Release-1.8.1.1

95 files changed, 1705 insertions, 1048 deletions

diff --git a/src/classdef.cpp b/src/classdef.cpp
index 43ffdb5..1aa20e1 100644
--- a/src/classdef.cpp
+++ b/src/classdef.cpp
@@ -42,12 +42,7 @@
 
 //-----------------------------------------------------------------------------
 
-//static inline MemberList *createNewMemberList(MemberList::ListType lt)
-//{
-//  MemberList *result = new MemberList(lt);
-//  return result;
-//}
-
+/** Private data associated with a ClassDef object. */
 class ClassDefImpl
 {
   public:
@@ -296,7 +291,7 @@ QCString ClassDef::getMemberListFileName() const
   return convertNameToFile(compoundTypeString()+name()+"-members");
 }
 
-QCString ClassDef::displayName() const
+QCString ClassDef::displayName(bool includeScope) const
 {
   //static bool optimizeOutputForJava = Config_getBool("OPTIMIZE_OUTPUT_JAVA");
   SrcLangExt lang = getLanguage();
@@ -308,7 +303,14 @@ QCString ClassDef::displayName() const
   }
   else 
   {
-    n=qualifiedNameWithTemplateParameters();
+    if (includeScope)
+    {
+      n=qualifiedNameWithTemplateParameters();
+    }
+    else
+    {
+      n=className();
+    }
   }
   QCString sep=getLanguageSpecificSeparator(lang);
   if (sep!="::")
@@ -3819,9 +3821,8 @@ int ClassDef::countInheritedDecMembersRec(MemberList::ListType lt,
       MemberList *ml = icd->getMemberList((MemberList::ListType)lt1);
       if (ml)
       {
-        //ml->countDecMembers();
-        //count+=ml->numDecMembers();
-        count+=ml->countInheritableMembers(inheritedFrom);
+        //count+=ml->countInheritableMembers(inheritedFrom);
+        count+=icd->countMembersIncludingGrouped((MemberList::ListType)lt1,inheritedFrom,TRUE);
         count+=icd->countInheritedDecMembersRec((MemberList::ListType)lt1,inheritedFrom);
       }
       if (lt2!=-1)
@@ -3829,15 +3830,15 @@ int ClassDef::countInheritedDecMembersRec(MemberList::ListType lt,
         ml = icd->getMemberList((MemberList::ListType)lt2);
         if (ml) 
         {
-          //ml->countDecMembers();
-          //count+=ml->numDecMembers();
-          count+=ml->countInheritableMembers(inheritedFrom);
+          //count+=ml->countInheritableMembers(inheritedFrom);
+          count+=icd->countMembersIncludingGrouped((MemberList::ListType)lt2,inheritedFrom,TRUE);
           count+=icd->countInheritedDecMembersRec((MemberList::ListType)lt2,inheritedFrom);
         }
       }
       ibcd=m_impl->inherits->next();
     }
   }
+#if 0
   if (m_impl->memberGroupSDict)
   {
     MemberGroupSDict::Iterator mgli(*m_impl->memberGroupSDict);
@@ -3850,6 +3851,7 @@ int ClassDef::countInheritedDecMembersRec(MemberList::ListType lt,
       }
     }
   }
+#endif
   return count;
 }
 
@@ -3859,11 +3861,11 @@ int ClassDef::countInheritedDecMembers(MemberList::ListType lt)
   MemberList *ml = getMemberList(lt);
   if (ml)
   {
-    //ml->countDecMembers();
-    //count = ml->numDecMembers();
-    count=ml->countInheritableMembers(this);
+    count = ml->countInheritableMembers(this);
   }
   if (count==0) // for this class the member list is empty
+                // see if we need to create a section for it under
+                // Additional Inherited Members
   {
     count = countInheritedDecMembersRec(lt,this);
   }
@@ -3897,7 +3899,7 @@ int ClassDef::countAdditionalInheritedMembers()
 
 void ClassDef::writeAdditionalInheritedMembers(OutputList &ol)
 {
-  //printf("writeAdditionalInheritedMembers()\n");
+  //printf("**** writeAdditionalInheritedMembers()\n");
   QListIterator<LayoutDocEntry> eli(
       LayoutDocManager::instance().docEntries(LayoutDocManager::Class));
   LayoutDocEntry *lde;
@@ -3917,30 +3919,31 @@ void ClassDef::writeAdditionalInheritedMembers(OutputList &ol)
 }
 
 int ClassDef::countMembersIncludingGrouped(MemberList::ListType lt,
-              ClassDef *inheritedFrom)
+              ClassDef *inheritedFrom,bool additional)
 {
   int count=0;
   MemberList *ml = getMemberList(lt);
   if (ml) 
   { 
-    //ml->countDecMembers(); 
-    //count=ml->numDecMembers(); 
     count=ml->countInheritableMembers(inheritedFrom);
   }
+  //printf("%s:countMembersIncludingGrouped: count=%d\n",name().data(),count);
   if (m_impl->memberGroupSDict)
   {
     MemberGroupSDict::Iterator mgli(*m_impl->memberGroupSDict);
     MemberGroup *mg;
     for (;(mg=mgli.current());++mgli)
     {
-      if (!mg->allMembersInSameSection() || !m_impl->subGrouping) // group is in its own section
+      bool hasOwnSection = !mg->allMembersInSameSection() || 
+                           !m_impl->subGrouping; // group is in its own section
+      if ((additional && hasOwnSection) || (!additional && !hasOwnSection))
       {
         count+=mg->countGroupedInheritedMembers(lt);
       }
     }
   }
-  //printf("%s:countMembersIncludingGrouped(%s)=%d\n",
-  //    name().data(),ml?ml->listTypeAsString().data():"<none>",count);
+  //printf("%s:countMembersIncludingGrouped(lt=%d,%s)=%d\n",
+  //    name().data(),lt,ml?ml->listTypeAsString().data():"<none>",count);
   return count;
 }
 
@@ -3951,7 +3954,9 @@ void ClassDef::writeInheritedMemberDeclarations(OutputList &ol,
 {
   ol.pushGeneratorState();
   ol.disableAllBut(OutputGenerator::Html);
-  bool process = countMembersIncludingGrouped(lt,inheritedFrom)>0;
+  bool process = countMembersIncludingGrouped(lt,inheritedFrom,FALSE)>0;
+  //printf("%s: writeInheritedMemberDec: lt=%d process=%d invert=%d\n",
+  //    name().data(),lt,process,invert);
   if (process^invert)
   {
     if (m_impl->inherits)
@@ -3964,7 +3969,10 @@ void ClassDef::writeInheritedMemberDeclarations(OutputList &ol,
         int lt1,lt2;
         convertProtectionLevel(lt,ibcd->prot,&lt1,&lt2);
         //printf("%s:convert %d->(%d,%d)\n",icd->name().data(),lt,lt1,lt2);
-        if (visitedClasses->find(icd)!=0) return;
+        if (visitedClasses->find(icd)!=0) 
+        {
+          return; // already processed before (in case of multiple inheritance)
+        }
         visitedClasses->insert(icd,icd);
         if (lt1!=-1)
         {
@@ -4024,7 +4032,6 @@ void ClassDef::addGroupedInheritedMembers(OutputList &ol,MemberList::ListType lt
     MemberGroup *mg;
     for (;(mg=mgli.current());++mgli)
     {
-      //printf("  candidate %s\n",mg->header().data());
       if (!mg->allMembersInSameSection() || !m_impl->subGrouping) // group is in its own section
       {
         mg->addGroupedInheritedMembers(ol,this,lt,inheritedFrom,inheritId);
diff --git a/src/classdef.h b/src/classdef.h
index 246404c..e7d5fb5 100644
--- a/src/classdef.h
+++ b/src/classdef.h
@@ -48,7 +48,7 @@ class StringDict;
 struct IncludeInfo;
 class ClassDefImpl;
 
-/*! \brief This class contains all information about a compound.
+/** A model of a compound symbol.
  *
  *  A compound can be a class, struct, union, interface, or exception.
  *  \note This class should be renamed to CompoundDef
@@ -56,7 +56,7 @@ class ClassDefImpl;
 class ClassDef : public Definition
 {
   public:
-    /*! The various compound types */
+    /** The various compound types */
     enum CompoundType { Class, //=Entry::CLASS_SEC, 
                         Struct, //=Entry::STRUCT_SEC, 
                         Union, //=Entry::UNION_SEC,
@@ -66,7 +66,7 @@ class ClassDef : public Definition
                         Exception //=Entry::EXCEPTION_SEC
                       };
 
-    /*! Creates a new compound definition.
+    /** Creates a new compound definition.
      *  \param fileName  full path and file name in which this compound was
      *                   found.
      *  \param startLine line number where the definition of this compound
@@ -88,121 +88,121 @@ class ClassDef : public Definition
              const char *name,CompoundType ct,
              const char *ref=0,const char *fName=0,
              bool isSymbol=TRUE,bool isJavaEnum=FALSE);
-    /*! Destroys a compound definition. */
+    /** Destroys a compound definition. */
    ~ClassDef();
 
     //-----------------------------------------------------------------------------------
     // --- getters 
     //-----------------------------------------------------------------------------------
 
-    /*! Used for RTTI, this is a class */
+    /** Used for RTTI, this is a class */
     DefType definitionType() const { return TypeClass; }
 
-    /*! Returns the unique base name (without extension) of the class's file on disk */
+    /** Returns the unique base name (without extension) of the class's file on disk */
     QCString getOutputFileBase() const;
     QCString getInstanceOutputFileBase() const; 
     QCString getFileBase() const;
 
-    /*! Returns the base name for the source code file */
+    /** Returns the base name for the source code file */
     QCString getSourceFileBase() const; 
 
-    /*! If this class originated from a tagfile, this will return the tag file reference */
+    /** If this class originated from a tagfile, this will return the tag file reference */
     QCString getReference() const;
 
-    /*! Returns TRUE if this class is imported via a tag file */
+    /** Returns TRUE if this class is imported via a tag file */
     bool isReference() const;
 
-    /*! Returns TRUE if this is a local class definition, see EXTRACT_LOCAL_CLASSES */
+    /** Returns TRUE if this is a local class definition, see EXTRACT_LOCAL_CLASSES */
     bool isLocal() const;
 
-    /*! returns the classes nested into this class */
+    /** returns the classes nested into this class */
     ClassSDict *getClassSDict();
 
-    /*! returns TRUE if this class has documentation */
+    /** returns TRUE if this class has documentation */
     bool hasDocumentation() const;
 
-    /*! Returns the name as it is appears in the documentation */
-    QCString displayName() const;
+    /** Returns the name as it is appears in the documentation */
+    QCString displayName(bool includeScope=TRUE) const;
 
-    /*! Returns the type of compound this is, i.e. class/struct/union/.. */
+    /** Returns the type of compound this is, i.e. class/struct/union/.. */
     CompoundType compoundType() const;
 
-    /*! Returns the type of compound as a string */
+    /** Returns the type of compound as a string */
     QCString compoundTypeString() const;
 
-    /*! Returns the list of base classes from which this class directly
+    /** Returns the list of base classes from which this class directly
      *  inherits.
      */
     BaseClassList *baseClasses() const;
     
-    /*! Returns the list of sub classes that directly derive from this class
+    /** Returns the list of sub classes that directly derive from this class
      */
     BaseClassList *subClasses() const;
 
-    /*! Returns a dictionary of all members. This includes any inherited 
+    /** Returns a dictionary of all members. This includes any inherited 
      *  members. Members are sorted alphabetically.
      */ 
     MemberNameInfoSDict *memberNameInfoSDict() const;
 
-    /*! Return the protection level (Public,Protected,Private) in which 
+    /** Return the protection level (Public,Protected,Private) in which 
      *  this compound was found.
      */
     Protection protection() const;
 
-    /*! returns TRUE iff a link is possible to this item within this project.
+    /** returns TRUE iff a link is possible to this item within this project.
      */
     bool isLinkableInProject() const;
 
-    /*! return TRUE iff a link to this class is possible (either within 
+    /** return TRUE iff a link to this class is possible (either within 
      *  this project, or as a cross-reference to another project).
      */
     bool isLinkable() const;
 
-    /*! the class is visible in a class diagram, or class hierarchy */
+    /** the class is visible in a class diagram, or class hierarchy */
     bool isVisibleInHierarchy();
     
-    /*! Returns the template arguments of this class 
+    /** Returns the template arguments of this class 
      *  Will return 0 if not applicable.
      */
     ArgumentList *templateArguments() const;
 
-    /*! Returns the namespace this compound is in, or 0 if it has a global
+    /** Returns the namespace this compound is in, or 0 if it has a global
      *  scope.
      */
     NamespaceDef *getNamespaceDef() const;
 
-    /*! Returns the file in which this compound's definition can be found.
+    /** Returns the file in which this compound's definition can be found.
      *  Should not return 0 (but it might be a good idea to check anyway).
      */
     FileDef      *getFileDef() const;
 
-    /*! Returns the Java package this class is in or 0 if not applicable. 
+    /** Returns the Java package this class is in or 0 if not applicable. 
      */ 
 
     MemberDef    *getMemberByName(const QCString &) const;
     
-    /*! Returns TRUE iff \a bcd is a direct or indirect base class of this
+    /** Returns TRUE iff \a bcd is a direct or indirect base class of this
      *  class. This function will recusively traverse all branches of the
      *  inheritance tree.
      */
     bool isBaseClass(ClassDef *bcd,bool followInstances,int level=0);
 
-    /*! returns TRUE iff \a md is a member of this class or of the
+    /** returns TRUE iff \a md is a member of this class or of the
      *  the public/protected members of a base class 
      */
     bool isAccessibleMember(MemberDef *md);
 
-    /*! Returns a sorted dictionary with all template instances found for
+    /** Returns a sorted dictionary with all template instances found for
      *  this template class. Returns 0 if not a template or no instances.
      */
     QDict<ClassDef> *getTemplateInstances() const;
 
-    /*! Returns the template master of which this class is an instance.
+    /** Returns the template master of which this class is an instance.
      *  Returns 0 if not applicable.
      */
     ClassDef *templateMaster() const;
 
-    /*! Returns TRUE if this class is a template */
+    /** Returns TRUE if this class is a template */
     bool isTemplate() const;
 
     IncludeInfo *includeInfo() const;
@@ -215,13 +215,13 @@ class ClassDef : public Definition
 
     bool isTemplateArgument() const;
 
-    /*! Returns the definition of a nested compound if
+    /** Returns the definition of a nested compound if
      *  available, or 0 otherwise.
      *  @param name The name of the nested compound
      */
     virtual Definition *findInnerCompound(const char *name);
 
-    /*! Returns the template parameter lists that form the template
+    /** Returns the template parameter lists that form the template
      *  declaration of this class.
      *  
      *  Example: <code>template<class T> class TC {};</code>
@@ -233,32 +233,32 @@ class ClassDef : public Definition
     QCString qualifiedNameWithTemplateParameters(
         QList<ArgumentList> *actualParams=0) const;
 
-    /*! Returns TRUE if there is at least one pure virtual member in this
+    /** Returns TRUE if there is at least one pure virtual member in this
      *  class.
      */
     bool isAbstract() const;
 
-    /*! Returns TRUE if this class is implemented in Objective-C */
+    /** Returns TRUE if this class is implemented in Objective-C */
     bool isObjectiveC() const;
 
-    /*! Returns TRUE if this class is implemented in C# */
+    /** Returns TRUE if this class is implemented in C# */
     bool isCSharp() const;
 
-    /*! Returns the class of which this is a category (Objective-C only) */
+    /** Returns the class of which this is a category (Objective-C only) */
     ClassDef *categoryOf() const;
 
-    /*! Returns the name of the class including outer classes, but not
+    /** Returns the name of the class including outer classes, but not
      *  including namespaces.
      */
     QCString className() const;
 
-    /*! Returns the members in the list identified by \a lt */
+    /** Returns the members in the list identified by \a lt */
     MemberList *getMemberList(MemberList::ListType lt);
 
-    /*! Returns the list containing the list of members sorted per type */
+    /** Returns the list containing the list of members sorted per type */
     const QList<MemberList> &getMemberLists() const;
 
-    /*! Returns the member groups defined for this class */
+    /** Returns the member groups defined for this class */
     MemberGroupSDict *getMemberGroupSDict() const;
 
     QDict<int> *getTemplateBaseClassNames() const;
@@ -342,6 +342,7 @@ class ClassDef : public Definition
     void removeMemberFromLists(MemberDef *md);
     void addGroupedInheritedMembers(OutputList &ol,MemberList::ListType lt,
                               ClassDef *inheritedFrom,const QCString &inheritId);
+    int countMembersIncludingGrouped(MemberList::ListType lt,ClassDef *inheritedFrom,bool additional);
     
     bool visited;
 
