
+
+div.bodywrapper {
+    margin: 0 0 0 230px;
+}
+
+div.body {
+    background-color: #ffffff;
+    color: #000000;
+    padding: 0 20px 30px 20px;
+}
+
+div.footer {
+    color: #ffffff;
+    width: 100%;
+    padding: 9px 0 9px 0;
+    text-align: center;
+    font-size: 75%;
+}
+
+div.footer a {
+    color: #ffffff;
+    text-decoration: underline;
+}
+
+div.related {
+    background-color: #133f52;
+    line-height: 30px;
+    color: #ffffff;
+}
+
+div.related a {
+    color: #ffffff;
+}
+
+div.sphinxsidebar {
+}
+
+div.sphinxsidebar h3 {
+    font-family: 'Trebuchet MS', sans-serif;
+    color: #ffffff;
+    font-size: 1.4em;
+    font-weight: normal;
+    margin: 0;
+    padding: 0;
+}
+
+div.sphinxsidebar h3 a {
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+}
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+    font-family: 'Trebuchet MS', sans-serif;
+    color: #ffffff;
+    font-size: 1.3em;
+    font-weight: normal;
+    margin: 5px 0 0 0;
+    padding: 0;
+}
+
+div.sphinxsidebar p {
+    color: #ffffff;
+}
+
+div.sphinxsidebar p.topless {
+    margin: 5px 10px 10px 10px;
+}
+
+div.sphinxsidebar ul {
+    margin: 10px;
+    padding: 0;
+    color: #ffffff;
+}
+
+div.sphinxsidebar a {
+    color: #98dbcc;
+}
+
+div.sphinxsidebar input {
+    border: 1px solid #98dbcc;
+    font-family: sans-serif;
+    font-size: 1em;
+}
+
+
+
+/* -- hyperlink styles ------------------------------------------------------ */
+
+a {
+    color: #355f7c;
+    text-decoration: none;
+}
+
+a:visited {
+    color: #355f7c;
+    text-decoration: none;
+}
+
+a:hover {
+    text-decoration: underline;
+}
+
+
+
+/* -- body styles ----------------------------------------------------------- */
+
+div.body h1,
+div.body h2,
+div.body h3,
+div.body h4,
+div.body h5,
+div.body h6 {
+    font-family: 'Trebuchet MS', sans-serif;
+    background-color: #f2f2f2;
+    font-weight: normal;
+    color: #20435c;
+    border-bottom: 1px solid #ccc;
+    margin: 20px -20px 10px -20px;
+    padding: 3px 0 3px 10px;
+}
+
+div.body h1 { margin-top: 0; font-size: 200%; }
+div.body h2 { font-size: 160%; }
+div.body h3 { font-size: 140%; }
+div.body h4 { font-size: 120%; }
+div.body h5 { font-size: 110%; }
+div.body h6 { font-size: 100%; }
+
+a.headerlink {
+    color: #c60f0f;
+    font-size: 0.8em;
+    padding: 0 4px 0 4px;
+    text-decoration: none;
+}
+
+a.headerlink:hover {
+    background-color: #c60f0f;
+    color: white;
+}
+
+div.body p, div.body dd, div.body li {
+    text-align: justify;
+    line-height: 130%;
+}
+
+div.admonition p.admonition-title + p {
+    display: inline;
+}
+
+div.admonition p {
+    margin-bottom: 5px;
+}
+
+div.admonition pre {
+    margin-bottom: 5px;
+}
+
+div.admonition ul, div.admonition ol {
+    margin-bottom: 5px;
+}
+
+div.note {
+    background-color: #eee;
+    border: 1px solid #ccc;
+}
+
+div.seealso {
+    background-color: #ffc;
+    border: 1px solid #ff6;
+}
+
+div.topic {
+    background-color: #eee;
+}
+
+div.warning {
+    background-color: #ffe4e4;
+    border: 1px solid #f66;
+}
+
+p.admonition-title {
+    display: inline;
+}
+
+p.admonition-title:after {
+    content: ":";
+}
+
+pre {
+    padding: 5px;
+    background-color: #eeffcc;
+    color: #333333;
+    line-height: 120%;
+    border: 1px solid #ac9;
+    border-left: none;
+    border-right: none;
+}
+
+tt {
+    background-color: #ecf0f3;
+    padding: 0 1px 0 1px;
+    font-size: 0.95em;
+}
+
+th {
+    background-color: #ede;
+}
+
+.warning tt {
+    background: #efc2c2;
+}
+
+.note tt {
+    background: #d6d6d6;
+}
+
+.viewcode-back {
+    font-family: sans-serif;
+}
+
+div.viewcode-block:target {
+    background-color: #f4debf;
+    border-top: 1px solid #ac9;
+    border-bottom: 1px solid #ac9;
+}
\ No newline at end of file
diff --git a/docs/doxygen.h b/docs/doxygen.h
new file mode 100644
index 0000000..52653bb
--- /dev/null
+++ b/docs/doxygen.h
@@ -0,0 +1,5 @@
+/**
+ * \mainpage ndnSIM documentation
+ *
+ * Please refer to <a href="../index.html">ndnSIM documentation page</a>
+ */
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 8f063e3..8291489 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -25,7 +25,7 @@
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = [ "sphinx.ext.autodoc", "sphinxcontrib.doxylink", "sphinxcontrib.aafig" ]
+extensions = [ "sphinx.ext.autodoc", "sphinxcontrib.doxylink", "sphinxcontrib.aafig", "sphinxcontrib.googleanalytics" ]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -242,6 +242,10 @@
 #texinfo_show_urls = 'footnote'
 
