diff --git a/doc/doxygen.conf b/doc/doxygen.conf
index de2b15014..f8294ed50 100644
--- a/doc/doxygen.conf
+++ b/doc/doxygen.conf
@@ -785,11 +785,13 @@ WARN_LOGFILE           = doc/doxygen.log
 
 INPUT                  = doc/modules \
                          doc/main.h \
-                         doc/introspected-doxygen.h \
                          examples \
                          utils \
                          src \
-                         contrib
+                         contrib \
+                         doc/introspected-doxygen.h \
+                         doc/introspected-command-line.h \
+
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
diff --git a/src/core/model/attribute-helper.h b/src/core/model/attribute-helper.h
index c1ef5c808..49865e308 100644
--- a/src/core/model/attribute-helper.h
+++ b/src/core/model/attribute-helper.h
@@ -34,7 +34,7 @@
 namespace ns3 {
 
 /**
- * \ingroup attribute
+ * \ingroup attributes
  * \defgroup attributehelper Attribute Helper
  *
  * All these macros can be used to generate automatically the code
diff --git a/src/core/model/attribute.h b/src/core/model/attribute.h
index 9e9597e7f..d2772fdde 100644
--- a/src/core/model/attribute.h
+++ b/src/core/model/attribute.h
@@ -42,7 +42,7 @@ class ObjectBase;
 /**
  *
  * \ingroup core
- * \defgroup attribute Attributes
+ * \defgroup attributes Attributes
  *
  * The \c ns-3 attribute system is the mechanism used in \c ns-3 to
  * organize, document, and modify the *values* used by the various
@@ -57,7 +57,7 @@ class ObjectBase;
 
 /**
  *
- * \ingroup attribute
+ * \ingroup attributes
  *
  * \brief Hold a value for an Attribute.
  *
@@ -104,7 +104,7 @@ public:
 /**
  * \brief allow setting and getting the value of an attribute.
  *
- * \ingroup attribute
+ * \ingroup attributes
  *
  * The goal of this class is to hide from the user how an attribute
  * is actually set or get to or from a class instance. Implementations
@@ -152,7 +152,7 @@ public:
 /**
  * \brief Represent the type of an attribute
  *
- * \ingroup attribute
+ * \ingroup attributes
  *
  * Each type of attribute has an associated unique AttributeChecker
  * subclass. The type of the subclass can be safely used by users
@@ -227,7 +227,7 @@ public:
 /**
  * \brief A class for an empty attribute value.
  *
- * \ingroup attribute
+ * \ingroup attributes
  */
 class EmptyAttributeValue : public AttributeValue
 {
@@ -275,7 +275,7 @@ public:
 };
 
 /**
- * \ingroup attribute
+ * \ingroup attributes
  *
  * \brief Create an empty AttributeAccessor.
  *
@@ -307,7 +307,7 @@ public:
 };
 
 /**
- * \ingroup attribute
+ * \ingroup attributes
  *
  * \brief Create an empty AttributeChecker.
  *
diff --git a/src/core/model/enum.cc b/src/core/model/enum.cc
index 929666aac..07893f15d 100644
--- a/src/core/model/enum.cc
+++ b/src/core/model/enum.cc
@@ -112,7 +112,7 @@ EnumChecker::GetValue (const std::string name) const
   auto it = std::find_if (m_valueSet.begin (), m_valueSet.end (),
                           [name] (Value v) { return v.second == name; } );
   NS_ASSERT_MSG (it != m_valueSet.end (),
-                 "name " << name << "not a valid enum value. Missed entry in MakeEnumChecker?");
+                 "name " << name << " not a valid enum value. Missed entry in MakeEnumChecker?");
   return it->first;
 }
 bool
diff --git a/src/core/model/nstime.h b/src/core/model/nstime.h
index 996a2fa8e..c0e977d78 100644
--- a/src/core/model/nstime.h
+++ b/src/core/model/nstime.h
@@ -1133,7 +1133,7 @@ ATTRIBUTE_VALUE_DEFINE (Time);
 ATTRIBUTE_ACCESSOR_DEFINE (Time);
 
 /**
- *  \ingroup time
+ *  \ingroup attribute_time
  *  \brief Helper to make a Time checker with bounded range.
  *  Both limits are inclusive
  *
@@ -1144,7 +1144,7 @@ ATTRIBUTE_ACCESSOR_DEFINE (Time);
 Ptr<const AttributeChecker> MakeTimeChecker (const Time min, const Time max);
 
 /**
- * \ingroup time
+ * \ingroup attribute_time
  * \brief Helper to make an unbounded Time checker.
  *
  * \return The AttributeChecker
@@ -1156,7 +1156,7 @@ Ptr<const AttributeChecker> MakeTimeChecker (void)
 }
 