@@ -386,13 +387,12 @@ class ClassDef : public Definition
     int countInheritedDecMembers(MemberList::ListType lt);
     int countAdditionalInheritedMembers();
     void writeAdditionalInheritedMembers(OutputList &ol);
-    int countMembersIncludingGrouped(MemberList::ListType lt,ClassDef *inheritedFrom);
     
     ClassDefImpl *m_impl;
 
 };
 
-/*! \brief Class that contains information about a usage relation. 
+/** Class that contains information about a usage relation. 
  */
 struct UsesClassDef
 {
@@ -412,21 +412,21 @@ struct UsesClassDef
       accessors->insert(s,(void *)666);
     }
   }
-  /*! Class definition that this relation uses. */
+  /** Class definition that this relation uses. */
   ClassDef *classDef;
 
-  /*! Dictionary of member variable names that form the edge labels of the
+  /** Dictionary of member variable names that form the edge labels of the
    *  usage relation.
    */
   QDict<void> *accessors;
 
-  /*! Template arguments used for the base class */
+  /** Template arguments used for the base class */
   QCString templSpecifiers;
 
   bool containment;
 };
 
-/*! \brief Dictionary of usage relations. 
+/** Dictionary of usage relations. 
  */
 class UsesClassDict : public QDict<UsesClassDef>
 {
@@ -435,7 +435,7 @@ class UsesClassDict : public QDict<UsesClassDef>
    ~UsesClassDict() {}
 };
 
-/*! \brief Iterator class to iterate over a dictionary of usage relations. 
+/** Iterator class to iterate over a dictionary of usage relations. 
  */
 class UsesClassDictIterator : public QDictIterator<UsesClassDef>
 {
@@ -445,7 +445,7 @@ class UsesClassDictIterator : public QDictIterator<UsesClassDef>
    ~UsesClassDictIterator() {}
 };
 
-/*! \brief Class that contains information about an inheritance relation. 
+/** Class that contains information about an inheritance relation. 
  */
 struct BaseClassDef
 {
@@ -453,29 +453,29 @@ struct BaseClassDef
                Specifier v,const char *t) : 
         classDef(cd), usedName(n), prot(p), virt(v), templSpecifiers(t) {}
 
-  /*! Class definition that this relation inherits from. */
+  /** Class definition that this relation inherits from. */
   ClassDef *classDef;
 
-  /*! name used in the inheritance list 
+  /** name used in the inheritance list 
    * (may be a typedef name instead of the class name)
    */
   QCString   usedName; 
   
-  /*! Protection level of the inheritance relation: 
+  /** Protection level of the inheritance relation: 
    *  Public, Protected, or Private 
    */
   Protection prot;     
 
-  /*! Virtualness of the inheritance relation:
+  /** Virtualness of the inheritance relation:
    *  Normal, or Virtual
    */
   Specifier  virt;
 
-  /*! Template arguments used for the base class */
+  /** Template arguments used for the base class */
   QCString templSpecifiers;
 };
 
-/*! \brief list of base classes 
+/** List of base classes.
  *  
  *  The classes are alphabetically sorted on name if inSort() is used.
  */
@@ -494,7 +494,7 @@ class BaseClassList : public QList<BaseClassDef>
     }
 };
 
-/*! \brief Iterator for a list of base classes
+/** Iterator for a list of base classes.
  */
 class BaseClassListIterator : public QListIterator<BaseClassDef>
 {
diff --git a/src/classlist.h b/src/classlist.h
index 9b76c39..71a62b6 100644
--- a/src/classlist.h
+++ b/src/classlist.h
@@ -26,6 +26,7 @@
 
 class Definition;
 
+/** A list of ClassDef objects. */
 class ClassList : public QList<ClassDef>
 { 
   public:
@@ -35,12 +36,14 @@ class ClassList : public QList<ClassDef>
    int compareItems(GCI item1,GCI item2);
 };
 
+/** An iterator for ClassDef objects in a ClassList. */
 class ClassListIterator : public QListIterator<ClassDef>
 {
   public:
     ClassListIterator(const ClassList &list);
 };
 
+/** An unsorted dictionary of ClassDef objects. */
 class ClassDict : public QDict<ClassDef>
 {
   public:
@@ -48,6 +51,7 @@ class ClassDict : public QDict<ClassDef>
    ~ClassDict() {}
 };
 
+/** A sorted dictionary of ClassDef objects. */
 class ClassSDict : public SDict<ClassDef>
 {
   public:
diff --git a/src/cmdmapper.cpp b/src/cmdmapper.cpp
index c4379e3..9a723c2 100644
--- a/src/cmdmapper.cpp
+++ b/src/cmdmapper.cpp
@@ -18,6 +18,13 @@
 
 #include "cmdmapper.h"
 
+/** Call representing a mapping from a command name to a command ID. */
+struct CommandMap
+{
+  const char *cmdName;
+  int cmdId;
+};
+
 CommandMap cmdMap[] =
 {
   { "a",             CMD_EMPHASIS },
@@ -198,6 +205,25 @@ CommandMap htmlTagMap[] =
 Mapper *Mappers::cmdMapper     = new Mapper(cmdMap,TRUE);
 Mapper *Mappers::htmlTagMapper = new Mapper(htmlTagMap,FALSE);
 
+int Mapper::map(const char *n)
+{
+  QCString name=n;
+  if (!m_cs) name=name.lower();
+  int *result;
+  return !name.isEmpty() && (result=m_map.find(name)) ? *result: 0;
+}
+
+Mapper::Mapper(const CommandMap *cm,bool caseSensitive) : m_map(89), m_cs(caseSensitive)
+{
+  m_map.setAutoDelete(TRUE);
+  const CommandMap *p = cm;
+  while (p->cmdName)
+  {
+    m_map.insert(p->cmdName,new int(p->cmdId));
+    p++;
+  }
+}
+
 void Mappers::freeMappers()
 {
   delete cmdMapper;     cmdMapper     = 0;
diff --git a/src/cmdmapper.h b/src/cmdmapper.h
index deb5f50..c53e2b1 100644
--- a/src/cmdmapper.h
+++ b/src/cmdmapper.h
@@ -21,11 +21,7 @@
 
 #include <qdict.h>
 
-struct CommandMap
-{
-  const char *cmdName;
-  int cmdId;
-};
+struct CommandMap;
 
 const int SIMPLESECT_BIT = 0x1000;
 
@@ -187,32 +183,18 @@ enum HtmlTagType
   XML_INHERITDOC   = XML_CmdMask + 22
 };
 
+/** Class representing a mapping from command names to command IDs. */
 class Mapper
 {
   public:
-    int map(const char *n)
-    {
-      QCString name=n;
-      if (!m_cs) name=name.lower();
-      int *result;
-      return !name.isEmpty() && (result=m_map.find(name)) ? *result: 0;
-    }
-
-    Mapper(const CommandMap *cm,bool caseSensitive) : m_map(89), m_cs(caseSensitive)
-    {
-      m_map.setAutoDelete(TRUE);
-      const CommandMap *p = cm;
-      while (p->cmdName)
-      {
-        m_map.insert(p->cmdName,new int(p->cmdId));
-        p++;
-      }
-    }
+    int map(const char *n);
+    Mapper(const CommandMap *cm,bool caseSensitive);
   private:
     QDict<int> m_map;
     bool m_cs;
 };
 
+/** Class representing a namespace for the doxygen and HTML command mappers. */
 struct Mappers
 {
   static void freeMappers();
diff --git a/src/commentcnv.l b/src/commentcnv.l
index f986531..689c274 100644
--- a/src/commentcnv.l
+++ b/src/commentcnv.l
@@ -107,12 +107,13 @@ static void replaceCommentMarker(const char *s,int len)
   }
   if (blanks>0)
   {
-    while (blanks>1)
+    while (blanks>2)
     {
       ADDCHAR(' ');
       blanks--;
     }
-    ADDCHAR('*');
+    if (blanks>1) ADDCHAR('*');
+    ADDCHAR(' ');
   }
   // copy comment line to output
   ADDARRAY(p,len-(p-s));
diff --git a/src/commentscan.l b/src/commentscan.l
index c7e36a5..26c381f 100644
--- a/src/commentscan.l
+++ b/src/commentscan.l
@@ -957,11 +957,18 @@ RCSTAG    "$"{ID}":"[^\n$]+"$"
 					}
 <Comment>"<summary>"			{ // start of a .NET XML style brief description
 					  setOutput(OutputBrief);
+                                          addOutput(yytext);
+  					}
+<Comment>"<remarks>"            	{ // start of a .NET XML style detailed description
+					  setOutput(OutputDoc);
+                                          addOutput(yytext);
   					}
-<Comment>"<remarks>"|"</summary>"	{ // start of a .NET XML style detailed description
+<Comment>"</summary>"	                { // start of a .NET XML style detailed description
+                                          addOutput(yytext);
 					  setOutput(OutputDoc);
   					}
 <Comment>"</remarks>"			{ // end of a brief or detailed description
+                                          addOutput(yytext);
   					}
 <Comment>{RCSTAG}			{ // RCS tag which end a brief description
   					  setOutput(OutputDoc);
@@ -988,6 +995,9 @@ RCSTAG    "$"{ID}":"[^\n$]+"$"
 					      // this command forces the end of brief description
 					      setOutput(OutputDoc);
 					    }
+                                            int i=0;
+                                            while (yytext[i]==' ' || yytext[i]=='\t') i++;
+                                            if (i>0) addOutput(QCString(yytext).left(i));
 					    if (cmdPtr->func && cmdPtr->func(cmdName))
 					    {
 					      // implicit split of the comment block into two
@@ -1010,7 +1020,7 @@ RCSTAG    "$"{ID}":"[^\n$]+"$"
 					    {
 					      // command without handler, to be processed
 					      // later by parsedoc.cpp
-					      addOutput(yytext);
+					      addOutput(yytext+i);
 					    }
 					  }
 					  else // command not relevant
@@ -1315,7 +1325,7 @@ RCSTAG    "$"{ID}":"[^\n$]+"$"
 <ClassDocArg2>.				{ // ignore other stuff
   					}
 
-<ClassDocArg3>[<]?{FILE}?[>]?		{ // third argument; include file name
+<ClassDocArg3>[<"]?{FILE}?[">]?		{ // third argument; include file name
  					  current->includeName = yytext;
 					  BEGIN( Comment );
 					}
@@ -2331,7 +2341,7 @@ static bool handleMemberOf(const QCString &)
 
 static bool handleRefItem(const QCString &)
 {
-  addOutput(" @refitem ");
+  addOutput("@refitem ");
   BEGIN(LineParam);
   return FALSE;
 }
@@ -2339,7 +2349,7 @@ static bool handleRefItem(const QCString &)
 static bool handleSection(const QCString &s)
 {
   setOutput(OutputDoc);
-  addOutput(" @"+s+" ");
+  addOutput("@"+s+" ");
   BEGIN(SectionLabel);
   if      (s=="section")       g_sectionLevel=1;
   else if (s=="subsection")    g_sectionLevel=2;
@@ -2358,28 +2368,28 @@ static bool handleSubpage(const QCString &s)
     warn(yyFileName,yyLineNr,
 	"warning: found \\subpage command in a comment block that is not marked as a page!");
   }
-  addOutput(" @"+s+" ");
+  addOutput("@"+s+" ");
   BEGIN(SubpageLabel);
   return FALSE;
 }
 
 static bool handleAnchor(const QCString &s)
 {
-  addOutput(" @"+s+" ");
+  addOutput("@"+s+" ");
   BEGIN(AnchorLabel);
   return FALSE;
 }
 
 static bool handleCite(const QCString &s)
 {
-  addOutput(" @"+s+" ");
+  addOutput("@"+s+" ");
   BEGIN(CiteLabel);
   return FALSE;
 }
 
 static bool handleFormatBlock(const QCString &s)
 {
-  addOutput(" @"+s+" ");
+  addOutput("@"+s+" ");
   //printf("handleFormatBlock(%s)\n",s.data());
   blockName=s;
   g_commentCount=0;
@@ -2389,7 +2399,7 @@ static bool handleFormatBlock(const QCString &s)
 
 static bool handleAddIndex(const QCString &)
 {
-  addOutput(" @addindex ");
+  addOutput("@addindex ");
   BEGIN(LineParam);
   return FALSE;
 }
diff --git a/src/compound.xsd b/src/compound.xsd
index 406f6f5..4007382 100644
--- a/src/compound.xsd
+++ b/src/compound.xsd
@@ -825,6 +825,8 @@
       <xsd:enumeration value="retain"/>
       <xsd:enumeration value="copy"/>
       <xsd:enumeration value="assign"/>
+      <xsd:enumeration value="weak"/>
+      <xsd:enumeration value="strong"/>
     </xsd:restriction>
   </xsd:simpleType>
 
diff --git a/src/compound_xsd.h b/src/compound_xsd.h
index 5e04417..eb4d978 100644
--- a/src/compound_xsd.h
+++ b/src/compound_xsd.h
@@ -825,6 +825,8 @@
 "      <xsd:enumeration value=\"retain\"/>\n"
 "      <xsd:enumeration value=\"copy\"/>\n"
 "      <xsd:enumeration value=\"assign\"/>\n"
+"      <xsd:enumeration value=\"weak\"/>\n"
+"      <xsd:enumeration value=\"strong\"/>\n"
 "    </xsd:restriction>\n"
 "  </xsd:simpleType>\n"
 "\n"
diff --git a/src/config.h b/src/config.h
index ccbf713..d18e87d 100644
--- a/src/config.h
+++ b/src/config.h
@@ -27,8 +27,7 @@
 #include "ftextstream.h"
 
 
-/*! \brief Abstract base class for any configuration option.
- *
+/** Abstract base class for any configuration option.
  */
 class ConfigOption
 {
@@ -92,8 +91,7 @@ class ConfigOption
     OptionType m_kind;
 };
 
-/*! \brief Section marker for grouping the configuration options
- *
+/** Section marker for grouping the configuration options.
  */
 class ConfigInfo : public ConfigOption
 {
@@ -117,8 +115,7 @@ class ConfigInfo : public ConfigOption
     void substEnvVars() {}
 };
 
-/*! \brief Option of the list type.
- *
+/** Class respresenting a list type option.
  */
 class ConfigList : public ConfigOption
 {
@@ -155,8 +152,7 @@ class ConfigList : public ConfigOption
     WidgetType m_widgetType;
 };
 
-/*! \brief Option of the enum type.
- *
+/** Class representing an enum type option.
  */
 class ConfigEnum : public ConfigOption
 {
@@ -197,8 +193,7 @@ class ConfigEnum : public ConfigOption
     QCString m_defValue;
 };
 
-/*! \brief Option of the string type.
- *
+/** Class representing a string type option.
  */
 class ConfigString : public ConfigOption
 {
@@ -240,8 +235,7 @@ class ConfigString : public ConfigOption
     WidgetType m_widgetType;
 };
 
-/*! \brief Option of the integer type.
- *
+/** Class representing an integer type option.
  */
 class ConfigInt : public ConfigOption
 {
@@ -291,8 +285,7 @@ class ConfigInt : public ConfigOption
     QCString m_valueString;
 };
 
-/*! \brief Option of the boolean type.
- *
+/** Class representing a Boolean type option.
  */
 class ConfigBool : public ConfigOption
 {
@@ -337,8 +330,7 @@ class ConfigBool : public ConfigOption
     QCString m_valueString;
 };
 
-/*! \brief Section marker for obsolete options
- *
+/** Section marker for obsolete options
  */
 class ConfigObsolete : public ConfigOption
 {
@@ -358,7 +350,7 @@ class ConfigObsolete : public ConfigOption
 #define Config_getEnum(val)    Config::instance()->getEnum(__FILE__,__LINE__,val)
 #define Config_getBool(val)    Config::instance()->getBool(__FILE__,__LINE__,val)
 