 doxylink = {
-  'ndnsim' : ('ndnSIM.tag', '../../doxygen/html/'),
+  'ndnsim' : ('ndnSIM.tag', 'doxygen/'),
 }
 
+googleanalytics_id = "UA-21372502-8"
+
+googleanalytics_enabled = True
+
diff --git a/docs/source/intro.rst b/docs/source/intro.rst
index 44991a2..91cf9e2 100644
--- a/docs/source/intro.rst
+++ b/docs/source/intro.rst
@@ -7,20 +7,58 @@
 Introduction
 ==============
 
-The ndnSIM is NS-3 module that implements Named Data Networking (NDN) communication model, the clean slate Internet design. ndnSIM is specially optimized for simulation purposes and has a cleaner and more extensible internal structure comparing to the existing NDN implementation (Project CCNx).  
+The ndnSIM is NS-3 module that implements Named Data Networking (NDN) communication model, the clean slate Internet design. ndnSIM is specially optimized for simulation purposes and has a cleaner and more extensible internal structure comparing to the existing NDN implementation (Project CCNx).
 
-Following the NDN architecture, ndnSIM is implemented as a new network-layer protocol model, which can run on top of any available link-layer protocol model (point-to-point, CSMA, wireless, etc.).  
+Following the NDN architecture, ndnSIM is implemented as a new network-layer protocol model, which can run on top of any available link-layer protocol model (point-to-point, CSMA, wireless, etc.).
 
 .. note::
-    It will also be possible to run ndnSIM on top of network-layer (IPv4, IPv6) and transport-layer (TCP, UDP) protocols. 
+    It will also be possible to run ndnSIM on top of network-layer (IPv4, IPv6) and transport-layer (TCP, UDP) protocols.
     However, it is not yet implemented and patches are welcome.
 
 .. This flexibility allows ndnSIM to simulate scenarios of various homogeneous and heterogeneous networks (e.g., NDN-only, NDN-over-IP, etc.).
 
-The simulator is implemented in a modular fashion, using separate C++ classes to model behavior of each network-layer entity in NDN: pending Interest table (PIT), forwarding information base (FIB), content store, network and application interfaces, Interest forwarding strategies, etc.
+The simulator is implemented in a modular fashion, using separate C++ classes to model behavior of each network-layer entity in NDN: :ndnsim:`pending Interest table (PIT) <CcnxPit>`, :ndnsim:`forwarding information base (FIB) <CcnxFib>`, :ndnsim:`content store <CcnxContentStore>`, :ndnsim:`network <CcnxNetDeviceFace>` and :ndnsim:`application <CcnxLocalFace>` interfaces, :ndnsim:`Interest forwarding strategies <CcnxForwardingStrategy>`, etc.
 This modular structure allows any component to be easily modified or replaced with no or minimal impact on other components.
 In addition, the simulator provides an extensive collection of interfaces and helpers to perform detailed tracing behavior of every component, as well as NDN traffic flow.
 
