docs: modifying documentation examples (now code in the documentation is taken from real code in examples/ folder)
diff --git a/examples/README.md b/examples/README.md
new file mode 100644
index 0000000..7654ac2
--- /dev/null
+++ b/examples/README.md
@@ -0,0 +1,3 @@
+Please refer to http://ndnsim.net/examples.html (../docs/source/examples.rst) 
+for detailed information about the examples.
+
diff --git a/examples/ndn-congestion-topo-plugin.cc b/examples/ndn-congestion-topo-plugin.cc
new file mode 100644
index 0000000..f5e9a5e
--- /dev/null
+++ b/examples/ndn-congestion-topo-plugin.cc
@@ -0,0 +1,109 @@
+/* -*-  Mode: C++; c-file-style: "gnu"; indent-tabs-mode:nil; -*- */
+/*
+ * Copyright (c) 2011-2012 University of California, Los Angeles
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License version 2 as
+ * published by the Free Software Foundation;
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+ *
+ * Author: Alexander Afanasyev <alexander.afanasyev@ucla.edu>
+ */
+// ndn-congestion-topo-plugin.cc
+#include "ns3/core-module.h"
+#include "ns3/network-module.h"
+#include "ns3/ndnSIM-module.h"
+
+using namespace ns3;
+
+/**
+ * This scenario simulates a grid topology (using topology reader module)
+ *
+ *   /------\	                                                 /------\
+ *   | Src1 |<--+                                            +-->| Dst1 |
+ *   \------/    \                                          /    \------/
+ *            	 \                                        /     
+ *                 +-->/------\   "bottleneck"  /------\<-+      
+ *                     | Rtr1 |<===============>| Rtr2 |         
+ *                 +-->\------/                 \------/<-+      
+ *                /                                        \
+ *   /------\    /                                          \    /------\
+ *   | Src2 |<--+                                            +-->| Dst2 |
+ *   \------/                                                    \------/
+ *
+ * To run scenario and see what is happening, use the following command:
+ *
+ *     NS_LOG=ndn.Consumer:ndn.Producer ./waf --run=ndn-congestion-topo-plugin
+ */
+
+int
+main (int argc, char *argv[])
+{
+  CommandLine cmd;
+  cmd.Parse (argc, argv);
+
+  AnnotatedTopologyReader topologyReader ("", 25);
+  topologyReader.SetFileName ("src/ndnSIM/examples/topology/topo-grid-3x3.txt");
+  topologyReader.Read ();
+
+  // Install CCNx stack on all nodes
+  ndn::StackHelper ccnxHelper;
+  ccnxHelper.InstallAll ();
+
+  // Installing global routing interface on all nodes
+  ndn::GlobalRoutingHelper ccnxGlobalRoutingHelper;
+  ccnxGlobalRoutingHelper.InstallAll ();
+
+  // Getting containers for the consumer/producer
+  Ptr<Node> consumer1 = Names::Find<Node> ("Src1");
+  Ptr<Node> consumer2 = Names::Find<Node> ("Src2");
+
+  Ptr<Node> producer1 = Names::Find<Node> ("Dst1");
+  Ptr<Node> producer2 = Names::Find<Node> ("Dst2");
+
+  ndn::AppHelper consumerHelper ("ns3::ndn::ConsumerCbr");
+  consumerHelper.SetAttribute ("Frequency", StringValue ("100")); // 100 interests a second
+
+  // on the first consumer node install a Consumer application
+  // that will express interests in /dst1 namespace
+  consumerHelper.SetPrefix ("/dst1");
+  consumerHelper.Install (consumer1);
+
+  // on the second consumer node install a Consumer application
+  // that will express interests in /dst2 namespace
+  consumerHelper.SetPrefix ("/dst2");
+  consumerHelper.Install (consumer2);
+  
+  ndn::AppHelper producerHelper ("ns3::ndn::Producer");
+  producerHelper.SetAttribute ("PayloadSize", StringValue("1024"));  
+
+  // Register /dst1 prefix with global routing controller and
+  // install producer that will satisfy Interests in /dst1 namespace
+  ccnxGlobalRoutingHelper.AddOrigins ("/dst1", producer1);
+  producerHelper.SetPrefix ("/dst1");
+  producerHelper.Install (producer1);
+
+  // Register /dst2 prefix with global routing controller and
+  // install producer that will satisfy Interests in /dst2 namespace
+  ccnxGlobalRoutingHelper.AddOrigins ("/dst2", producer2);
+  producerHelper.SetPrefix ("/dst2");
+  producerHelper.Install (producer2);
+