-/*! \brief Singleton for configuration variables.
+/** Singleton for configuration variables.
  *
  *  This object holds the global static variables
  *  read from a user-supplied configuration file.
diff --git a/src/config.xml b/src/config.xml
index e455ffd..b59b213 100644
--- a/src/config.xml
+++ b/src/config.xml
@@ -541,7 +541,7 @@ is used as the file version. See the manual for examples.
     <option type='string' id='LAYOUT_FILE' format='file' docs='
 The LAYOUT_FILE tag can be used to specify a layout file which will be parsed 
 by doxygen. The layout file controls the global structure of the generated 
-output files in an output format independent way. The create the layout file 
+output files in an output format independent way. To create the layout file 
 that represents doxygen&apos;s defaults, run doxygen with the -l option. 
 You can optionally specify a file name after the option, if omitted 
 DoxygenLayout.xml will be used as the name of the layout file. 
@@ -763,7 +763,7 @@ of functions and classes directly in the documentation.
     <option type='bool' id='STRIP_CODE_COMMENTS' docs='
 Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct 
 doxygen to hide any special comment blocks from generated source code 
-fragments. Normal C and C++ comments will always remain visible. 
+fragments. Normal C, C++ and Fortran comments will always remain visible. 
 ' defval='1'/>
     <option type='bool' id='REFERENCED_BY_RELATION' docs='
 If the REFERENCED_BY_RELATION tag is set to YES 
diff --git a/src/configoptions.cpp b/src/configoptions.cpp
index 9ae97af..462de19 100644
--- a/src/configoptions.cpp
+++ b/src/configoptions.cpp
@@ -778,7 +778,7 @@ void addConfigOptions(Config *cfg)
                  "LAYOUT_FILE",
                  "The LAYOUT_FILE tag can be used to specify a layout file which will be parsed\n"
                  "by doxygen. The layout file controls the global structure of the generated\n"
-                 "output files in an output format independent way. The create the layout file\n"
+                 "output files in an output format independent way. To create the layout file\n"
                  "that represents doxygen's defaults, run doxygen with the -l option.\n"
                  "You can optionally specify a file name after the option, if omitted\n"
                  "DoxygenLayout.xml will be used as the name of the layout file."
@@ -1076,7 +1076,7 @@ void addConfigOptions(Config *cfg)
                  "STRIP_CODE_COMMENTS",
                  "Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct\n"
                  "doxygen to hide any special comment blocks from generated source code\n"
-                 "fragments. Normal C and C++ comments will always remain visible.",
+                 "fragments. Normal C, C++ and Fortran comments will always remain visible.",
                  TRUE
                 );
   //----
diff --git a/src/cppvalue.h b/src/cppvalue.h
index d3e2a1d..7289ce0 100644
--- a/src/cppvalue.h
+++ b/src/cppvalue.h
@@ -22,11 +22,10 @@
 #include <stdio.h>
 #include <qglobal.h> 
 
+/** A class representing a C-preprocessor value. */
 class CPPValue
 {
   public:
-  
-  
     enum Type { Int, Float };
   
     CPPValue(long val=0) : type(Int) { v.l = val; }
diff --git a/src/dbusxmlscanner.cpp b/src/dbusxmlscanner.cpp
index f116d5e..ddfe9ac 100644
--- a/src/dbusxmlscanner.cpp
+++ b/src/dbusxmlscanner.cpp
@@ -64,6 +64,7 @@
 
 const QString EXTENSION_URI("http://psiamp.org/dtd/doxygen_dbusxml.dtd");
 
+/** DBus implementation of the generic QXmlDefaultHandler. */
 class DBusXMLHandler : public QXmlDefaultHandler
 {
 public:
diff --git a/src/dbusxmlscanner.h b/src/dbusxmlscanner.h
index fd48cbc..545071c 100644
--- a/src/dbusxmlscanner.h
+++ b/src/dbusxmlscanner.h
@@ -20,7 +20,7 @@
 
 #include "parserintf.h"
 
-/** \brief D-Bus XML parser.
+/** D-Bus XML parser.
  *
  *  This is the D-Bus XML parser for doxygen.
  */
diff --git a/src/debug.cpp b/src/debug.cpp
index 1c3c1c1..8757be2 100644
--- a/src/debug.cpp
+++ b/src/debug.cpp
@@ -25,6 +25,7 @@
 
 //------------------------------------------------------------------------
 
+/** Helper struct representing a mapping from debug label to a debug ID */
 struct LabelMap
 {
   const char *name;
@@ -49,6 +50,7 @@ static LabelMap s_labels[] =
   { 0,             (Debug::DebugMask)0  }
 };
 
+/** Class representing a mapping from debug labels to debug IDs. */
 class LabelMapper
 {
   public:
diff --git a/src/debug.h b/src/debug.h
index f624628..c3d78de 100644
--- a/src/debug.h
+++ b/src/debug.h
@@ -19,6 +19,7 @@
 #ifndef _DEBUG_H
 #define _DEBUG_H
 
+/** Class containing a print function for diagnostics. */
 class Debug
 {
   public:
diff --git a/src/define.h b/src/define.h
index b5e4f6e..6579403 100644
--- a/src/define.h
+++ b/src/define.h
@@ -24,6 +24,7 @@
 
 class FileDef;
 
+/** A class representing a macro definition. */
 class Define
 {
   public:
@@ -47,6 +48,7 @@ class Define
     bool nonRecursive;
 };
 
+/** A list of Define objects. */
 class DefineList : public QList<Define>
 {
   public:
@@ -58,6 +60,7 @@ class DefineList : public QList<Define>
     }
 };
 
+/** A list of Define objects associated with a specific name. */
 class DefineName : public QList<Define>
 {
   public:
@@ -73,6 +76,7 @@ class DefineName : public QList<Define>
     QCString name;
 };
 
+/** A list of DefineName objects. */
 class DefineNameList : public QList<DefineName>
 {
   public:
@@ -85,7 +89,10 @@ class DefineNameList : public QList<DefineName>
     }
 };
 
+/** An unsorted dictionary of Define objects. */
 typedef QDict<Define> DefineDict;
+
+/** A sorted dictionary of DefineName object. */
 typedef QDict<DefineName> DefineNameDict;
 
 #endif
diff --git a/src/definition.cpp b/src/definition.cpp
index e1f7d60..1631c16 100644
--- a/src/definition.cpp
+++ b/src/definition.cpp
@@ -44,6 +44,8 @@
 
 //-----------------------------------------------------------------------------------------
 
+
+/** Private data associated with a Definition object. */
 class DefinitionImpl
 {
   public:
@@ -669,6 +671,7 @@ static bool readCodeFragment(const char *fileName,
                       int &startLine,int &endLine,QCString &result)
 {
   static bool filterSourceFiles = Config_getBool("FILTER_SOURCE_FILES");
+  static int tabSize = Config_getInt("TAB_SIZE");
   //printf("readCodeFragment(%s,%d,%d)\n",fileName,startLine,endLine);
   if (fileName==0 || fileName[0]==0) return FALSE; // not a valid file name
   QCString filter = getFileFilter(fileName,TRUE);
@@ -717,7 +720,7 @@ static bool readCodeFragment(const char *fileName,
           }
           else if (c=='\t') 
           {
-            col+=Config_getInt("TAB_SIZE") - (col%Config_getInt("TAB_SIZE"));
+            col+=tabSize - (col%tabSize);
           }
           else if (pc=='/' && c=='/') // skip single line comment
           {
@@ -1448,12 +1451,12 @@ QCString Definition::navigationPathAsString() const
   {
     if (definitionType()==Definition::TypeGroup && ((const GroupDef*)this)->groupTitle())
     {
-      result+="<a class=\"el\" href=\""+getOutputFileBase()+Doxygen::htmlFileExtension+"\">"+
+      result+="<a class=\"el\" href=\"$relpath$"+getOutputFileBase()+Doxygen::htmlFileExtension+"\">"+
               ((const GroupDef*)this)->groupTitle()+"</a>";
     }
     else if (definitionType()==Definition::TypePage && !((const PageDef*)this)->title().isEmpty())
     {
-      result+="<a class=\"el\" href=\""+getOutputFileBase()+Doxygen::htmlFileExtension+"\">"+
+      result+="<a class=\"el\" href=\"$relpath$"+getOutputFileBase()+Doxygen::htmlFileExtension+"\">"+
               ((const PageDef*)this)->title()+"</a>";
     }
     else if (definitionType()==Definition::TypeClass)
@@ -1463,13 +1466,13 @@ QCString Definition::navigationPathAsString() const
       {
         name = name.left(name.length()-2);
       }
-      result+="<a class=\"el\" href=\""+getOutputFileBase()+Doxygen::htmlFileExtension;
+      result+="<a class=\"el\" href=\"$relpath$"+getOutputFileBase()+Doxygen::htmlFileExtension;
       if (!anchor().isEmpty()) result+="#"+anchor();
       result+="\">"+name+"</a>";
     }
     else
     {
-      result+="<a class=\"el\" href=\""+getOutputFileBase()+Doxygen::htmlFileExtension+"\">"+
+      result+="<a class=\"el\" href=\"$relpath$"+getOutputFileBase()+Doxygen::htmlFileExtension+"\">"+
               m_impl->localName+"</a>";
     }
   }
@@ -1486,11 +1489,13 @@ void Definition::writeNavigationPath(OutputList &ol) const
   ol.pushGeneratorState();
   ol.disableAllBut(OutputGenerator::Html);
 
-  ol.writeString("<div id=\"nav-path\" class=\"navpath\">\n");
-  ol.writeString("  <ul>\n");
-  ol.writeString(navigationPathAsString());
-  ol.writeString("  </ul>\n");
-  ol.writeString("</div>\n");
+  QCString navPath;
+  navPath += "<div id=\"nav-path\" class=\"navpath\">\n"
+             "  <ul>\n";
+  navPath += navigationPathAsString();
+  navPath += "  </ul>\n"
+             "</div>\n";
+  ol.writeNavigationPath(navPath);
 
   ol.popGeneratorState();
 }
diff --git a/src/definition.h b/src/definition.h
index 116208c..33a5bbb 100644
--- a/src/definition.h
+++ b/src/definition.h
@@ -38,15 +38,7 @@ struct SectionInfo;
 class Definition;
 class DefinitionImpl;
 
-#if 0
-struct ReachableDefinition
-{
-  ReachableDefinition(Definition *d,int dist) : def(d), distance(dist) {}
-  Definition *def;
-  int distance;
-};
-#endif
-
+/** Data associated with a detailed description. */
 struct DocInfo
 {
     QCString doc;  
@@ -54,6 +46,7 @@ struct DocInfo
     QCString file;
 };
 
+/** Data associated with a brief description. */
 struct BriefInfo
 {
     QCString doc;  
@@ -62,14 +55,15 @@ struct BriefInfo
     QCString file;
 };
 
+/** Data associated with description found in the body. */
 struct BodyInfo
 {
-    int      startLine;   // line number of the start of the definition
-    int      endLine;     // line number of the end of the definition
-    FileDef *fileDef;     // file definition containing the function body
+    int      startLine;   //!< line number of the start of the definition
+    int      endLine;     //!< line number of the end of the definition
+    FileDef *fileDef;     //!< file definition containing the function body
 };
     
-/*! Abstract interface for a Definition or DefinitionList */
+/** Abstract interface for a Definition or DefinitionList */
 class DefinitionIntf
 {
   public:
@@ -92,7 +86,8 @@ class DefinitionIntf
     virtual DefType definitionType() const = 0;
 };
 
-/*! The common base class of all entity definitions found in the sources. 
+/** The common base class of all entity definitions found in the sources. 
+ *
  *  This can be a class or a member function, or a file, or a namespace, etc.
  *  Use definitionType() to find which type of definition this is.
  */
@@ -117,7 +112,7 @@ class Definition : public DefinitionIntf, public LockableObj
     const QCString& name() const { return m_name; }
 
     /*! Returns the name of the definition as it appears in the output */
-    virtual QCString displayName() const = 0;
+    virtual QCString displayName(bool includeScope=TRUE) const = 0;
 
     /*! Returns the local name without any scope qualifiers. */
     QCString localName() const;
@@ -362,6 +357,7 @@ class Definition : public DefinitionIntf, public LockableObj
     int m_defLine;
 };
 
+/** A list of Definition objects. */
 class DefinitionList : public QList<Definition>, public DefinitionIntf
 {
   public:
@@ -376,6 +372,7 @@ class DefinitionList : public QList<Definition>, public DefinitionIntf
 
 };
 
+/** An iterator for Definition objects in a DefinitionList. */
 class DefinitionListIterator : public QListIterator<Definition>
 {
   public:
diff --git a/src/diagram.cpp b/src/diagram.cpp
index 07fb4aa..fe6f1f5 100644
--- a/src/diagram.cpp
+++ b/src/diagram.cpp
@@ -36,6 +36,108 @@
 
 //-----------------------------------------------------------------------------
 
+class DiagramItemList;
+
+/** Class representing a single node in the built-in class diagram */
+class DiagramItem 
+{
+  public:
+    DiagramItem(DiagramItem *p,int number,ClassDef *cd,
+                Protection prot,Specifier virt,const char *ts);
+   ~DiagramItem();
+    QCString label() const;
+    QCString fileName() const;
+    DiagramItem *parentItem() { return parent; } 
+    DiagramItemList *getChildren() { return children; }
+    void move(int dx,int dy) { x+=dx; y+=dy; }
+    int xPos() const { return x; }
+    int yPos() const { return y; }
+    int avgChildPos() const;
+    int numChildren() const;
+    void addChild(DiagramItem *di);
+    int number() const { return num; }
+    Protection protection() const { return prot; }
+    Specifier virtualness() const { return virt; }
+    void putInList() { inList=TRUE; }
+    bool isInList() const { return inList; } 
+    ClassDef *getClassDef() const { return classDef; }
+  private:
+    DiagramItemList *children;
+    DiagramItem *parent;
+    int x,y;
+    int num;
+    Protection prot;
+    Specifier virt;
+    QCString templSpec;
+    bool inList;
+    ClassDef *classDef;
+};
+
+/** Class representing a list of DiagramItem object. */
+class DiagramItemList : public QList<DiagramItem>
+{
+  public:
+    DiagramItemList() : QList<DiagramItem>() {}
+   ~DiagramItemList() {}
+};
+
+/** Class representing a row in the built-in class diagram */
+class DiagramRow : public QList<DiagramItem> 
+{
+  public:
+    DiagramRow(TreeDiagram *d,int l) : QList<DiagramItem>() 
+    { 
+      diagram=d; 
+      level=l;
+      setAutoDelete(TRUE); 
+    }
+    void insertClass(DiagramItem *parent,ClassDef *cd,bool doBases,
+                     Protection prot,Specifier virt,const char *ts);
+    uint number() { return level; }
+  private:
+    TreeDiagram *diagram;
+    uint level;
+};
+
+/** Class representing iterator for the rows in the built-in class diagram. */
+class DiagramRowIterator : public QListIterator<DiagramRow>
+{
+  public:
+    DiagramRowIterator(const QList<DiagramRow> &d) 
+      : QListIterator<DiagramRow>(d) {}
+};
+
+/** Class represeting the tree layout for the built-in class diagram. */
+class TreeDiagram : public QList<DiagramRow>
+{
+  public:
+    TreeDiagram(ClassDef *root,bool doBases);
+   ~TreeDiagram();
+    void computeLayout();
+    uint computeRows();
+    //uint computeCols();
+    void moveChildren(DiagramItem *root,int dx);
+    void computeExtremes(uint *labelWidth,uint *xpos);
+    void drawBoxes(FTextStream &t,Image *image,
+                   bool doBase,bool bitmap,
+                   uint baseRows,uint superRows,
+                   uint cellWidth,uint cellHeight,
+                   QCString relPath="",
+                   bool generateMap=TRUE);
+    void drawConnectors(FTextStream &t,Image *image,
+                   bool doBase,bool bitmap,
+                   uint baseRows,uint superRows,
+                   uint cellWidth,uint cellheight);
+  private:
+    bool layoutTree(DiagramItem *root,int row);
+    TreeDiagram &operator=(const TreeDiagram &);
+    TreeDiagram(const TreeDiagram &);
+};
+
+
+
+//-----------------------------------------------------------------------------
+
 const uint maxTreeWidth = 8;
 const int gridWidth  = 100;
 const int gridHeight = 100;
diff --git a/src/diagram.h b/src/diagram.h
index 3e2cac2..e26f16c 100644
--- a/src/diagram.h
+++ b/src/diagram.h
@@ -16,108 +16,17 @@
  *
  */
 
+#ifndef DIAGRAM_H
+#define DIAGRAM_H
+
 #include "qtbc.h"
 #include "types.h"
 
 class ClassDef;
-class DiagramRow;
 class TreeDiagram;
-class ClassDiagram;
-class DiagramItemList;
-class Image;
 class FTextStream;
 