+
+.. aafig::
+    :aspect: 60
+    :scale: 120
+
+             +----------------+			      +-----------+
+             | "Applications" |			      | NetDevice |
+             +----------------+			      +-----------+
+		     ^ 					    ^
+    .................|......................................|......................
+    .		     v			     	            v			  .
+    .		+------------------+	     +----------------------+		  .
+    .           |    "CcnxFace"    |	     |      "CcnxFace"      |		  .
+    .           | "(CcnxLocalFace)"|	     | "(CcnxNetDeviceFace)"|		  .
+    .		+------------------+         +----------------------+		  .
+    .		               ^                   ^				  .
+    .			       |                   |				  .
+    .			       v                   v				  .
+    .			    XXXXXXXXXXXXXXXXXXXXXXXXXXXXX			  .
+    .			    XX                         XX			  .
+    .			    XX    Core NDN protocol    XX  			  .
+    .                       XX    "(CcnxL3Protocol)"   XX
+    .			    XX                         XX			  .
+    .			    XXXXXXXXXXXXXXXXXXXXXXXXXXXXX			  .
+    .			      ^       ^       ^       ^				  .
+    .			      |	      |	      |	      |				  .
+    .     +-------------------+   +---+       +---+   +------------+		  .
+    .	  | 		    	  |		  |    		   |		  .
+    .	  v			  v		  v		   v		  .
+    . +-------------------+      +-------+      +-------+        +-------------+  .
+    . | "CcnxContentStore"|      |  PIT  |      |  FIB  |        | "Pluggable" |  .
+    . +-------------------+      +-------+      +-------+        | "Forwarding"|  .
+    .							         | "Strategy"  |  .
+    .							         +-------------+  .
+    .										  .
+    ...............................................................................
+
+
 The wire format of Interest and Data packets follows the format of the existing `CCNx Project's NDN implementation`_ (CCNx Binary Encoding), allowing reuse of the existing traffic analysis tools, as well as driving simulations using real NDN traffic traces.
 
 .. _CCNx Project's NDN implementation: http://www.ccnx.org/
@@ -31,12 +69,12 @@
 Portability
 ------------
 
-ndnSIM has been successfully compiled and used under Ubuntu Linux 11.04 (stock gcc), Mac OS 10.6/10.7 (gcc-4.2 apple/llvm, macports gcc 4.6), FreeBSD 8.2 (requires gcc from ports - the stock gcc will not work!).  
+ndnSIM has been successfully compiled and used under Ubuntu Linux 11.04 (stock gcc), Mac OS 10.6/10.7 (gcc-4.2 apple/llvm, macports gcc 4.6), FreeBSD 8.2 (requires gcc from ports - the stock gcc will not work!).
 
 Requirements
 -------------
 
-1. ndnSIM requires the latest version of NS-3 simulator (as of May 31st, 2012, development branch of NS-3). 
+1. ndnSIM requires the latest version of NS-3 simulator (as of May 31st, 2012, development branch of NS-3).
 
 2. ndnSIM requires boost libraries:
 
@@ -54,7 +92,7 @@
    * For Ubuntu::
 
        sudo apt-get install python-dev python-pygraphviz python-kiwi
-       sudo apt-get install python-pygoocanvas python-gnome2 
+       sudo apt-get install python-pygoocanvas python-gnome2
        sudo apt-get install python-gnomedesktop python-rsvg ipython
 
    * For MacOS (macports)::
@@ -126,9 +164,11 @@
 
 Overall structure of ndnSIM is described in our technical report.
 
-It is also possible to build doxygen documentation of ndnSIM API (in ``ns-3/doc/html/``), provided that ``doxygen`` and ``graphviz`` modules are installed on system::
+`ndnSIM API documentation <doxygen/index.html>`_
 
-    ./waf doxygen
+.. It is also possible to build doxygen documentation of ndnSIM API (in ``ns-3/doc/html/``), provided that ``doxygen`` and ``graphviz`` modules are installed on system::
+
+..     ./waf doxygen
 
 
 A very short guide to the code