+  // Calculate and install FIBs
+  ccnxGlobalRoutingHelper.CalculateRoutes ();
+
+  Simulator::Stop (Seconds (20.0));
+
+  Simulator::Run ();
+  Simulator::Destroy ();
+
+  return 0;
+}
diff --git a/examples/ndn-grid-topo-plugin.cc b/examples/ndn-grid-topo-plugin.cc
new file mode 100644
index 0000000..aa761da
--- /dev/null
+++ b/examples/ndn-grid-topo-plugin.cc
@@ -0,0 +1,99 @@
+/* -*-  Mode: C++; c-file-style: "gnu"; indent-tabs-mode:nil; -*- */
+/*
+ * Copyright (c) 2011-2012 University of California, Los Angeles
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License version 2 as
+ * published by the Free Software Foundation;
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+ *
+ * Author: Alexander Afanasyev <alexander.afanasyev@ucla.edu>
+ */
+// ndn-grid-topo-plugin.cc
+#include "ns3/core-module.h"
+#include "ns3/network-module.h"
+#include "ns3/ndnSIM-module.h"
+
+using namespace ns3;
+
+/**
+ * This scenario simulates a grid topology (using topology reader module)
+ *
+ * (consumer) -- ( ) ----- ( )
+ *     |          |         |
+ *    ( ) ------ ( ) ----- ( )
+ *     |          |         |
+ *    ( ) ------ ( ) -- (producer)
+ *
+ * All links are 1Mbps with propagation 10ms delay. 
+ *
+ * FIB is populated using NdnGlobalRoutingHelper.
+ *
+ * Consumer requests data from producer with frequency 10 interests per second
+ * (interests contain constantly increasing sequence number).
+ *
+ * For every received interest, producer replies with a data packet, containing
+ * 1024 bytes of virtual payload.
+ *
+ * To run scenario and see what is happening, use the following command:
+ *
+ *     NS_LOG=ndn.Consumer:ndn.Producer ./waf --run=ndn-grid-topo-plugin
+ */
+
+int
+main (int argc, char *argv[])
+{
+  CommandLine cmd;
+  cmd.Parse (argc, argv);
+
+  AnnotatedTopologyReader topologyReader ("", 25);
+  topologyReader.SetFileName ("src/ndnSIM/examples/topology/topo-grid-3x3.txt");
+  topologyReader.Read ();
+
+  // Install CCNx stack on all nodes
+  ndn::StackHelper ccnxHelper;
+  ccnxHelper.InstallAll ();
+
+  // Installing global routing interface on all nodes
+  ndn::GlobalRoutingHelper ccnxGlobalRoutingHelper;
+  ccnxGlobalRoutingHelper.InstallAll ();
+
+  // Getting containers for the consumer/producer
+  Ptr<Node> producer = Names::Find<Node> ("Node8");
+  NodeContainer consumerNodes;
+  consumerNodes.Add (Names::Find<Node> ("Node0"));
+
+  // Install CCNx applications
+  std::string prefix = "/prefix";
+
+  ndn::AppHelper consumerHelper ("ns3::ndn::ConsumerCbr");
+  consumerHelper.SetPrefix (prefix);
+  consumerHelper.SetAttribute ("Frequency", StringValue ("100")); // 100 interests a second
+  consumerHelper.Install (consumerNodes);
+
+  ndn::AppHelper producerHelper ("ns3::ndn::Producer");
+  producerHelper.SetPrefix (prefix);
+  producerHelper.SetAttribute ("PayloadSize", StringValue("1024"));
+  producerHelper.Install (producer);
+
+  // Add /prefix origins to ndn::GlobalRouter
+  ccnxGlobalRoutingHelper.AddOrigins (prefix, producer);
+
+  // Calculate and install FIBs
+  ccnxGlobalRoutingHelper.CalculateRoutes ();
+
+  Simulator::Stop (Seconds (20.0));
+
+  Simulator::Run ();
+  Simulator::Destroy ();
+
+  return 0;
+}
diff --git a/examples/ndn-grid.cc b/examples/ndn-grid.cc
index 35e1df7..bb2d7db 100644
--- a/examples/ndn-grid.cc
+++ b/examples/ndn-grid.cc
@@ -1,6 +1,6 @@
 /* -*-  Mode: C++; c-file-style: "gnu"; indent-tabs-mode:nil; -*- */
 /*
- * Copyright (c) 2011 University of California, Los Angeles
+ * Copyright (c) 2011-2012 University of California, Los Angeles
  *
  * This program is free software; you can redistribute it and/or modify
  * it under the terms of the GNU General Public License version 2 as
@@ -15,20 +15,17 @@
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
  *
- * Author: Ilya Moiseenko <iliamo@cs.ucla.edu>
- *         Alexander Afanasyev <alexander.afanasyev@ucla.edu>
+ * Author: Alexander Afanasyev <alexander.afanasyev@ucla.edu>
  */
-
+// ndn-grid.cc
 #include "ns3/core-module.h"
 #include "ns3/network-module.h"
 #include "ns3/point-to-point-module.h"
+#include "ns3/point-to-point-layout-module.h"
 #include "ns3/ndnSIM-module.h"
-#include "ns3/point-to-point-grid.h"
 