-class DiagramItem 
-{
-  public:
-    DiagramItem(DiagramItem *p,int number,ClassDef *cd,
-                Protection prot,Specifier virt,const char *ts);
-   ~DiagramItem();
-    QCString label() const;
-    QCString fileName() const;
-    DiagramItem *parentItem() { return parent; } 
-    DiagramItemList *getChildren() { return children; }
-    void move(int dx,int dy) { x+=dx; y+=dy; }
-    int xPos() const { return x; }
-    int yPos() const { return y; }
-    int avgChildPos() const;
-    int numChildren() const;
-    void addChild(DiagramItem *di);
-    int number() const { return num; }
-    Protection protection() const { return prot; }
-    Specifier virtualness() const { return virt; }
-    void putInList() { inList=TRUE; }
-    bool isInList() const { return inList; } 
-    ClassDef *getClassDef() const { return classDef; }
-  private:
-    DiagramItemList *children;
-    DiagramItem *parent;
-    int x,y;
-    int num;
-    Protection prot;
-    Specifier virt;
-    QCString templSpec;
-    bool inList;
-    ClassDef *classDef;
-};
-
-class DiagramItemList : public QList<DiagramItem>
-{
-  public:
-    DiagramItemList() : QList<DiagramItem>() {}
-   ~DiagramItemList() {}
-};
-
-class DiagramRow : public QList<DiagramItem> 
-{
-  public:
-    DiagramRow(TreeDiagram *d,int l) : QList<DiagramItem>() 
-    { 
-      diagram=d; 
-      level=l;
-      setAutoDelete(TRUE); 
-    }
-    void insertClass(DiagramItem *parent,ClassDef *cd,bool doBases,
-                     Protection prot,Specifier virt,const char *ts);
-    uint number() { return level; }
-  private:
-    TreeDiagram *diagram;
-    uint level;
-};
-
-class DiagramRowIterator : public QListIterator<DiagramRow>
-{
-  public:
-    DiagramRowIterator(const QList<DiagramRow> &d) 
-      : QListIterator<DiagramRow>(d) {}
-};
-
-class TreeDiagram : public QList<DiagramRow>
-{
-  public:
-    TreeDiagram(ClassDef *root,bool doBases);
-   ~TreeDiagram();
-    void computeLayout();
-    uint computeRows();
-    //uint computeCols();
-    void moveChildren(DiagramItem *root,int dx);
-    void computeExtremes(uint *labelWidth,uint *xpos);
-    void drawBoxes(FTextStream &t,Image *image,
-                   bool doBase,bool bitmap,
-                   uint baseRows,uint superRows,
-                   uint cellWidth,uint cellHeight,
-                   QCString relPath="",
-                   bool generateMap=TRUE);
-    void drawConnectors(FTextStream &t,Image *image,
-                   bool doBase,bool bitmap,
-                   uint baseRows,uint superRows,
-                   uint cellWidth,uint cellheight);
-  private:
-    bool layoutTree(DiagramItem *root,int row);
-    TreeDiagram &operator=(const TreeDiagram &);
-    TreeDiagram(const TreeDiagram &);
-};
-
+/** Class representing a built-in class diagram. */
 class ClassDiagram
 {
   public:
@@ -131,3 +40,6 @@ class ClassDiagram
     TreeDiagram *base;
     TreeDiagram *super;
 };
+
+#endif
+
diff --git a/src/dirdef.cpp b/src/dirdef.cpp
index 4ee4a9a..1114bb8 100644
--- a/src/dirdef.cpp
+++ b/src/dirdef.cpp
@@ -887,79 +887,7 @@ void computeDirDependencies()
     dir->computeDependencies();
   }
 
-#if 0
-  printf("-------------------------------------------------------------\n");
-  // print dependencies (for debugging)
-  for (sdi.toFirst();(dir=sdi.current());++sdi)
-  {
-    if (dir->usedDirs())
-    {
-      QDictIterator<UsedDir> udi(*dir->usedDirs());
-      UsedDir *usedDir;
-      for (udi.toFirst();(usedDir=udi.current());++udi)
-      {
-        printf("%s depends on %s due to ",
-            dir->shortName().data(),usedDir->dir()->shortName().data());
-        QDictIterator<FileDef> fdi(usedDir->files());
-        FileDef *fd;
-        for (fdi.toFirst();(fd=fdi.current());++fdi)
-        {
-          printf("%s ",fd->name().data());
-        }
-        printf("\n");
-      }
-    }
-  }
-  printf("^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^\n");
-#endif
-}
-
-#if 0
-void writeDirDependencyGraph(const char *dirName)
-{
-  QString path;
-  DirDef *dir;
-  DirSDict::Iterator sdi(*Doxygen::directories);
-  QFile htmlPage(QCString(dirName)+"/dirdeps.html");
-  if (htmlPage.open(IO_WriteOnly))
-  {
-    QTextStream out(&htmlPage);
-    out << "<html><body>";
-    for (sdi.toFirst();(dir=sdi.current());++sdi)
-    {
-      path=dirName;
-      path+="/";
-      path+=dir->getOutputFileBase();
-      path+="_dep.dot";
-      out << "<h4>" << dir->displayName() << "</h4>" << endl;
-      out << "<img src=\"" << dir->getOutputFileBase() << "_dep.gif\">" << endl;
-      QFile f(path);
-      if (f.open(IO_WriteOnly))
-      {
-        QTextStream t(&f);
-        dir->writeDepGraph(t);
-      }
-      f.close();
-
-      QCString imgExt = Config_getEnum("DOT_IMAGE_FORMAT");
-      QCString outFile = QCString(dirName)+"/"+
-                         dir->getOutputFileBase()+"_dep."+imgExt; 
-      DotRunner dotRun(path);
-      dotRun.addJob(imgExt,outFile);
-      dotRun.run();
-      
-      //QCString dotArgs(4096);
-      //dotArgs.sprintf("%s -Tgif -o %s",path.data(),outFile.data());
-      //if (portable_system(Config_getString("DOT_PATH")+"dot",dotArgs,FALSE)!=0)
-      //{
-      //  err("Problems running dot. Check your installation!\n");
-      //}
-    }
-    out << "</body></html>";
-  }
-  htmlPage.close();
 }
-#endif
 
 void generateDirDocs(OutputList &ol)
 {
diff --git a/src/dirdef.h b/src/dirdef.h
index e7a6b0e..9a5346c 100644
--- a/src/dirdef.h
+++ b/src/dirdef.h
@@ -34,14 +34,14 @@ class FTextStream;
 
 class DirDef;
 
-/** A list of directories */
+/** A list of directories. */
 class DirList : public QList<DirDef>
 {
   public:
    int compareItems(GCI item1,GCI item2);
 };
 
-/** A directory */
+/** A model of a directory symbol. */
 class DirDef : public Definition
 {
   public:
@@ -54,7 +54,7 @@ class DirDef : public Definition
     QCString anchor() const { return QCString(); }
     bool isLinkableInProject() const;
     bool isLinkable() const;
-    QCString displayName() const { return m_dispName; }
+    QCString displayName(bool=TRUE) const { return m_dispName; }
     QCString shortName() const { return m_shortName; }
     void addSubDir(DirDef *subdir);
     FileList *   getFiles() const        { return m_fileList; }
@@ -105,6 +105,7 @@ class DirDef : public Definition
     QDict<UsedDir> *m_usedDirs;
 };
 
+/** Class representing a pair of FileDef objects */
 class FilePair 
 {
   public:
@@ -116,6 +117,7 @@ class FilePair
     FileDef *m_dst;
 };
 
+/** A sorted dictionary of FilePair objects. */
 class FilePairDict : public SDict<FilePair>
 {
   public:
@@ -123,7 +125,7 @@ class FilePairDict : public SDict<FilePair>
     int compareItems(GCI item1,GCI item2);
 };
 
-/** Usage information of a directory . */
+/** Usage information of a directory. */
 class UsedDir
 {
   public:
@@ -141,7 +143,7 @@ class UsedDir
     bool m_inherited;
 };
 
-/** A usage relation between two direction. */
+/** A usage relation between two directories. */
 class DirRelation
 {
   public:
@@ -163,6 +165,7 @@ inline int DirList::compareItems(GCI item1,GCI item2)
   return stricmp(((DirDef *)item1)->shortName(),((DirDef *)item2)->shortName());
 }
 
+/** A sorted dictionary of DirDef objects. */
 class DirSDict : public SDict<DirDef>
 {
   public:
diff --git a/src/docparser.cpp b/src/docparser.cpp
index abf0943..4beb405 100644
--- a/src/docparser.cpp
+++ b/src/docparser.cpp
@@ -74,6 +74,7 @@ static const char *sectionLevelToName[] =
 static Definition *           g_scope;
 static QCString               g_context;
 static bool                   g_inSeeBlock;
+static bool                   g_xmlComment;
 static bool                   g_insideHtmlLink;
 static QStack<DocNode>        g_nodeStack;
 static QStack<DocStyleChange> g_styleStack;
@@ -95,12 +96,15 @@ static QCString               g_includeFileText;
 static uint                   g_includeFileOffset;
 static uint                   g_includeFileLength;
 
-// parser's context to store all global variables
+
+/** Parser's context to store all global variables. 
+ */
 struct DocParserContext
 {
   Definition *scope;
   QCString context;
   bool inSeeBlock;
+  bool xmlComment;
   bool insideHtmlLink;
   QStack<DocNode> nodeStack;
   QStack<DocStyleChange> styleStack;
@@ -140,6 +144,7 @@ static void docParserPushContext(bool saveParamInfo=TRUE)
   ctx->scope              = g_scope;
   ctx->context            = g_context;
   ctx->inSeeBlock         = g_inSeeBlock;
+  ctx->xmlComment         = g_xmlComment;
   ctx->insideHtmlLink     = g_insideHtmlLink;
   ctx->nodeStack          = g_nodeStack;
   ctx->styleStack         = g_styleStack;
@@ -177,6 +182,7 @@ static void docParserPopContext(bool keepParamInfo=FALSE)
   g_scope               = ctx->scope;
   g_context             = ctx->context;
   g_inSeeBlock          = ctx->inSeeBlock;
+  g_xmlComment          = ctx->xmlComment;
   g_insideHtmlLink      = ctx->insideHtmlLink;
   g_nodeStack           = ctx->nodeStack;
   g_styleStack          = ctx->styleStack;
@@ -646,20 +652,6 @@ static bool insideTable(DocNode *n)
 
 //---------------------------------------------------------------------------
 
-///*! Returns TRUE iff node n is a child of a language node */
-//static bool insideLang(DocNode *n)
-//{
-//  while (n)
-//  {
-//    if (n->kind()==DocNode::Kind_Language) return TRUE;
-//    n=n->parent();
-//  }
-//  return FALSE;
-//}
-
-
-//---------------------------------------------------------------------------
-
 /*! Looks for a documentation block with name commandName in the current
  *  context (g_context). The resulting documentation string is
  *  put in pDoc, the definition in which the documentation was found is
@@ -3593,13 +3585,15 @@ int DocHtmlTable::parseXml()
   return retval==RetVal_EndTable ? RetVal_OK : retval;
 }
 
+/** Helper class to compute the grid for an HTML style table */
 struct ActiveRowSpan
 {
   ActiveRowSpan(int rows,int col) : rowsLeft(rows), column(col) {}
   int rowsLeft;
-  int column;
+  int column;  
 };
 
+/** List of ActiveRowSpan classes. */
 typedef QList<ActiveRowSpan> RowSpanList;
 
 /** determines the location of all cells in a grid, resolving row and
@@ -5577,8 +5571,9 @@ int DocPara::handleHtmlStartTag(const QCString &tagName,const HtmlAttribList &ta
       handleStyleEnter(this,m_children,DocStyleChange::Bold,&g_token->attribs);
       break;
     case HTML_CODE:
-      if (getLanguageFromFileName(g_fileName)==SrcLangExt_CSharp) 
-        // for C# code we treat <code> as an XML tag
+      if (getLanguageFromFileName(g_fileName)==SrcLangExt_CSharp || g_xmlComment) 
+        // for C# source or inside a <summary> or <remark> section we 
+        // treat <code> as an XML tag (so similar to @code)
       {
         doctokenizerYYsetStateXmlCode();
         retval = handleStartCode();
@@ -5719,6 +5714,8 @@ int DocPara::handleHtmlStartTag(const QCString &tagName,const HtmlAttribList &ta
 
     case XML_SUMMARY:
     case XML_REMARKS:
+      g_xmlComment=TRUE;
+      // fall through
     case XML_VALUE:
     case XML_PARA:
       if (!m_children.isEmpty())
@@ -6860,6 +6857,7 @@ DocNode *validatingParseDoc(const char *fileName,int startLine,
   g_styleStack.clear();
   g_initialStyleStack.clear();
   g_inSeeBlock = FALSE;
+  g_xmlComment = FALSE;
   g_insideHtmlLink = FALSE;
   g_includeFileText = "";
   g_includeFileOffset = 0;
@@ -6923,6 +6921,7 @@ DocNode *validatingParseText(const char *input)
   g_styleStack.clear();
   g_initialStyleStack.clear();
   g_inSeeBlock = FALSE;
+  g_xmlComment = FALSE;
   g_insideHtmlLink = FALSE;
   g_includeFileText = "";
   g_includeFileOffset = 0;
diff --git a/src/docparser.h b/src/docparser.h
index ad5dd03..ab7c523 100644
--- a/src/docparser.h
+++ b/src/docparser.h
@@ -79,7 +79,7 @@ void docFindSections(const char *input,
 
 //---------------------------------------------------------------------------
 
-/*! @brief Abstract node interface with type information. */
+/** Abstract node interface with type information. */
 class DocNode
 {
   public:
@@ -167,7 +167,7 @@ class DocNode
     bool m_insidePre;
 };
 
-/*! @brief Default accept implementation for compound nodes in the abstract
+/** Default accept implementation for compound nodes in the abstract
  *  syntax tree.
  */
 template<class T> class CompAccept
@@ -191,7 +191,7 @@ template<class T> class CompAccept
 };
 
 
-/*! @brief Node representing a word 
+/** Node representing a word 
  */
 class DocWord : public DocNode
 {
@@ -205,7 +205,7 @@ class DocWord : public DocNode
     QCString  m_word;
 };
 
-/*! @brief Node representing a word that can be linked to something
+/** Node representing a word that can be linked to something
  */
 class DocLinkedWord : public DocNode
 {
@@ -231,7 +231,7 @@ class DocLinkedWord : public DocNode
     QCString  m_tooltip;
 };
 
-/*! @brief Node representing an URL (or email address) */
+/** Node representing an URL (or email address) */
 class DocURL : public DocNode
 {
   public:
@@ -247,7 +247,7 @@ class DocURL : public DocNode
     bool m_isEmail;
 };
 
-/*! @brief Node representing a line break */
+/** Node representing a line break */
 class DocLineBreak : public DocNode
 {
   public:
@@ -258,7 +258,7 @@ class DocLineBreak : public DocNode
   private:
 };
 
-/*! @brief Node representing a horizonal ruler */
+/** Node representing a horizonal ruler */
 class DocHorRuler : public DocNode
 {
   public:
@@ -269,7 +269,7 @@ class DocHorRuler : public DocNode
   private:
 };
 
-/*! @brief Node representing an anchor */
+/** Node representing an anchor */
 class DocAnchor : public DocNode
 {
   public:
@@ -284,7 +284,7 @@ class DocAnchor : public DocNode
     QCString  m_file;
 };
 
-/*! @brief Node representing a citation of some bibliographic reference */
+/** Node representing a citation of some bibliographic reference */
 class DocCite : public DocNode
 {
   public:
@@ -306,7 +306,7 @@ class DocCite : public DocNode
 };
 
 
-/*! @brief Node representing a style change */
+/** Node representing a style change */
 class DocStyleChange : public DocNode
 {
   public:
@@ -333,7 +333,7 @@ class DocStyleChange : public DocNode
     HtmlAttribList m_attribs;
 };
 
-/*! @brief Node representing a special symbol */
+/** Node representing a special symbol */
 class DocSymbol : public DocNode
 {
   public:
@@ -355,7 +355,7 @@ class DocSymbol : public DocNode
     char     m_letter;
 };
 
-/*! @brief Node representing some amount of white space */
+/** Node representing some amount of white space */
 class DocWhiteSpace : public DocNode
 {
   public:
@@ -368,7 +368,7 @@ class DocWhiteSpace : public DocNode
     QCString  m_chars;
 };
 
-/*! @brief Node representing a verbatim, unparsed text fragment */
+/** Node representing a verbatim, unparsed text fragment */
 class DocVerbatim : public DocNode
 {
   public:
@@ -397,7 +397,7 @@ class DocVerbatim : public DocNode
 };
 
 
-/*! @brief Node representing an included text block from file */
+/** Node representing an included text block from file */
 class DocInclude : public DocNode
 {
   public:
@@ -436,7 +436,7 @@ class DocInclude : public DocNode
     QCString  m_blockId;
 };
 
-/*! @brief Node representing a include/dontinclude operator block */
+/** Node representing a include/dontinclude operator block */
 class DocIncOperator : public DocNode
 {
   public:
@@ -471,7 +471,7 @@ class DocIncOperator : public DocNode
     QCString  m_exampleFile;
 };
 
-/*! @brief Node representing an item of a cross-referenced list */
+/** Node representing an item of a cross-referenced list */
 class DocFormula : public DocNode
 {
   public:
@@ -491,7 +491,7 @@ class DocFormula : public DocNode
     int      m_id;
 };
 