 /**
- * \ingroup time
+ * \ingroup attribute_time
  * \brief Helper to make a Time checker with a lower bound.
  *
  *  \param [in] min Minimum allowed value.
diff --git a/src/core/model/simulator.cc b/src/core/model/simulator.cc
index f0c467c16..bac4c2100 100644
--- a/src/core/model/simulator.cc
+++ b/src/core/model/simulator.cc
@@ -55,6 +55,7 @@ NS_LOG_COMPONENT_DEFINE ("Simulator");
 
 /**
  * \ingroup simulator
+ * \anchor GlobalValueSimulatorImplementationType
  * The specific simulator implementation to use.
  *
  * Must be derived from SimulatorImpl.
@@ -67,6 +68,7 @@ static GlobalValue g_simTypeImpl = GlobalValue
 
 /**
  * \ingroup scheduler
+ * \anchor GlobalValueSchedulerType
  * The specific event scheduler implementation to use.
  *
  * Must be derived from Scheduler.
diff --git a/src/core/model/system-path.cc b/src/core/model/system-path.cc
index c27a69cec..ab0308262 100644
--- a/src/core/model/system-path.cc
+++ b/src/core/model/system-path.cc
@@ -310,7 +310,7 @@ MakeTemporaryDirectoryName (void)
   //
   // The final path to the directory is going to look something like
   //
-  //   /tmp/ns3-14.30.29.32767
+  //   /tmp/ns3.14.30.29.32767
   //
   // The first segment comes from one of the temporary directory env
   // variables or /tmp if not found.  The directory name starts with an
diff --git a/src/core/model/system-path.h b/src/core/model/system-path.h
index b9bb111de..2e3a9e1eb 100644
--- a/src/core/model/system-path.h
+++ b/src/core/model/system-path.h
@@ -110,6 +110,22 @@ std::list<std::string> ReadFiles (std::string path);
  * Call ns3::SystemPath::MakeDirectories to create it. Yes, there is a
  * well-known security race in this API but we don't care in ns-3.
  *
+ * The final path to the directory is going to look something like
+ *
+ *     /tmp/ns3.14.30.29.32767
+ *
+ * The first part, "/tmp/" is the absolute path found by inspecting
+ * the environment variables `TMP`and `TEMP`, in order. If neither
+ * exists the hard-codes root path `/tmp/` is used.
+ *
+ * The directory name itself starts with the "ns3" identifier telling folks
+ * who is making all of the temp directories.
+ *
+ * The next three number give the hour, minute and second, separated by
+ * periods.
+ *
+ * The final number is randomly generated, to avoid name collisions.
+ *
  * \return A path which identifies a temporary directory.
  */
 std::string MakeTemporaryDirectoryName (void);
diff --git a/src/network/model/node.cc b/src/network/model/node.cc
index 503829588..070f1602a 100644
--- a/src/network/model/node.cc
+++ b/src/network/model/node.cc
@@ -39,6 +39,8 @@ NS_LOG_COMPONENT_DEFINE ("Node");
 NS_OBJECT_ENSURE_REGISTERED (Node);
 