 using namespace ns3;
 
-NS_LOG_COMPONENT_DEFINE ("ndn.Grid");
-
 /**
  * This scenario simulates a grid topology (using PointToPointGrid module)
  *
@@ -38,8 +35,6 @@
  *     |          |         |
  *    ( ) ------ ( ) -- (producer)
  *
- * Grid size could be specified using --nGrid parameter (default 3)
- *
  * All links are 1Mbps with propagation 10ms delay. 
  *
  * FIB is populated using NdnGlobalRoutingHelper.
@@ -50,85 +45,64 @@
  * For every received interest, producer replies with a data packet, containing
  * 1024 bytes of virtual payload.
  *
- * Simulation time is 20 seconds, unless --finish parameter is specified
- *
  * To run scenario and see what is happening, use the following command:
  *
- *     NS_LOG=NdnSimple:NdnConsumer ./waf --run=ndn-grid
+ *     NS_LOG=ndn.Consumer:ndn.Producer ./waf --run=ndn-grid
  */
 
-
-int 
+int
 main (int argc, char *argv[])
 {
+  // Setting default parameters for PointToPoint links and channels
   Config::SetDefault ("ns3::PointToPointNetDevice::DataRate", StringValue ("1Mbps"));
   Config::SetDefault ("ns3::PointToPointChannel::Delay", StringValue ("10ms"));
   Config::SetDefault ("ns3::DropTailQueue::MaxPackets", StringValue ("20"));
-  
-  uint32_t nGrid = 3;
-  Time finishTime = Seconds (20.0); 
 
+  // Read optional command-line parameters (e.g., enable visualizer with ./waf --run=<> --visualize
   CommandLine cmd;
-  cmd.AddValue ("nGrid", "Number of grid nodes", nGrid);
-  cmd.AddValue ("finish", "Finish time", finishTime);
   cmd.Parse (argc, argv);
 
+  // Creating 3x3 topology
   PointToPointHelper p2p;
-
-  PointToPointGridHelper grid (nGrid, nGrid, p2p);
+  PointToPointGridHelper grid (3, 3, p2p);
   grid.BoundingBox(100,100,200,200);
 
-  // Install NDN stack on all nodes
-  NS_LOG_INFO ("Installing Ndn stack on all nodes");
-  ndn::StackHelper ndnHelper;
-  ndnHelper.SetContentStore ("ns3::ndn::cs::Lru", "MaxSize", "10");
-  // ndnHelper.SetContentStore ("ns3::ndn::cs::Random", "MaxSize", "10");
-  ndnHelper.InstallAll ();
+  // Install CCNx stack on all nodes
+  ndn::StackHelper ccnxHelper;
+  ccnxHelper.InstallAll ();
 