-/*! @brief Node representing an entry in the index. */
+/** Node representing an entry in the index. */
 class DocIndexEntry : public DocNode
 {
   public:
@@ -512,8 +512,8 @@ class DocIndexEntry : public DocNode
 
 //-----------------------------------------------------------------------
 
-/*! @brief Node representing a copy of documentation block. */
-class DocCopy : /*public CompAccept<DocCopy>,*/ public DocNode
+/** Node representing a copy of documentation block. */
+class DocCopy : public DocNode
 {
   public:
     DocCopy(DocNode *parent,const QCString &link,bool copyBrief,bool copyDetails) 
@@ -530,7 +530,7 @@ class DocCopy : /*public CompAccept<DocCopy>,*/ public DocNode
     bool     m_copyDetails;
 };
 
-/*! @brief Node representing an auto List */
+/** Node representing an auto List */
 class DocAutoList : public CompAccept<DocAutoList>, public DocNode
 {
   public:
@@ -548,7 +548,7 @@ class DocAutoList : public CompAccept<DocAutoList>, public DocNode
     int      m_depth;
 };
 
-/*! @brief Node representing an item of a auto list */
+/** Node representing an item of a auto list */
 class DocAutoListItem : public CompAccept<DocAutoListItem>, public DocNode
 {
   public:
@@ -565,7 +565,7 @@ class DocAutoListItem : public CompAccept<DocAutoListItem>, public DocNode
 
 
 
-/*! @brief Node representing a simple section title */
+/** Node representing a simple section title */
 class DocTitle : public CompAccept<DocTitle>, public DocNode
 {
   public:
@@ -578,11 +578,10 @@ class DocTitle : public CompAccept<DocTitle>, public DocNode
   private:
 };
 
-/*! @brief Node representing an item of a cross-referenced list */
+/** Node representing an item of a cross-referenced list */
 class DocXRefItem : public CompAccept<DocXRefItem>, public DocNode
 {
   public:
-    //enum Type { Bug, Test, Todo, Deprecated };
     DocXRefItem(DocNode *parent,int id,const char *key);
     Kind kind() const          { return Kind_XRefItem; }
     QCString file() const       { return m_file; }
@@ -602,7 +601,7 @@ class DocXRefItem : public CompAccept<DocXRefItem>, public DocNode
     QCString  m_relPath;
 };
 
-/*! @brief Node representing an image */
+/** Node representing an image */
 class DocImage : public CompAccept<DocImage>, public DocNode
 {
   public:
@@ -631,7 +630,7 @@ class DocImage : public CompAccept<DocImage>, public DocNode
     QCString  m_url;
 };
 
-/*! @brief Node representing a dot file */
+/** Node representing a dot file */
 class DocDotFile : public CompAccept<DocDotFile>, public DocNode
 {
   public:
@@ -655,7 +654,7 @@ class DocDotFile : public CompAccept<DocDotFile>, public DocNode
     QCString  m_context;
 };
 
-/*! @brief Node representing a msc file */
+/** Node representing a msc file */
 class DocMscFile : public CompAccept<DocMscFile>, public DocNode
 {
   public:
@@ -680,7 +679,7 @@ class DocMscFile : public CompAccept<DocMscFile>, public DocNode
 };
 
 
-/*! @brief Node representing a link to some item */
+/** Node representing a link to some item */
 class DocLink : public CompAccept<DocLink>, public DocNode
 {
   public:
@@ -701,7 +700,7 @@ class DocLink : public CompAccept<DocLink>, public DocNode
     QCString  m_refText;
 };
 
-/*! @brief Node representing a reference to some item */
+/** Node representing a reference to some item */
 class DocRef : public CompAccept<DocRef>, public DocNode
 {
   public:
@@ -730,7 +729,7 @@ class DocRef : public CompAccept<DocRef>, public DocNode
     QCString   m_text;
 };
 
-/*! @brief Node representing an internal reference to some item */
+/** Node representing an internal reference to some item */
 class DocInternalRef : public CompAccept<DocInternalRef>, public DocNode
 {
   public:
@@ -748,24 +747,7 @@ class DocInternalRef : public CompAccept<DocInternalRef>, public DocNode
     QCString   m_anchor;
 };
 
-/*! @brief Node representing a Language specific section */
-//class DocLanguage : public CompAccept<DocLanguage>, public DocNode
-//{
-//  public:
-//    DocLanguage(DocNode *parent,const QCString &id) : 
-//      m_parent(parent), m_id(id) {}
-//    QCString id() const         { return m_id; }
-//    Kind kind() const          { return Kind_Language; }
-//    DocNode *parent() const    { return m_parent; }
-//    void accept(DocVisitor *v) { CompAccept<DocLanguage>::accept(this,v); }
-//    int parse();
-//    
-//  private:
-//    DocNode * m_parent;
-//    QCString   m_id;
-//};
-
-/*! @brief Node representing a Hypertext reference */
+/** Node representing a Hypertext reference */
 class DocHRef : public CompAccept<DocHRef>, public DocNode
 {
   public:
@@ -785,7 +767,7 @@ class DocHRef : public CompAccept<DocHRef>, public DocNode
     QCString   m_relPath;
 };
 
-/*! @brief Node Html heading */
+/** Node Html heading */
 class DocHtmlHeader : public CompAccept<DocHtmlHeader>, public DocNode
 {
   public:
@@ -802,7 +784,7 @@ class DocHtmlHeader : public CompAccept<DocHtmlHeader>, public DocNode
     HtmlAttribList m_attribs;
 };
 
-/*! @brief Node representing a Html description item */
+/** Node representing a Html description item */
 class DocHtmlDescTitle : public CompAccept<DocHtmlDescTitle>, public DocNode
 {
   public:
@@ -817,7 +799,7 @@ class DocHtmlDescTitle : public CompAccept<DocHtmlDescTitle>, public DocNode
     HtmlAttribList m_attribs;
 };
 
-/*! @brief Node representing a Html description list */
+/** Node representing a Html description list */
 class DocHtmlDescList : public CompAccept<DocHtmlDescList>, public DocNode
 {
   public:
@@ -832,7 +814,7 @@ class DocHtmlDescList : public CompAccept<DocHtmlDescList>, public DocNode
     HtmlAttribList m_attribs;
 };
 
-/*! @brief Node representing a normal section */
+/** Node representing a normal section */
 class DocSection : public CompAccept<DocSection>, public DocNode
 {
   public:
@@ -855,7 +837,7 @@ class DocSection : public CompAccept<DocSection>, public DocNode
     QCString  m_file;
 };
 
-/*! @brief Node representing a reference to a section */
+/** Node representing a reference to a section */
 class DocSecRefItem : public CompAccept<DocSecRefItem>, public DocNode
 {
   public:
@@ -874,7 +856,7 @@ class DocSecRefItem : public CompAccept<DocSecRefItem>, public DocNode
     QCString  m_anchor;
 };
 
-/*! @brief Node representing a list of section references */
+/** Node representing a list of section references */
 class DocSecRefList : public CompAccept<DocSecRefList>, public DocNode
 {
   public:
@@ -886,7 +868,7 @@ class DocSecRefList : public CompAccept<DocSecRefList>, public DocNode
   private:
 };
 
-/*! @brief Node representing an internal section of documentation */
+/** Node representing an internal section of documentation */
 class DocInternal : public CompAccept<DocInternal>, public DocNode
 {
   public:
@@ -898,7 +880,7 @@ class DocInternal : public CompAccept<DocInternal>, public DocNode
   private:
 };
 
-/*! @brief Node representing a simple list */
+/** Node representing a simple list */
 class DocSimpleList : public CompAccept<DocSimpleList>, public DocNode
 {
   public:
@@ -910,7 +892,7 @@ class DocSimpleList : public CompAccept<DocSimpleList>, public DocNode
   private:
 };
 
-/*! @brief Node representing a Html list */
+/** Node representing a Html list */
 class DocHtmlList : public CompAccept<DocHtmlList>, public DocNode
 {
   public:
@@ -929,7 +911,7 @@ class DocHtmlList : public CompAccept<DocHtmlList>, public DocNode
     HtmlAttribList m_attribs;
 };
 
-/*! Node representing a simple section */
+/** Node representing a simple section */
 class DocSimpleSect : public CompAccept<DocSimpleSect>, public DocNode
 {
   public:
@@ -954,7 +936,7 @@ class DocSimpleSect : public CompAccept<DocSimpleSect>, public DocNode
     DocTitle *      m_title;
 };
 
-/*! Node representing a separator between two simple sections of the
+/** Node representing a separator between two simple sections of the
  *  same type. 
  */
 class DocSimpleSectSep : public DocNode
@@ -967,7 +949,7 @@ class DocSimpleSectSep : public DocNode
   private:
 };
 
-/*! Node representing a parameter section */
+/** Node representing a parameter section */
 class DocParamSect : public CompAccept<DocParamSect>, public DocNode
 {
     friend class DocParamList;
@@ -998,7 +980,7 @@ class DocParamSect : public CompAccept<DocParamSect>, public DocNode
     bool            m_hasTypeSpecifier;
 };
 
-/*! Node representing a paragraph in the documentation tree */
+/** Node representing a paragraph in the documentation tree */
 class DocPara : public CompAccept<DocPara>, public DocNode
 {
   public:
@@ -1042,7 +1024,7 @@ class DocPara : public CompAccept<DocPara>, public DocNode
     bool     m_isLast;
 };
 
-/*! @brief Node representing a parameter list. */
+/** Node representing a parameter list. */
 class DocParamList : public DocNode
 {
   public:
@@ -1084,7 +1066,7 @@ class DocParamList : public DocNode
     bool                    m_isLast;
 };
 
-/*! @brief Node representing a simple list item */
+/** Node representing a simple list item */
 class DocSimpleListItem : public DocNode
 {
   public:
@@ -1104,7 +1086,7 @@ class DocSimpleListItem : public DocNode
     DocPara *m_paragraph;
 };
 
-/*! @brief Node representing a HTML list item */
+/** Node representing a HTML list item */
 class DocHtmlListItem : public CompAccept<DocHtmlListItem>, public DocNode
 {
   public:
@@ -1122,7 +1104,7 @@ class DocHtmlListItem : public CompAccept<DocHtmlListItem>, public DocNode
     int            m_itemNum;
 };
 
-/*! @brief Node representing a HTML description data */
+/** Node representing a HTML description data */
 class DocHtmlDescData : public CompAccept<DocHtmlDescData>, public DocNode
 {
   public:
@@ -1136,7 +1118,7 @@ class DocHtmlDescData : public CompAccept<DocHtmlDescData>, public DocNode
     HtmlAttribList m_attribs;
 };
 
-/*! @brief Node representing a HTML table cell */
+/** Node representing a HTML table cell */
 class DocHtmlCell : public CompAccept<DocHtmlCell>, public DocNode
 {
     friend class DocHtmlTable;
@@ -1173,7 +1155,7 @@ class DocHtmlCell : public CompAccept<DocHtmlCell>, public DocNode
     int            m_colIdx;
 };
 
-/*! @brief Node representing a HTML table caption */
+/** Node representing a HTML table caption */
 class DocHtmlCaption : public CompAccept<DocHtmlCaption>, public DocNode
 {
   public:
@@ -1189,7 +1171,7 @@ class DocHtmlCaption : public CompAccept<DocHtmlCaption>, public DocNode
     bool           m_atTop;
 };
 
-/*! @brief Node representing a HTML table row */
+/** Node representing a HTML table row */
 class DocHtmlRow : public CompAccept<DocHtmlRow>, public DocNode
 {
     friend class DocHtmlTable;
@@ -1216,7 +1198,7 @@ class DocHtmlRow : public CompAccept<DocHtmlRow>, public DocNode
     int m_rowIdx;
 };
 
-/*! @brief Node representing a HTML table */
+/** Node representing a HTML table */
 class DocHtmlTable : public CompAccept<DocHtmlTable>, public DocNode
 {
   public:
@@ -1239,7 +1221,7 @@ class DocHtmlTable : public CompAccept<DocHtmlTable>, public DocNode
     int m_numCols;
 };
 
-/*! @brief Node representing an HTML blockquote */
+/** Node representing an HTML blockquote */
 class DocHtmlBlockQuote : public CompAccept<DocHtmlBlockQuote>, public DocNode
 {
   public:
@@ -1254,7 +1236,7 @@ class DocHtmlBlockQuote : public CompAccept<DocHtmlBlockQuote>, public DocNode
     HtmlAttribList m_attribs;
 };
 
-/*! @brief Root node of a text fragment */
+/** Root node of a text fragment */
 class DocText : public CompAccept<DocText>, public DocNode
 {
   public:
@@ -1264,7 +1246,7 @@ class DocText : public CompAccept<DocText>, public DocNode
     void parse();
 };
 
-/*! @brief Root node of documentation tree */
+/** Root node of documentation tree */
 class DocRoot : public CompAccept<DocRoot>, public DocNode
 {
   public:
diff --git a/src/docsets.h b/src/docsets.h
index 977991e..799e289 100644
--- a/src/docsets.h
+++ b/src/docsets.h
@@ -25,7 +25,8 @@
 class QFile;
 class Definition;
 
-/*! A class that generates docset files.
+/** A class that generates docset files.
+ *
  *  These files can be used to create context help 
  *  for use within Apple's Xcode 3.0 development environment
  */
diff --git a/src/doctokenizer.h b/src/doctokenizer.h
index 35fdbe2..5036f19 100644
--- a/src/doctokenizer.h
+++ b/src/doctokenizer.h
@@ -63,6 +63,7 @@ enum Tokens
   RetVal_EndBlockQuote  = 0x10014
 };
 
+/** @brief Data associated with a token used by the comment block parser. */
 struct TokenInfo
 {
   // unknown token
diff --git a/src/doctokenizer.l b/src/doctokenizer.l
index d9f845a..ae4c173 100644
--- a/src/doctokenizer.l
+++ b/src/doctokenizer.l
@@ -490,7 +490,7 @@ REFWORD   {LABELID}|{REFWORD2}|{REFWORD3}
                            return TK_LISTITEM;
                          }
                        }
-<St_Para>({BLANK}*\n)+{OLISTITEM}     { /* list item on next line */ 
+<St_Para>{BLANK}*\n{OLISTITEM}     { /* list item on next line */ 
                          if (!Doxygen::markdownSupport)
                          {
                            REJECT;
diff --git a/src/dot.cpp b/src/dot.cpp
index a4cef13..9deae32 100644
--- a/src/dot.cpp
+++ b/src/dot.cpp
@@ -195,6 +195,7 @@ static const char *umlEdgeStyleMap[] =
   "solid"          // usage
 };
 
+/** Helper struct holding the properties of a edge in a dot graph. */
 struct EdgeProperties
 {
   const char * const *edgeColorMap;
@@ -746,6 +747,7 @@ static bool checkDeliverables(const QCString &file1,
 
 //--------------------------------------------------------------------
 
+/** Class representing a list of DotNode objects. */
 class DotNodeList : public QList<DotNode>
 {
   public:
diff --git a/src/dot.h b/src/dot.h
index e4acd5a..ddcd1c3 100644
--- a/src/dot.h
+++ b/src/dot.h
@@ -42,7 +42,7 @@ class DotRunnerQueue;
 
 enum GraphOutputFormat { BITMAP , EPS };
 
-/** @brief Attributes of an edge of a dot graph */
+/** Attributes of an edge of a dot graph */
 struct EdgeInfo
 {
   enum Colors { Blue=0, Green=1, Red=2, Purple=3, Grey=4, Orange=5 };
@@ -56,7 +56,7 @@ struct EdgeInfo
   int m_labColor;
 };
 
-/** @brief A node in a dot graph */
+/** A node in a dot graph */
 class DotNode
 {
   public:
@@ -138,7 +138,7 @@ inline int DotNode::findParent( DotNode *n )
     return m_parents->find(n);
 }
 
-/** @brief Represents a graphical class hierarchy */
+/** Represents a graphical class hierarchy */
 class DotGfxHierarchyTable
 {
   public:
@@ -156,7 +156,7 @@ class DotGfxHierarchyTable
     DotNodeList    *m_rootSubgraphs;
 };
 
-/** @brief Representation of a class inheritance or dependency graph */
+/** Representation of a class inheritance or dependency graph */
 class DotClassGraph
 {
   public:
@@ -188,7 +188,7 @@ class DotClassGraph
     bool               m_lrRank;
 };
 
-/** @brief Representation of an include dependency graph */
+/** Representation of an include dependency graph */
 class DotInclDepGraph
 {
   public:
@@ -215,7 +215,7 @@ class DotInclDepGraph
     bool            m_inverse;
 };
 
-/** @brief Representation of an call graph */
+/** Representation of an call graph */
 class DotCallGraph
 {
   public:
@@ -242,7 +242,7 @@ class DotCallGraph
     Definition *    m_scope;
 };
 