 /**
+ * \relates Node
+ * \anchor GlobalValueChecksumEnabled
  * \brief A global switch to enable all checksums for all protocols.
  */
 static GlobalValue g_checksumEnabled  = GlobalValue ("ChecksumEnabled",
diff --git a/src/wifi/model/extended-capabilities.h b/src/wifi/model/extended-capabilities.h
index 848c89917..c64738a12 100644
--- a/src/wifi/model/extended-capabilities.h
+++ b/src/wifi/model/extended-capabilities.h
@@ -30,8 +30,6 @@ namespace ns3 {
  * \ingroup wifi
  *
  * This class knows how to serialise and deserialise the Extended Capabilities Information Element
- *
- * \see attribute_ExtendedCapabilities
  */
 class ExtendedCapabilities : public WifiInformationElement
 {
diff --git a/src/wifi/model/he-operation.h b/src/wifi/model/he-operation.h
index 1b2f17f74..f21a7efe9 100644
--- a/src/wifi/model/he-operation.h
+++ b/src/wifi/model/he-operation.h
@@ -31,8 +31,6 @@ namespace ns3 {
  *
  * This class knows how to serialise and deserialise
  * the HE Operation Information Element
- *
- * \see attribute_HeOperation
  */
 class HeOperation : public WifiInformationElement
 {
diff --git a/src/wifi/model/ht-capabilities.h b/src/wifi/model/ht-capabilities.h
index acb3599c0..5907a2083 100644
--- a/src/wifi/model/ht-capabilities.h
+++ b/src/wifi/model/ht-capabilities.h
@@ -37,8 +37,6 @@ namespace ns3 {
  * \ingroup wifi
  *
  * This class knows how to serialise and deserialise the HT Capabilities Information Element
- *
- * \see attribute_HtCapabilities
  */
 class HtCapabilities : public WifiInformationElement
 {
diff --git a/src/wifi/model/ht-operation.h b/src/wifi/model/ht-operation.h
index 8923f2b4a..39d87fd8d 100644
--- a/src/wifi/model/ht-operation.h
+++ b/src/wifi/model/ht-operation.h
@@ -46,8 +46,6 @@ enum HtProtectionType
  *
  * This class knows how to serialise and deserialise
  * the HT Operation Information Element
- *
- * \see attribute_HtOperation
  */
 class HtOperation : public WifiInformationElement
 {
diff --git a/src/wifi/model/vht-operation.h b/src/wifi/model/vht-operation.h
index 464ae2229..494dfcb81 100644
--- a/src/wifi/model/vht-operation.h
+++ b/src/wifi/model/vht-operation.h
@@ -31,8 +31,6 @@ namespace ns3 {
  *
  * This class knows how to serialise and deserialise
  * the VHT Operation Information Element
- *
- * \see attribute_VhtOperation
  */
 class VhtOperation : public WifiInformationElement
 {
diff --git a/utils/print-introspected-doxygen.cc b/utils/print-introspected-doxygen.cc
index 27c006300..26ded86f3 100644
--- a/utils/print-introspected-doxygen.cc
+++ b/utils/print-introspected-doxygen.cc
@@ -73,6 +73,10 @@ namespace
   std::string functionStop;        ///< end of a method/function
   std::string headingStart;        ///< start of section heading (h3)
   std::string headingStop;         ///< end of section heading (h3)
+  // Linking:  [The link text displayed](\ref TheTarget) 
+  std::string hrefStart;           ///< start of a link
+  std::string hrefMid;             ///< middle part of a link
+  std::string hrefStop;            ///< end of a link
   std::string indentHtmlOnly;      ///< small indent
   std::string listLineStart;       ///< start unordered list item
   std::string listLineStop;        ///< end unordered list item
@@ -81,6 +85,7 @@ namespace
   std::string note;                ///< start a note section
   std::string page;                ///< start a separate page
   std::string reference;           ///< reference tag
+  std::string referenceNo;         ///< block automatic references
   std::string returns;             ///< the return value
   std::string sectionStart;        ///< start of a section or group
   std::string seeAlso;             ///< Reference to other docs
@@ -126,6 +131,10 @@ SetMarkup (bool outputText)
       functionStop                 = "\n\n";
       headingStart                 = "";
       headingStop                  = "";
+      // Linking:  The link text displayed (see TheTarget) 
+      hrefStart                    = "";
+      hrefMid                      = "(see ";
+      hrefStop                     = ")";
       indentHtmlOnly               = "";
       listLineStart                = "    * ";
       listLineStop                 = "";
@@ -134,6 +143,7 @@ SetMarkup (bool outputText)
       note                         = "Note: ";
       page                         = "Page ";
       reference                    = " ";
+      referenceNo                  = " ";
       returns                      = "  Returns: ";
       sectionStart                 = "Section ";
       seeAlso                      = "  See: ";
@@ -166,6 +176,10 @@ SetMarkup (bool outputText)
       functionStop                 = "";
       headingStart                 = "<h3>";
       headingStop                  = "</h3>";
+      // Linking:  [The link text displayed](\ref TheTarget) 
+      hrefStart                    = "[";
+      hrefMid                      = "](\\ref ";
+      hrefStop                     = ")";
       indentHtmlOnly               = "  ";
       listLineStart                = "<li>";
       listLineStop                 = "</li>";
@@ -174,6 +188,7 @@ SetMarkup (bool outputText)
       note                         = "\\note ";
       page                         = "\\page ";
       reference                    = " \\ref ";
+      referenceNo                  = " %";
       returns                      = "\\returns ";
       sectionStart                 = "\\ingroup ";
       seeAlso                      = "\\see ";
@@ -983,12 +998,14 @@ void
 PrintAllTypeIds (std::ostream & os)
 {
   NS_LOG_FUNCTION_NOARGS ();
-  os << commentStart << page << "TypeIdList All TypeIds\n"
+  os << commentStart << page << "TypeIdList All ns3::TypeId's\n"
      << std::endl;
-  os << "This is a list of all" << reference << "TypeIds.\n"
-     << "For more information see the" << reference << "TypeId "
-     << "section of this API documentation and the TypeId section "
-     << "in the Configuration and Attributes chapter of the Manual.\n"
+  os << "This is a list of all" << reference << "ns3::TypeId's.\n"
+     << "For more information see the" << reference << "ns3::TypeId "
+     << "section of this API documentation and the"
+     << referenceNo << "TypeId section "
+     << "in the Configuration and "
+     << referenceNo << "Attributes chapter of the Manual.\n"
      << std::endl;
 
   os << listStart << std::endl;
@@ -1015,6 +1032,7 @@ PrintAllTypeIds (std::ostream & os)
 	 << std::endl;
       