-  ndn::GlobalRoutingHelper ndnGlobalRoutingHelper;
-  ndnGlobalRoutingHelper.InstallAll ();
-  
+  // Installing global routing interface on all nodes
+  ndn::GlobalRoutingHelper ccnxGlobalRoutingHelper;
+  ccnxGlobalRoutingHelper.InstallAll ();
+
   // Getting containers for the consumer/producer
-  Ptr<Node> producer = grid.GetNode (nGrid-1, nGrid-1);
+  Ptr<Node> producer = grid.GetNode (2, 2);
   NodeContainer consumerNodes;
   consumerNodes.Add (grid.GetNode (0,0));
-  
-  // Install Ndn applications
-  NS_LOG_INFO ("Installing Applications");
+
+  // Install CCNx applications
   std::string prefix = "/prefix";
-  
+
   ndn::AppHelper consumerHelper ("ns3::ndn::ConsumerCbr");
   consumerHelper.SetPrefix (prefix);
-  consumerHelper.SetAttribute ("Frequency", StringValue ("100")); // 10 interests a second
-  ApplicationContainer consumers = consumerHelper.Install (consumerNodes);
-  
+  consumerHelper.SetAttribute ("Frequency", StringValue ("10")); // 10 interests a second
+  consumerHelper.Install (consumerNodes);
+
   ndn::AppHelper producerHelper ("ns3::ndn::Producer");
   producerHelper.SetPrefix (prefix);
   producerHelper.SetAttribute ("PayloadSize", StringValue("1024"));
-  ApplicationContainer producers = producerHelper.Install (producer);
+  producerHelper.Install (producer);
 
   // Add /prefix origins to ndn::GlobalRouter
-  ndnGlobalRoutingHelper.AddOrigins (prefix, producer);
+  ccnxGlobalRoutingHelper.AddOrigins (prefix, producer);
 
   // Calculate and install FIBs
-  ndnGlobalRoutingHelper.CalculateRoutes ();
-  
-  Simulator::Stop (finishTime);
-    
-  NS_LOG_INFO ("Run Simulation.");
-  Simulator::Run ();
+  ccnxGlobalRoutingHelper.CalculateRoutes ();
 
-  for (NodeList::Iterator node = NodeList::Begin ();
-       node != NodeList::End ();
-       node ++)
-    {
-      std::cout << "Node #" << (*node)->GetId () << std::endl;
-      (*node)->GetObject<ndn::ContentStore> ()->Print (std::cout);
-      std::cout << std::endl;
-    }
-  
+  Simulator::Stop (Seconds (20.0));
+
+  Simulator::Run ();
   Simulator::Destroy ();
-  NS_LOG_INFO ("Done!");
-    
+
   return 0;
 }
diff --git a/examples/ndn-simple.cc b/examples/ndn-simple.cc
index eaa9d09..78993ee 100644
--- a/examples/ndn-simple.cc
+++ b/examples/ndn-simple.cc
@@ -17,7 +17,7 @@
  *
  * Author: Alexander Afanasyev <alexander.afanasyev@ucla.edu>
  */
-
+// ndn-simple.cc
 #include "ns3/core-module.h"
 #include "ns3/network-module.h"
 #include "ns3/point-to-point-module.h"
@@ -40,26 +40,21 @@
  * For every received interest, producer replies with a data packet, containing
  * 1024 bytes of virtual payload.
  *
- * Simulation time is 20 seconds, unless --finish parameter is specified
- *
  * To run scenario and see what is happening, use the following command:
  *
- *     NS_LOG=ndn.Simple:ndn.Consumer ./waf --run=ndn-simple
+ *     NS_LOG=ndn.Consumer:ndn.Producer ./waf --run=ndn-simple
  */
 