-/** @brief Representation of an directory dependency graph */
+/** Representation of an directory dependency graph */
 class DotDirDeps
 {
   public:
@@ -260,7 +260,7 @@ class DotDirDeps
     DirDef *m_dir;
 };
 
-/** @brief Representation of a group collaboration graph */
+/** Representation of a group collaboration graph */
 class DotGroupCollaboration
 {
   public :
@@ -318,7 +318,7 @@ class DotGroupCollaboration
     QList<Edge>     m_edges;
 };
 
-/** @brief Helper class to run dot from doxygen.
+/** Helper class to run dot from doxygen.
  */
 class DotRunner
 {
@@ -358,7 +358,7 @@ class DotRunner
     CleanupItem m_cleanupItem;
 };
 
-/** @brief Helper class to insert a set of map file into an output file */
+/** Helper class to insert a set of map file into an output file */
 class DotFilePatcher
 {
   public:
@@ -389,6 +389,7 @@ class DotFilePatcher
     QCString m_patchFile;
 };
 
+/** Queue of dot jobs to run. */
 class DotRunnerQueue
 {
   public:
@@ -401,6 +402,7 @@ class DotRunnerQueue
     mutable QMutex  m_mutex;
 };
 
+/** Worker thread to execute a dot run */
 class DotWorkerThread : public QThread
 {
   public:
@@ -413,7 +415,7 @@ class DotWorkerThread : public QThread
     QList<DotRunner::CleanupItem> m_cleanupItems;
 };
 
-/** @brief singleton that manages dot relation actions */
+/** Singleton that manages dot relation actions */
 class DotManager
 {
   public:
diff --git a/src/doxygen.cpp b/src/doxygen.cpp
index fad7102..d942656 100644
--- a/src/doxygen.cpp
+++ b/src/doxygen.cpp
@@ -235,7 +235,7 @@ static void findMember(EntryNav *rootNav,
                        bool isFunc
                       );
 
-
+/** A struct contained the data for an STL class */
 struct STLInfo
 {
   const char *className;
@@ -821,6 +821,7 @@ static void addIncludeFile(ClassDef *cd,FileDef *ifd,Entry *root)
       if (!iName.isEmpty()) // user specified include file
       {
         if (iName.at(0)=='<') local=FALSE; // explicit override
+        else if (iName.at(0)=='"') local=TRUE;
         if (iName.at(0)=='"' || iName.at(0)=='<')
         {
           iName=iName.mid(1,iName.length()-2); // strip quotes or brackets
@@ -2356,12 +2357,16 @@ static MemberDef *addVariableToFile(
          )
         // variable already in the scope
       {
+        bool isPHPArray = md->getLanguage()==SrcLangExt_PHP &&
+                          md->argsString()!=root->args && 
+                          root->args.find('[')!=-1;
+        bool staticsInDifferentFiles = 
+                          root->stat && md->isStatic() && 
+                          root->fileName!=md->getDefFileName();
+
         if (md->getFileDef() &&
-            ! // not a php array
-             (
-               (md->getLanguage()==SrcLangExt_PHP) &&
-               (md->argsString()!=root->args && root->args.find('[')!=-1)
-             )
+            !isPHPArray && // not a php array
+            !staticsInDifferentFiles
            ) 
           // not a php array variable
         {
@@ -2835,7 +2840,7 @@ static void buildTypedefList(EntryNav *rootNav)
 
 static void buildVarList(EntryNav *rootNav)
 {
-  //printf("buildVarList(%s)\n",rootNav->name().data());
+  //printf("buildVarList(%s) section=%08x\n",rootNav->name().data(),rootNav->section());
   int isFuncPtr=-1;
   if (!rootNav->name().isEmpty() &&
       (rootNav->type().isEmpty() || g_compoundKeywordDict.find(rootNav->type())==0) &&
@@ -2877,11 +2882,18 @@ static void addMethodToClass(EntryNav *rootNav,ClassDef *cd,
   Entry *root = rootNav->entry();
   FileDef *fd=rootNav->fileDef();
 
-  int l,i=-1;
+  int l;
   static QRegExp re("([a-z_A-Z0-9: ]*[ &*]+[ ]*");
+  int ts=root->type.find('<');
+  int te=root->type.findRev('>');
+  int i=re.match(root->type,0,&l);
+  if (i!=-1 && ts!=-1 && ts<te && ts<i && i<te) // avoid changing A<int(int*)>, see bug 677315
+  {
+    i=-1;
+  }
 
   if (cd->getLanguage()==SrcLangExt_Cpp && // only C has pointers
-      !root->type.isEmpty() && (i=re.match(root->type,0,&l))!=-1) // function variable
+      !root->type.isEmpty() && i!=-1) // function variable
   {
     root->args+=root->type.right(root->type.length()-i-l);
     root->type=root->type.left(i+l);
@@ -3113,12 +3125,17 @@ static void buildFunctionList(EntryNav *rootNav)
       }
 
       static QRegExp re("([a-z_A-Z0-9: ]*[ &*]+[ ]*");
+      int ts=root->type.find('<');
+      int te=root->type.findRev('>');
+      int ti;
       if (!rootNav->parent()->name().isEmpty() &&
           (rootNav->parent()->section() & Entry::COMPOUND_MASK) && 
           cd &&
           // do some fuzzy things to exclude function pointers 
           (root->type.isEmpty() || 
-           (root->type.find(re,0)==-1 || root->args.find(")[")!=-1) ||     // type contains ..(..* and args not )[.. -> function pointer
+           ((ti=root->type.find(re,0))==-1 ||      // type does not contain ..(..* 
+            (ts!=-1 && ts<te && ts<ti && ti<te) || // outside of < ... >
+           root->args.find(")[")!=-1) ||           // and args not )[.. -> function pointer
            root->type.find(")(")!=-1 || root->type.find("operator")!=-1 || // type contains ..)(.. and not "operator"
            cd->getLanguage()!=SrcLangExt_Cpp                               // language other than C
           )
@@ -3181,11 +3198,16 @@ static void buildFunctionList(EntryNav *rootNav)
                 sameNumTemplateArgs = FALSE;
               }
             }
+
+            bool staticsInDifferentFiles = 
+                    root->stat && md->isStatic() && root->fileName!=md->getDefFileName();
+
             if (
                 matchArguments2(md->getOuterScope(),mfd,mdAl.pointer(),
                                 rnd ? rnd : Doxygen::globalScope,rfd,root->argList,
                                 FALSE) &&
-                sameNumTemplateArgs
+                sameNumTemplateArgs && 
+                !staticsInDifferentFiles
                )
             {
               GroupDef *gd=0;
@@ -5231,7 +5253,6 @@ static bool findGlobalMember(EntryNav *rootNav,
           }
         }
 
-
         //printf("%s<->%s\n",
         //    argListToString(md->argumentList()).data(),
         //    argListToString(root->argList).data());
@@ -5255,7 +5276,7 @@ static bool findGlobalMember(EntryNav *rootNav,
         }
       }
     } 
-    if (!found && root->relatesType != Duplicate) // no match
+    if (!found && root->relatesType != Duplicate && root->section==Entry::FUNCTION_SEC) // no match
     {
       QCString fullFuncDecl=decl;
       if (root->argList) fullFuncDecl+=argListToString(root->argList,TRUE);
@@ -5263,12 +5284,13 @@ static bool findGlobalMember(EntryNav *rootNav,
          QCString("warning: no matching file member found for \n")+substitute(fullFuncDecl,"%","%%");
       if (mn->count()>0)
       {
-        warnMsg+="Possible candidates:\n";
+        warnMsg+="\nPossible candidates:\n";
         for (mni.toFirst();(md=mni.current());++mni)
         {
-          warnMsg+="  ";
+          warnMsg+=" '";
           warnMsg+=substitute(md->declaration(),"%","%%");
-          warnMsg+='\n';
+          warnMsg+="' at line "+QCString().setNum(md->getDefLine())+
+                   " of file"+md->getDefFileName()+"\n";
         }
       }
       warn(root->fileName,root->startLine,warnMsg);
@@ -6003,7 +6025,7 @@ static void findMember(EntryNav *rootNav,
                   LockingPtr<ArgumentList> templAl = md->templateArguments();
                   if (templAl!=0)
                   {
-                    warnMsg+="  template ";
+                    warnMsg+="  'template ";
                     warnMsg+=tempArgListToString(templAl.pointer());
                     warnMsg+='\n';
                   }
@@ -6020,9 +6042,8 @@ static void findMember(EntryNav *rootNav,
                     warnMsg+=md->argsString();
                   if (noMatchCount>1) 
                   {
-                    QCString lineFile;
-                    lineFile.sprintf(" at line %d of file ",md->getDefLine());
-                    warnMsg+=lineFile+md->getDefFileName();
+                    warnMsg+="' at line "+QCString().setNum(md->getDefLine()) +
+                             " of file "+md->getDefFileName();
                   }
 
                   warnMsg+='\n';
@@ -8785,20 +8806,6 @@ static void copyExtraFiles()
 //! parse the list of input files
 static void parseFiles(Entry *root,EntryNav *rootNav)
 {
-#if 0
-  void *cd = 0;
-  QCString inpEncoding = Config_getString("INPUT_ENCODING");
-  bool needsTranscoding = !inpEncoding.isEmpty();
-  if (needsTranscoding)
-  {
-    if (!(cd = portable_iconv_open("UTF-8", inpEncoding)))
-    {
-       err("error: unsupported character enconding: '%s'",inpEncoding.data());
-       exit(1);
-    }
-  }
-#endif
-
   QCString *s=g_inputFiles.first();
   while (s)
   {
@@ -10293,18 +10300,6 @@ void parseInput()
    *             Parse source files                                         * 
    **************************************************************************/
 
-  //printNavTree(rootNav,0);
-
-  // we are done with input scanning now, so free up the buffers used by flex
-  // (can be around 4MB)
-  preFreeScanner();
-  scanFreeScanner();
-  pyscanFreeScanner();
-
-  //delete rootNav;
-  //g_storage.close();
-  //exit(1);
-
   if (Config_getBool("BUILTIN_STL_SUPPORT"))
   {
     addSTLClasses(rootNav);
@@ -10312,6 +10307,13 @@ void parseInput()
 
   parseFiles(root,rootNav);
   g_storage->close();
+
+  // we are done with input scanning now, so free up the buffers used by flex
+  // (can be around 4MB)
+  preFreeScanner();
+  scanFreeScanner();
+  pyscanFreeScanner();
+
   if (!g_storage->open(IO_ReadOnly))
   {
     err("Failed to open temporary storage file %s for reading",
@@ -10530,6 +10532,13 @@ void parseInput()
 
   msg("Adding members to index pages...\n");
   addMembersToIndex();
+
+  if (Config_getBool("OPTIMIZE_OUTPUT_VHDL") && 
+      Config_getBool("HAVE_DOT") &&
+      Config_getEnum("DOT_IMAGE_FORMAT")=="svg")
+  {
+    VhdlDocGen::writeOverview();
+  }
 }
 
 void generateOutput()
diff --git a/src/doxygen.css b/src/doxygen.css
index 32d4d9c..6ce8bb9 100644
--- a/src/doxygen.css
+++ b/src/doxygen.css
@@ -184,8 +184,24 @@ div.line {
 	padding-left: 53px;
 	padding-bottom: 0px;
 	margin: 0px;
+	-webkit-transition-property: background-color, box-shadow;
+	-webkit-transition-duration: 0.5s;
+	-moz-transition-property: background-color, box-shadow;
+	-moz-transition-duration: 0.5s;
+	-ms-transition-property: background-color, box-shadow;
+	-ms-transition-duration: 0.5s;
+	-o-transition-property: background-color, box-shadow;
+	-o-transition-duration: 0.5s;
+	transition-property: background-color, box-shadow;
+	transition-duration: 0.5s;
 }
 
+div.line.glow {
+	background-color: cyan;
+	box-shadow: 0 0 10px cyan;
+}
+
+
 span.lineno {
 	padding-right: 4px;
 	text-align: right;
@@ -486,6 +502,8 @@ table.memberdecls {
         -ms-transition: box-shadow 0.5s linear;
         -o-transition: box-shadow 0.5s linear;
         transition: box-shadow 0.5s linear;
+        display: table !important;
+        width: 100%;
 }
 
 .memitem.glow {
@@ -575,6 +593,9 @@ dl.reflist dd {
 .paramname em {
 	font-style: normal;
 }
+.paramname code {
+        line-height: 14px;
+}
 
 .params, .retval, .exception, .tparams {
         margin-left: 0px;
@@ -662,6 +683,10 @@ div.directory {
         outline:none;
 }
 
+.directory td.entry a img {
+        border: none;
+}
+
 .directory td.desc {
         width: 100%;
         padding-left: 6px;
@@ -857,9 +882,7 @@ div.summary a
 
 div.ingroups
 {
-	margin-left: 5px;
 	font-size: 8pt;
-	padding-left: 5px;
 	width: 50%;
 	text-align: left;
 }
diff --git a/src/doxygen.md b/src/doxygen.md
new file mode 100644
index 0000000..6931329
--- /dev/null
+++ b/src/doxygen.md
@@ -0,0 +1,59 @@
+Doxygen Internals {#mainpage}
+=================
+
+Introduction
+------------
+
+This page provides a high-level overview of the internals of doxygen, with
+links to the relevant parts of the code.
+
+The generic starting point of the application is ofcource the main() function.
+
+Configuration options
+---------------------
+
+Configuration file data is stored in singleton class Config and can be
+accessed using wrapper macros 
+Config_getString(), Config_getInt(), Config_getList(),
+Config_getEnum(), and Config_getBool() depending on the type of the
+option. 
+
+The format of the configuration file (options and types) is defined
+by the file `config.xml`. As part of the build process, 
+the python script `configgen.py` will create a file configoptions.cpp 
+from this, which serves as the input for the configuration file parser
+that is invoked using Config::parse()
+
+Gathering Input files
+---------------------
+
+After the configuration is known, the input files are searched using
+searchInputFiles() and any tag files are read using readTagFile()
+
+Parsing Input files
+-------------------
+
+The function parseFiles() takes care of parsing all files.
+It uses the ParserManager singleton factory to create a suitable parser object
+for each file. Each parser implements the abstract interface ParserInterface.
+
+If the parser indicates it needs preprocessing
+via ParserInterface::needsPreprocessing(), doxygen will call preprocessFile()
+on the file before calling ParserInterface::parseInput().
+
+The result of parsing is a tree of Entry objects 
+These Entry objects are wrapped in a EntryNav object and stored on disk using
+Entry::createNavigationIndex() on the root node of the tree.
+
+Each Entry object roughly contains the raw data for a symbol and is later
+converted into a Definition object.
+
+When a parser finds a special comment block in the input, it will do a first
+pass parsing via parseCommentBlock(). During this pass the comment block
+is split into multiple parts if needed. Some data that is later needed is
+extracted like section labels, xref items, and formulas. 
+Also Markdown markup is processed using processMarkdown() during this pass.
+
+
+
+
diff --git a/src/doxygen_css.h b/src/doxygen_css.h
index e883f8e..0c4f9c1 100644
--- a/src/doxygen_css.h
+++ b/src/doxygen_css.h
@@ -184,8 +184,24 @@
 "	padding-left: 53px;\n"
 "	padding-bottom: 0px;\n"
 "	margin: 0px;\n"
+"	-webkit-transition-property: background-color, box-shadow;\n"
+"	-webkit-transition-duration: 0.5s;\n"
+"	-moz-transition-property: background-color, box-shadow;\n"
+"	-moz-transition-duration: 0.5s;\n"
+"	-ms-transition-property: background-color, box-shadow;\n"
+"	-ms-transition-duration: 0.5s;\n"
+"	-o-transition-property: background-color, box-shadow;\n"
+"	-o-transition-duration: 0.5s;\n"
+"	transition-property: background-color, box-shadow;\n"
+"	transition-duration: 0.5s;\n"
 "}\n"
 "\n"
+"div.line.glow {\n"
+"	background-color: cyan;\n"
+"	box-shadow: 0 0 10px cyan;\n"
+"}\n"
+"\n"
+"\n"
 "span.lineno {\n"
 "	padding-right: 4px;\n"
 "	text-align: right;\n"
@@ -486,6 +502,8 @@
 "        -ms-transition: box-shadow 0.5s linear;\n"
 "        -o-transition: box-shadow 0.5s linear;\n"
 "        transition: box-shadow 0.5s linear;\n"
+"        display: table !important;\n"
+"        width: 100%;\n"
 "}\n"
 "\n"
 ".memitem.glow {\n"
@@ -575,6 +593,9 @@
 ".paramname em {\n"
 "	font-style: normal;\n"
 "}\n"
+".paramname code {\n"
+"        line-height: 14px;\n"
+"}\n"
 "\n"
 ".params, .retval, .exception, .tparams {\n"
 "        margin-left: 0px;\n"
@@ -662,6 +683,10 @@
 "        outline:none;\n"
 "}\n"
 "\n"
+".directory td.entry a img {\n"
+"        border: none;\n"
+"}\n"
+"\n"
 ".directory td.desc {\n"
 "        width: 100%;\n"
 "        padding-left: 6px;\n"
@@ -857,9 +882,7 @@
 "\n"
 "div.ingroups\n"
 "{\n"
-"	margin-left: 5px;\n"
 "	font-size: 8pt;\n"
-"	padding-left: 5px;\n"
 "	width: 50%;\n"
 "	text-align: left;\n"
 "}\n"
diff --git a/src/eclipsehelp.h b/src/eclipsehelp.h
index cbae366..2531a9f 100644
--- a/src/eclipsehelp.h
+++ b/src/eclipsehelp.h
@@ -32,8 +32,7 @@
 class QFile;
 class Definition;
 