     }
+  os << listStop << std::endl;
   os << commentStop << std::endl;
 
 }  // PrintAllTypeIds ()
@@ -1034,8 +1052,8 @@ PrintAllAttributes (std::ostream & os)
   NS_LOG_FUNCTION_NOARGS ();
   os << commentStart << page << "AttributeList All Attributes\n"
      << std::endl;
-  os << "This is a list of all" << reference << "attribute by class.  "
-     << "For more information see the" << reference << "attribute "
+  os << "This is a list of all" << reference << "ns3::Attributes by class.  "
+     << "For more information see the" << reference << "ns3:Attributes "
      << "section of this API documentation and the Attributes sections "
      << "in the Tutorial and Manual.\n"
      << std::endl;
@@ -1101,11 +1119,12 @@ PrintAllGlobals (std::ostream & os)
       os << indentHtmlOnly
 	 <<   listLineStart
 	 <<     boldStart
-	 <<       anchor
-	 <<       "GlobalValue" << (*i)->GetName () << " " << (*i)->GetName ()
+         <<       hrefStart << (*i)->GetName ()
+         <<       hrefMid << "GlobalValue" << (*i)->GetName ()
+         <<       hrefStop
 	 <<     boldStop
-	 <<     ": "            << (*i)->GetHelp ()
-	 <<     ".  Default value: " << val.Get () << "."
+	 <<     ": " << (*i)->GetHelp ()
+	 <<     ".  Default value: " << val.Get () << ". "
 	 <<   listLineStop
 	 << std::endl;
     }
@@ -1491,17 +1510,6 @@ PrintAttributeImplementations (std::ostream & os)
       { "Address",        "Address",        true,  "address.h"          },
       { "Box",            "Box",            true,  "box.h"              },
       { "DataRate",       "DataRate",       true,  "data-rate.h"        },
-      { "DsssParameterSet",
-                          "DsssParameterSet",
-                                            true,  "dsss-parameter-set.h"},
-      { "EdcaParameterSet",
-                          "EdcaParameterSet",
-                                            true,  "edca-parameter-set.h"},
-      { "ErpInformation", "ErpInformation", true,  "erp-information.h"  },
-      { "ExtendedCapabilities", "ExtendedCapabilities", true,  "extended-capabilities.h"  },
-      { "HeCapabilities", "HeCapabilities", true,  "he-capabilities.h"  },
-      { "VhtCapabilities","VhtCapabilities",true,  "vht-capabilities.h" },
-      { "HtCapabilities", "HtCapabilities", true,  "ht-capabilities.h"  },
       { "IeMeshId",       "IeMeshId",       true,  "ie-dot11s-id.h"     },
       { "Ipv4Address",    "Ipv4Address",    true,  "ipv4-address.h"     },
       { "Ipv4Mask",       "Ipv4Mask",       true,  "ipv4-address.h"     },
@@ -1522,20 +1530,16 @@ PrintAttributeImplementations (std::ostream & os)
       { "Vector",         "Vector",         true,  "vector.h"           },
       { "Vector2D",       "Vector2D",       true,  "vector.h"           },
       { "Vector3D",       "Vector3D",       true,  "vector.h"           },
-      { "HeOperation",    "HeOperation",    true,  "he-operation.h"    },
-      { "VhtOperation",   "VhtOperation",   true,  "vht-operation.h"    },
-      { "HtOperation",    "HtOperation",    true,  "ht-operation.h"  },
       { "Waypoint",       "Waypoint",       true,  "waypoint.h"         },
       { "WifiMode",       "WifiMode",       true,  "wifi-mode.h"        },
       
       // All three (Value, Access and Checkers) defined, but custom
-      { "Boolean",        "Boolean",        false, "boolean.h"          },
+      { "Boolean",        "bool",           false, "boolean.h"          },
       { "Callback",       "Callback",       true,  "callback.h"         },
       { "Double",         "double",         false, "double.h"           },
       { "Enum",           "int",            false, "enum.h"             },
       { "Integer",        "int64_t",        false, "integer.h"          },
       { "Pointer",        "Pointer",        false, "pointer.h"          },
-      { "RandomVariable", "RandomVariable", true,  "random-variable-stream.h"  },
       { "String",         "std::string",    false, "string.h"           },
       { "Time",           "Time",           true,  "nstime.h"           },
       { "Uinteger",       "uint64_t",       false, "uinteger.h"         },
@@ -1595,7 +1599,7 @@ int main (int argc, char *argv[])
   if (!outputText)
     {
       std::cout << "/* -*- Mode:C++; c-file-style:\"gnu\"; "
-	           "indent-tabs-mode:nil; -*- */"
+	           "indent-tabs-mode:nil; -*- */\n"
 		<< std::endl;
     }