-NS_LOG_COMPONENT_DEFINE ("ndn.Simple");
-
 int 
 main (int argc, char *argv[])
 {
+  // setting default parameters for PointToPoint links and channels
   Config::SetDefault ("ns3::PointToPointNetDevice::DataRate", StringValue ("1Mbps"));
   Config::SetDefault ("ns3::PointToPointChannel::Delay", StringValue ("10ms"));
   Config::SetDefault ("ns3::DropTailQueue::MaxPackets", StringValue ("20"));
-  
-  Time finishTime = Seconds (20.0); 
 
+  // Read optional command-line parameters (e.g., enable visualizer with ./waf --run=<> --visualize
   CommandLine cmd;
-  cmd.AddValue ("finish", "Finish time", finishTime);
   cmd.Parse (argc, argv);
 
   // Creating nodes
@@ -71,37 +66,31 @@
   p2p.Install (nodes.Get (0), nodes.Get (1));
   p2p.Install (nodes.Get (1), nodes.Get (2));
 
-  // Install Ndn stack on all nodes
-  NS_LOG_INFO ("Installing Ndn stack");
-  ndn::StackHelper ndnHelper;
-  ndnHelper.SetDefaultRoutes (true);
-  ndnHelper.InstallAll ();
+  // Install CCNx stack on all nodes
+  ndn::StackHelper ccnxHelper;
+  ccnxHelper.SetDefaultRoutes (true);
+  ccnxHelper.InstallAll ();
 
-  NS_LOG_INFO ("Installing Ndn applications");
+  // Installing applications
+
+  // Consumer
   ndn::AppHelper consumerHelper ("ns3::ndn::ConsumerCbr");
   // Consumer will request /prefix/0, /prefix/1, ...
-  consumerHelper.SetPrefix ("/prefix/0");
-  consumerHelper.SetAttribute ("Frequency", StringValue ("1")); // 10 interests a second
-  ApplicationContainer consumers = consumerHelper.Install (nodes.Get (0)); // first node
-  consumers.Stop (Seconds (0.3));
-
   consumerHelper.SetPrefix ("/prefix");
-  consumers = consumerHelper.Install (nodes.Get (0)); // first node
-  consumers.Start (Seconds (1));
-  consumers.Stop  (Seconds (1.3));
-  
+  consumerHelper.SetAttribute ("Frequency", StringValue ("10")); // 10 interests a second
+  consumerHelper.Install (nodes.Get (0)); // first node
+
+  // Producer
   ndn::AppHelper producerHelper ("ns3::ndn::Producer");
   // Producer will reply to all requests starting with /prefix
   producerHelper.SetPrefix ("/prefix");
   producerHelper.SetAttribute ("PayloadSize", StringValue("1024"));
-  ApplicationContainer producers = producerHelper.Install (nodes.Get (2)); // last node
-  
-  Simulator::Stop (finishTime);
-    
-  NS_LOG_INFO ("Run Simulation.");
+  producerHelper.Install (nodes.Get (2)); // last node
+
+  Simulator::Stop (Seconds (20.0));
+
   Simulator::Run ();
   Simulator::Destroy ();
-  NS_LOG_INFO ("Done!");
-    
+
   return 0;
 }
diff --git a/examples/wscript b/examples/wscript
index decba8f..31127c9 100644
--- a/examples/wscript
+++ b/examples/wscript
@@ -4,8 +4,15 @@
     obj = bld.create_ns3_program('ndn-simple', ['ndnSIM'])
     obj.source = 'ndn-simple.cc'
 
-    obj = bld.create_ns3_program('ndn-grid', ['ndnSIM', 'point-to-point', 'point-to-point-layout'])
+    obj = bld.create_ns3_program('ndn-grid', ['ndnSIM', 'point-to-point-layout'])
     obj.source = 'ndn-grid.cc'
 
     obj = bld.create_ns3_program('trie', ['ndnSIM'])
     obj.source = 'trie.cc'
+    
+    if 'topology' in bld.env['NDN_plugins']:
+        obj = bld.create_ns3_program('ndn-grid-topo-plugin', ['ndnSIM'])
+        obj.source = 'ndn-grid-topo-plugin.cc'
+
+        obj = bld.create_ns3_program('ndn-congestion-topo-plugin', ['ndnSIM'])
+        obj.source = 'ndn-congestion-topo-plugin.cc'