-/*!
- * \brief Generator of Eclipse help files
+/** Generator for Eclipse help files.
  *
  * This class generates the Eclipse specific help files.
  * These files can be used to generate a help plugin readable
diff --git a/src/entry.h b/src/entry.h
index d312cec..9a39963 100644
--- a/src/entry.h
+++ b/src/entry.h
@@ -33,7 +33,7 @@ class StorageIntf;
 class ArgumentList;
 struct ListItemInfo;
 
-/*! \brief This class stores information about an inheritance relation
+/** This class stores information about an inheritance relation
  */ 
 struct BaseInfo 
 {
@@ -45,8 +45,8 @@ struct BaseInfo
   Specifier  virt; //!< virtualness
 };
 
-/*! \brief This struct is used to capture the tag file information 
- *         for an Entry. 
+/** This struct is used to capture the tag file information 
+ *  for an Entry. 
  */
 struct TagInfo 
 {
@@ -55,8 +55,8 @@ struct TagInfo
   QCString anchor;
 };
 
-/*! \brief Represents an unstructured piece of information, about an
- *         entity found in the sources. 
+/** Represents an unstructured piece of information, about an
+ *  entity found in the sources. 
  *
  *  parseMain() in scanner.l will generate a tree of these
  *  entries.
@@ -137,9 +137,11 @@ class Entry
       Copy        = 0x00080000,
       Retain      = 0x00100000,
       Assign      = 0x00200000,
-      Composition = 0x00400000,
-      Aggregation = 0x00800000,
-      Association = 0x01000000
+      Strong      = 0x00400000,
+      Weak        = 0x00800000,
+      Composition = 0x01000000,
+      Aggregation = 0x02000000,
+      Association = 0x04000000
     };
     enum ClassSpecifier
     {
@@ -299,6 +301,11 @@ class Entry
     Entry &operator=(const Entry &); 
 };
 
+/** Wrapper for a node in the Entry tree.
+ *
+ *  Allows navigating through the Entry tree and load and storing Entry
+ *  objects persistently to disk.
+ */
 class EntryNav
 {
   public:
diff --git a/src/example.h b/src/example.h
index a780326..2ee1429 100644
--- a/src/example.h
+++ b/src/example.h
@@ -24,6 +24,7 @@
 class ClassDef;
 class MemberName;
 
+/** Data associated with an example. */
 struct Example
 {
   QCString anchor;
@@ -31,6 +32,7 @@ struct Example
   QCString file;
 };
 
+/** A sorted dictionary of Example objects. */
 class ExampleSDict : public SDict<Example>
 {
   public:
diff --git a/src/filedef.cpp b/src/filedef.cpp
index c0aa4cf..674cc89 100644
--- a/src/filedef.cpp
+++ b/src/filedef.cpp
@@ -40,6 +40,7 @@
 
 //---------------------------------------------------------------------------
 
+/** Class implementing CodeOutputInterface by throwing away everything. */
 class DevNullCodeDocInterface : public CodeOutputInterface
 {
   public:
diff --git a/src/filedef.h b/src/filedef.h
index 08b8480..2368b36 100644
--- a/src/filedef.h
+++ b/src/filedef.h
@@ -40,6 +40,7 @@ class MemberGroupSDict;
 class PackageDef;
 class DirDef;
 
+/** Class representing the data associated with a \#include statement. */
 struct IncludeInfo
 {
   IncludeInfo() { fileDef=0; local=FALSE; indirect=FALSE; }
@@ -51,16 +52,14 @@ struct IncludeInfo
   bool indirect;
 };
 
-/*! \class FileDef filedef.h
-    \brief A File definition.
-    
-    An object of this class contains all file information that is gathered.
-    This includes the members and compounds defined in the file.
-    
-    The member writeDocumentation() can be used to generate the page of
-    documentation to HTML and LaTeX.
-*/
-
+/** A model of a file symbol. 
+ *   
+ *  An object of this class contains all file information that is gathered.
+ *  This includes the members and compounds defined in the file.
+ *   
+ *  The member writeDocumentation() can be used to generate the page of
+ *  documentation to HTML and LaTeX.
+ */
 class FileDef : public Definition
 {
   friend class FileName;
@@ -80,7 +79,7 @@ class FileDef : public Definition
       else 
         return Definition::name(); 
     } 
-    QCString displayName() const { return name(); }
+    QCString displayName(bool=TRUE) const { return name(); }
     QCString fileName() const { return filename; }
     
     QCString getOutputFileBase() const 
@@ -221,8 +220,6 @@ class FileDef : public Definition
     QIntDict<Definition> *srcDefDict;
     QIntDict<MemberDef>  *srcMemberDict;
     bool                  isSource;
-    //bool                  m_isJava;
-    //bool                  m_isCSharp;
     QCString              fileVersion;
     PackageDef           *package;
     DirDef               *dir;
@@ -233,7 +230,7 @@ class FileDef : public Definition
     bool                  m_subGrouping;
 };
 
-
+/** Class representing a list of FileDef objects. */
 class FileList : public QList<FileDef>
 {
   public:
@@ -273,6 +270,7 @@ class OutputNameDict : public QDict<FileList>
 
 class Directory;
 
+/** Class representing an entry (file or sub directory) in a directory */
 class DirEntry
 {
   public:
@@ -303,6 +301,7 @@ class DirEntry
     bool m_isLast;
 };
 
+/** Class representing a directory tree of DirEntry objects. */
 class Directory : public DirEntry
 {
   public:
@@ -319,7 +318,6 @@ class Directory : public DirEntry
     QList<DirEntry> m_children;
 };
 
-//void generateFileTree(QTextStream &t);
 void generateFileTree();
 
 #endif
diff --git a/src/filename.h b/src/filename.h
index 29e90c0..e305e0e 100644
--- a/src/filename.h
+++ b/src/filename.h
@@ -22,6 +22,7 @@
 #include <qdict.h>
 #include "filedef.h"
 
+/** Class representing all files with a certain base name */
 class FileName : public FileList
 { 
   public:
@@ -37,12 +38,14 @@ class FileName : public FileList
     QCString fName;
 };
 
+/** Iterator for FileDef objects in a FileName list. */
 class FileNameIterator : public QListIterator<FileDef>
 {
   public:
     FileNameIterator(const FileName &list);
 };
 
+/** Class representing a list of FileName objects. */
 class FileNameList : public QList<FileName>
 {
   public:
@@ -52,12 +55,14 @@ class FileNameList : public QList<FileName>
     int compareItems(GCI item1,GCI item2);
 };
 
+/** Iterator for FileName objects in a FileNameList. */
 class FileNameListIterator : public QListIterator<FileName>
 {
   public:
     FileNameListIterator( const FileNameList &list );
 };
 
+/** Unsorted dictionary of FileName objects. */
 class FileNameDict : public QDict<FileName>
 {
   public:
diff --git a/src/formula.h b/src/formula.h
index ca68e6e..a912b76 100644
--- a/src/formula.h
+++ b/src/formula.h
@@ -22,6 +22,7 @@
 #include <qlist.h>
 #include <qdict.h>
 
+/** Class representing a formula in the output. */
 class Formula
 {
   public:
@@ -35,12 +36,14 @@ class Formula
     QCString form;
 };
 
+/** A list of Formula objects. */
 class FormulaList : public QList<Formula>
 {
   public:
     void generateBitmaps(const char *path);
 };
 
+/** Iterator for Formula objects in a FormulaList. */
 class FormulaListIterator : public QListIterator<Formula>
 {
   public:
@@ -48,6 +51,7 @@ class FormulaListIterator : public QListIterator<Formula>
       QListIterator<Formula>(l) {}
 };
 
+/** Unsorted dictionary of Formula objects. */
 class FormulaDict : public QDict<Formula>
 {
   public:
diff --git a/src/fortrancode.l b/src/fortrancode.l
index 4de3bf2..d8c788e 100644
--- a/src/fortrancode.l
+++ b/src/fortrancode.l
@@ -270,6 +270,7 @@ static void codifyLines(char *text)
   char *p=text,*sp=p;
   char c;
   bool done=FALSE;
+  const char *  tmp_currentFontClass = g_currentFontClass;
   while (!done)
   {
     sp=p;
@@ -284,6 +285,10 @@ static void codifyLines(char *text)
       {
 	startCodeLine();
       }
+      if (tmp_currentFontClass)
+      {
+        startFontClass(tmp_currentFontClass);
+      }
     }
     else
     {
@@ -923,7 +928,12 @@ PREFIX    (RECURSIVE{BS_}|PURE{BS_}|ELEMENTAL{BS_}){0,2}(RECURSIVE|PURE|ELEMENTA
                                         }
 
  /*-------- comments ---------------------------------------------------*/
-<Start>\n?{BS}"!>"                      { // start comment line or comment block
+<Start>\n?{BS}"!>"|"!<"                 { // start comment line or comment block
+                                          yy_push_state(YY_START);
+					  BEGIN(DocBlock);
+                                          docBlock=yytext;
+					}
+<Declaration>{BS}"!<"                   { // start comment line or comment block
                                           yy_push_state(YY_START);
 					  BEGIN(DocBlock);
                                           docBlock=yytext;
@@ -932,7 +942,7 @@ PREFIX    (RECURSIVE{BS_}|PURE{BS_}|ELEMENTAL{BS_}){0,2}(RECURSIVE|PURE|ELEMENTA
 <DocBlock>.*    			{ // contents of current comment line
                                           docBlock+=yytext;
   					}
-<DocBlock>"\n"{BS}("!>"|"!"+)		{ //| comment block (next line is also comment line)
+<DocBlock>"\n"{BS}("!>"|"!<"|"!!")	{ //| comment block (next line is also comment line)
 					  docBlock+=yytext; 
    					}
 <DocBlock>"\n"        			{ // comment block ends at the end of this line
@@ -956,7 +966,7 @@ PREFIX    (RECURSIVE{BS_}|PURE{BS_}|ELEMENTAL{BS_}){0,2}(RECURSIVE|PURE|ELEMENTA
                                          yy_pop_state();
 					}
 
-<*>"!"[^>\n].*|"!"$ 			{ // normal comment
+<*>"!"[^><\n].*|"!"$ 			{ // normal comment
 					  if(YY_START == String) REJECT; // ignore in strings
   					  startFontClass("comment");
   					  codifyLines(yytext);
diff --git a/src/ftvhelp.cpp b/src/ftvhelp.cpp
index 85caa36..c180c4e 100644
--- a/src/ftvhelp.cpp
+++ b/src/ftvhelp.cpp
@@ -722,7 +722,7 @@ void FTVHelp::addContentsItem(bool isDir,
                               Definition *def
                               )
 {
-  //printf("addContentsItem(%s,%s,%s,%s)\n",name,ref,file,anchor);
+  //printf("%p: m_indent=%d addContentsItem(%s,%s,%s,%s)\n",this,m_indent,name,ref,file,anchor);
   QList<FTVNode> *nl = &m_indentNodes[m_indent];
   FTVNode *newNode = new FTVNode(isDir,ref,file,anchor,name,separateIndex,addToNavIndex,def);
   if (!nl->isEmpty())
@@ -1053,9 +1053,18 @@ static void generateJSLink(FTextStream &t,FTVNode *n)
   }
 }
 
+static QCString convertFileId2Var(const QCString &fileId)
+{
+  QCString varId = fileId;
+  int i=varId.findRev('/');
+  if (i>=0) varId = varId.mid(i+1);
+  return substitute(varId,"-","_");
+}
+
 static bool generateJSTree(NavIndexEntryList &navIndex,FTextStream &t, 
                            const QList<FTVNode> &nl,int level,bool &first)
 {
+  static QCString htmlOutput = Config_getString("HTML_OUTPUT");
   QCString indentStr;
   indentStr.fill(' ',level*2);
   bool found=FALSE;
@@ -1088,18 +1097,14 @@ static bool generateJSTree(NavIndexEntryList &navIndex,FTextStream &t,
       {
         QCString fileId = n->file;
         if (dupOfParent(n)) fileId+="_dup";
-        QFile f(Config_getString("HTML_OUTPUT")+"/"+fileId+".js");
+        QFile f(htmlOutput+"/"+fileId+".js");
         if (f.open(IO_WriteOnly))
         {
           FTextStream tt(&f);
-          QCString varId = fileId;
-          int i=fileId.findRev('/');
-          if (i>=0) varId = varId.mid(i+1);
-          tt << "var " << varId << " =" << endl;
+          tt << "var " << convertFileId2Var(fileId) << " =" << endl;
           generateJSTree(navIndex,tt,n->children,1,firstChild);
           tt << endl << "];"; 
         }
-        // write file name without extension as marker
         t << "\"" << fileId << "\" ]";
       }
       else // no children
@@ -1167,54 +1172,54 @@ static void generateJSNavTree(const QList<FTVNode> &nodeList)
       t << "]" << endl;
     else 
       t << endl << "  ] ]" << endl;
-    t << "];" << endl;
-    t << endl << navtree_script;
-  }
-
-  // write the navigation index (and sub-indices)
-  navIndex.sort();
-  int subIndex=0;
-  int elemCount=0;
-  const int maxElemCount=250;
-  QFile fidx(htmlOutput+"/navtreeindex.js");
-  QFile fsidx(htmlOutput+"/navtreeindex0.js");
-  if (fidx.open(IO_WriteOnly) && fsidx.open(IO_WriteOnly))
-  {
-    FTextStream tidx(&fidx);
-    FTextStream tsidx(&fsidx);
-    tidx << "var NAVTREEINDEX =" << endl;
-    tidx << "[" << endl;
-    tsidx << "var NAVTREEINDEX" << subIndex << " =" << endl;
-    tsidx << "{" << endl;
-    QListIterator<NavIndexEntry> li(navIndex);
-    NavIndexEntry *e;
-    for (li.toFirst();(e=li.current());) // for each entry
+    t << "];" << endl << endl;
+
+    // write the navigation index (and sub-indices)
+    navIndex.sort();
+    int subIndex=0;
+    int elemCount=0;
+    const int maxElemCount=250;
+    //QFile fidx(htmlOutput+"/navtreeindex.js");
+    QFile fsidx(htmlOutput+"/navtreeindex0.js");
+    if (/*fidx.open(IO_WriteOnly) &&*/ fsidx.open(IO_WriteOnly))
     {
-      if (elemCount==0)
-      {
-        tidx << "\"" << e->url << "\"," << endl;
-      }
-      tsidx << "\"" << e->url << "\":[" << e->path << "]";
-      ++li;
-      if (li.current()) tsidx << ","; // not last entry
-      tsidx << endl;
-
-      elemCount++;
-      if (li.current() && elemCount>=maxElemCount) // switch to new sub-index
+      //FTextStream tidx(&fidx);
+      FTextStream tsidx(&fsidx);
+      t << "var NAVTREEINDEX =" << endl;
+      t << "[" << endl;
+      tsidx << "var NAVTREEINDEX" << subIndex << " =" << endl;
+      tsidx << "{" << endl;
+      QListIterator<NavIndexEntry> li(navIndex);
+      NavIndexEntry *e;
+      for (li.toFirst();(e=li.current());) // for each entry
       {
-        tsidx << "};" << endl;
-        elemCount=0;
-        fsidx.close();
-        subIndex++;
-        fsidx.setName(htmlOutput+"/navtreeindex"+QCString().setNum(subIndex)+".js");
-        if (!fsidx.open(IO_WriteOnly)) break;
-        tsidx.setDevice(&fsidx);
-        tsidx << "var NAVTREEINDEX" << subIndex << " =" << endl;
-        tsidx << "{" << endl;
+        if (elemCount==0)
+        {
+          t << "\"" << e->url << "\"," << endl;
+        }
+        tsidx << "\"" << e->url << "\":[" << e->path << "]";
+        ++li;
+        if (li.current()) tsidx << ","; // not last entry
+        tsidx << endl;
+  
+        elemCount++;
+        if (li.current() && elemCount>=maxElemCount) // switch to new sub-index
+        {
+          tsidx << "};" << endl;
+          elemCount=0;
+          fsidx.close();
+          subIndex++;
+          fsidx.setName(htmlOutput+"/navtreeindex"+QCString().setNum(subIndex)+".js");
+          if (!fsidx.open(IO_WriteOnly)) break;
+          tsidx.setDevice(&fsidx);
+          tsidx << "var NAVTREEINDEX" << subIndex << " =" << endl;
+          tsidx << "{" << endl;
+        }
       }
+      tsidx << "};" << endl;
+      t << "];" << endl;
     }
-    tsidx << "};" << endl;
-    tidx << "];" << endl;
+    t << endl << navtree_script;
   }
 }
 
diff --git a/src/ftvhelp.h b/src/ftvhelp.h
index 1169238..8f24b3d 100644
--- a/src/ftvhelp.h
+++ b/src/ftvhelp.h
@@ -34,7 +34,7 @@ class Definition;
 struct FTVNode;
 class FTextStream;
 
-/*! A class that generates a dynamic tree view side panel.
+/** A class that generates a dynamic tree view side panel.
  */
 class FTVHelp : public IndexIntf
 {
diff --git a/src/groupdef.h b/src/groupdef.h
index 5c83b81..6b41979 100644
--- a/src/groupdef.h
+++ b/src/groupdef.h
@@ -42,6 +42,7 @@ class DirList;
 class FTVHelp;
 class Entry;
 
+/** A model of a group of symbols. */
 class GroupDef : public Definition
 {
   public:
@@ -50,7 +51,7 @@ class GroupDef : public Definition
     DefType definitionType() const { return TypeGroup; }
     QCString getOutputFileBase() const;
     QCString anchor() const { return QCString(); }
-    QCString displayName() const { return hasGroupTitle() ? title : Definition::name(); }
+    QCString displayName(bool=TRUE) const { return hasGroupTitle() ? title : Definition::name(); }
     const char *groupTitle() const { return title; }
     void setGroupTitle( const char *newtitle );
     bool hasGroupTitle( ) const { return titleSet; }
@@ -153,6 +154,7 @@ class GroupDef : public Definition
 
 };
 
+/** A sorted dictionary of GroupDef objects. */
 class GroupSDict : public SDict<GroupDef>
 {
   public:
@@ -164,6 +166,7 @@ class GroupSDict : public SDict<GroupDef>
     }
 };
 
+/** A list of GroupDef objects. */
 class GroupList : public QList<GroupDef>
 {
   public:
@@ -173,6 +176,7 @@ class GroupList : public QList<GroupDef>
     }
 };
 
+/** An iterator for GroupDef objects in a GroupList. */
 class GroupListIterator : public QListIterator<GroupDef>
 {
   public:
diff --git a/src/growbuf.h b/src/growbuf.h
index 6798692..f1bf315 100644
--- a/src/growbuf.h
+++ b/src/growbuf.h
@@ -4,6 +4,7 @@
 #include <stdlib.h>
 #include <string.h>
 
+/** Class representing a string buffer optimised for growing. */
 class GrowBuf
 {
   public:
diff --git a/src/htags.h b/src/htags.h
index 458adec..4a164a6 100644
--- a/src/htags.h
+++ b/src/htags.h
@@ -17,6 +17,7 @@
 
 class QCString;
 
+/** This class is a namespace for HTAGS related functions */
 struct Htags
 {
   static bool useHtags;
diff --git a/src/htmldocvisitor.cpp b/src/htmldocvisitor.cpp
index c3bdd9f..e048858 100644
--- a/src/htmldocvisitor.cpp
+++ b/src/htmldocvisitor.cpp
@@ -572,8 +572,8 @@ void HtmlDocVisitor::visit(DocFormula *f)
     m_t << "\" alt=\"";
     filterQuotedCdataAttr(f->text());
     m_t << "\"";
-    /// @todo cache image dimensions on formula generation and give height/width
-    /// for faster preloading and better rendering of the page
+    // TODO: cache image dimensions on formula generation and give height/width
+    // for faster preloading and better rendering of the page
     m_t << " src=\"" << f->relPath() << f->name() << ".png\"/>";
 
   }
diff --git a/src/htmlgen.cpp b/src/htmlgen.cpp
index 63bff45..6cf31ad 100644
--- a/src/htmlgen.cpp
+++ b/src/htmlgen.cpp
@@ -2722,6 +2722,11 @@ void HtmlGenerator::writeSplitBar(const char *name)
   t << writeSplitBarAsString(name,relPath);
 }
 
+void HtmlGenerator::writeNavigationPath(const char *s)
+{
+  t << substitute(s,"$relpath$",relPath);
+}
+
 void HtmlGenerator::startContents()
 {
   t << "<div class=\"contents\">" << endl;
@@ -3037,14 +3042,21 @@ void HtmlGenerator::endLabels()
   t << "</span>";
 }
 
-void HtmlGenerator::writeInheritedSectionTitle(const char *id,
-                  const char *file,const char *anchor,const char *title,
-                  const char *name)
+void HtmlGenerator::writeInheritedSectionTitle(
+                  const char *id,    const char *ref, 
+                  const char *file,  const char *anchor,
+                  const char *title, const char *name)
 {
   DBG_HTML(t << "<!-- writeInheritedSectionTitle -->" << endl;)
   QCString a = anchor;
   if (!a.isEmpty()) a.prepend("#");
-  QCString classLink = QCString("<a class=\"el\" href=\"")+correctURL(file,relPath)+Doxygen::htmlFileExtension+a+"\">"+name+"</a>";
+  QCString classLink = QCString("<a class=\"el\" href=\"");
+  if (ref)
+  {
+    classLink+= externalLinkTarget() + externalRef(relPath,ref,TRUE);
+  }
+  classLink+=file+Doxygen::htmlFileExtension+a;
+  classLink+=QCString("\">")+name+"</a>";
   t << "<tr class=\"inherit_header " << id << "\">"
     << "<td colspan=\"2\" onclick=\"javascript:toggleInherit('" << id << "')\">"
     << "<img src=\"" << relPath << "closed.png\" alt=\"-\"/>&nbsp;" 
diff --git a/src/htmlgen.h b/src/htmlgen.h
index 58c534c..83599f4 100644
--- a/src/htmlgen.h
+++ b/src/htmlgen.h
@@ -29,6 +29,7 @@
 class QFile;
 class FTextStream;
 
+/** Generator for HTML output */
 class HtmlGenerator : public OutputGenerator
 {
   public:
@@ -137,8 +138,9 @@ class HtmlGenerator : public OutputGenerator
     void insertMemberAlign(bool);
     void startMemberDescription(const char *anchor,const char *inheritId);
     void endMemberDescription();
-    void writeInheritedSectionTitle(const char *id,const char *file,
-                      const char *anchor,const char *title,const char *name);
+    void writeInheritedSectionTitle(const char *id,   const char *ref,
+                                    const char *file, const char *anchor,
+                                    const char *title,const char *name);
 
     void writeRuler()    { t << "<hr/>"; }
     void writeAnchor(const char *,const char *name) 
@@ -200,6 +202,7 @@ class HtmlGenerator : public OutputGenerator
     void startQuickIndices() {}
     void endQuickIndices();
     void writeSplitBar(const char *name);
+    void writeNavigationPath(const char *s);
     void writeLogo();
     void writeQuickLinks(bool compact,HighlightedItem hli,const char *file);
     void startContents();
diff --git a/src/htmlhelp.cpp b/src/htmlhelp.cpp
index 2860296..86d4e42 100644
--- a/src/htmlhelp.cpp
+++ b/src/htmlhelp.cpp
@@ -34,6 +34,7 @@
 
 //----------------------------------------------------------------------------
 
+/** Class representing a field in the HTML help index. */
 struct IndexField
 {
   QCString name;
@@ -43,6 +44,7 @@ struct IndexField
   bool     reversed;
 };
 
+/** Sorted dictionary of IndexField objects. */
 class IndexFieldSDict : public SDict<IndexField>
 {
   public:
@@ -54,8 +56,8 @@ class IndexFieldSDict : public SDict<IndexField>
     }
 };
 
-/*! A helper class for HtmlHelp that manages a two level index in 
- * alphabetical order 
+/** A helper class for HtmlHelp that manages a two level index in 
+ *  alphabetical order.
  */
 class HtmlHelpIndex
 {
diff --git a/src/htmlhelp.h b/src/htmlhelp.h
index 669dd24..524f8f1 100644
--- a/src/htmlhelp.h
+++ b/src/htmlhelp.h
@@ -30,7 +30,8 @@ class QFile;
 class Definition;
 class HtmlHelpIndex;
 
-/*! A class that generated the HTML Help specific files.
+/** A class that generated the HTML Help specific files.
+ *
  *  These files can be used with the Microsoft HTML Help workshop
  *  to generate compressed HTML files (.chm).
  */
diff --git a/src/image.cpp b/src/image.cpp
index 20fa868..8afab58 100644
--- a/src/image.cpp
+++ b/src/image.cpp
@@ -25,6 +25,7 @@
 
 typedef unsigned char  Byte;
 
+/** Helper struct representing a RGBA color */
 struct Color
 {
   Byte red;
diff --git a/src/image.h b/src/image.h
index a73be0d..5fb98e6 100644
--- a/src/image.h
+++ b/src/image.h
@@ -20,6 +20,7 @@
 #define _IMAGE_H
 #include <qglobal.h>
 
+/** Class representing a bitmap image generated by doxygen. */
 class Image
 {
   public:
@@ -49,6 +50,7 @@ class Image
     uchar *data;
 };
 
+/** Class representing a bitmap image colored based on hue/sat/gamma settings. */
 class ColoredImage
 {
   public:
diff --git a/src/index.cpp b/src/index.cpp
index ea240f4..b2301a2 100644
--- a/src/index.cpp
+++ b/src/index.cpp
@@ -288,10 +288,16 @@ void endFileWithNavPath(Definition *d,OutputList &ol)
 }
 
 //----------------------------------------------------------------------
-template<class T> void addMembersToIndex(T *def,LayoutDocManager::LayoutPart part,const QCString &name,const QCString &anchor,bool addToIndex=TRUE)
+template<class T> 
+void addMembersToIndex(T *def,LayoutDocManager::LayoutPart part,
+                       const QCString &name,const QCString &anchor,
+                       bool addToIndex=TRUE,bool preventSeparateIndex=FALSE)
 {
   bool hasMembers = def->getMemberLists().count()>0 || def->getMemberGroupSDict()!=0;
-  Doxygen::indexList.addContentsItem(hasMembers,name,def->getReference(),def->getOutputFileBase(),anchor,hasMembers,addToIndex);
+  Doxygen::indexList.addContentsItem(hasMembers,name,
+                                     def->getReference(),def->getOutputFileBase(),anchor,
+                                     hasMembers && !preventSeparateIndex,
+                                     addToIndex);
   int numClasses=0;
   ClassSDict *classes = def->getClassSDict();
   if (classes)
@@ -321,19 +327,41 @@ template<class T> void addMembersToIndex(T *def,LayoutDocManager::LayoutPart par
           MemberDef *md;
           for (mi.toFirst();(md=mi.current());++mi)
           {
+            LockingPtr<MemberList> enumList = md->enumFieldList();
+            bool isDir = enumList!=0 && md->isEnumerate();
             if (md->name().find('@')==-1)
             {
               if (md->getOuterScope()==def)
               {
-                Doxygen::indexList.addContentsItem(FALSE,
+                Doxygen::indexList.addContentsItem(isDir,
                   md->name(),md->getReference(),md->getOutputFileBase(),md->anchor(),FALSE,addToIndex);
               }
               else // inherited member
               {
-                Doxygen::indexList.addContentsItem(FALSE,
+                Doxygen::indexList.addContentsItem(isDir,
                   md->name(),def->getReference(),def->getOutputFileBase(),md->anchor(),FALSE,addToIndex);
               }
             }
+            if (isDir)
+            {
+              Doxygen::indexList.incContentsDepth();
+              MemberListIterator emli(*enumList);
+              MemberDef *emd;
+              for (emli.toFirst();(emd=emli.current());++emli)
+              {
+                if (emd->getOuterScope()==def)
+                {
+                  Doxygen::indexList.addContentsItem(FALSE,
+                      emd->name(),emd->getReference(),emd->getOutputFileBase(),emd->anchor(),FALSE,addToIndex);
+                }
+                else // inherited member
+                {
+                  Doxygen::indexList.addContentsItem(FALSE,
+                      emd->name(),def->getReference(),def->getOutputFileBase(),emd->anchor(),FALSE,addToIndex);
+                }
+              }
+              Doxygen::indexList.decContentsDepth();
+            }
           }
         }
       }
@@ -351,8 +379,8 @@ template<class T> void addMembersToIndex(T *def,LayoutDocManager::LayoutPart par
             if (cd->isLinkable())
             {
               bool isNestedClass = def->definitionType()==Definition::TypeClass;
-              addMembersToIndex(cd,LayoutDocManager::Class,cd->className(),cd->anchor(),
-                                addToIndex && isNestedClass);
+              addMembersToIndex(cd,LayoutDocManager::Class,cd->displayName(FALSE),cd->anchor(),
+                                addToIndex && isNestedClass,preventSeparateIndex);
             }
           }
         }
@@ -526,6 +554,12 @@ static bool fileVisibleInIndex(FileDef *fd,bool &genSourceFile)
          );
 }
 
+static bool classVisibleInIndex(ClassDef *cd)
+{
+  static bool allExternals = Config_getBool("ALLEXTERNALS");
+  return (allExternals && cd->isLinkable()) || cd->isLinkableInProject();
+}
+
 //----------------------------------------------------------------------------
 static void writeDirTreeNode(OutputList &ol, DirDef *dd, int level, FTVHelp* ftv,bool addToIndex)
 {
@@ -616,7 +650,7 @@ static void writeDirTreeNode(OutputList &ol, DirDef *dd, int level, FTVHelp* ftv
           ol.parseText(fd->displayName());
           ol.endIndexItem(reference,outputBase);
           ol.endIndexListItem();
-          if (ftv)
+          if (ftv && doc)
           {
             ftv->addContentsItem(FALSE,
                 fd->displayName(),
@@ -705,7 +739,7 @@ static void writeDirHierarchy(OutputList &ol, FTVHelp* ftv,bool addToIndex)
           ftv->addContentsItem(FALSE,fd->displayName(),
               reference, outputBase, 0,
               FALSE,FALSE,fd); 
-          if (addToIndex)
+          if (addToIndex && doc)
           {
             addMembersToIndex(fd,LayoutDocManager::File,
                               fd->displayName(),QCString());
@@ -918,9 +952,11 @@ static void writeHierarchicalIndex(OutputList &ol)
   ol.pushGeneratorState();
   //2.{
   ol.disable(OutputGenerator::Html);
+  Doxygen::indexList.disable();
 
   writeClassHierarchy(ol,0,addToIndex);
 
+  Doxygen::indexList.enable();
   ol.popGeneratorState();
   //2.}
 
@@ -1256,9 +1292,9 @@ void writeClassTree(ClassSDict *clDict,FTVHelp *ftv,bool addToIndex,bool globalO
       }
 
       if (!globalOnly || 
-          cd->getOuterScope()==0 || 
-          cd->getOuterScope()==Doxygen::globalScope 
-         )
+           cd->getOuterScope()==0 || 
+           cd->getOuterScope()==Doxygen::globalScope 
+         ) 
       {
         int count=0;
         if (cd->getClassSDict())
@@ -1273,14 +1309,18 @@ void writeClassTree(ClassSDict *clDict,FTVHelp *ftv,bool addToIndex,bool globalO
             }
           }
         }
-        if (cd->isLinkableInProject() && cd->templateMaster()==0) 
+        if (classVisibleInIndex(cd) && cd->templateMaster()==0) 
         { 
-          ftv->addContentsItem(count>0,cd->className(),cd->getReference(),
-              cd->getOutputFileBase(),0,FALSE,TRUE,cd); 
+          ftv->addContentsItem(count>0,cd->displayName(FALSE),cd->getReference(),
+              cd->getOutputFileBase(),cd->anchor(),FALSE,TRUE,cd); 
           if (addToIndex && 
-              (cd->getOuterScope()==0 || cd->getOuterScope()->definitionType()!=Definition::TypeClass))
+              !cd->isEmbeddedInOuterScope() &&
+              (cd->getOuterScope()==0 || 
+               cd->getOuterScope()->definitionType()!=Definition::TypeClass
+              )
+             )
           {
-            addMembersToIndex(cd,LayoutDocManager::Class,cd->className(),cd->anchor());
+            addMembersToIndex(cd,LayoutDocManager::Class,cd->displayName(FALSE),cd->anchor());
           }
           if (count>0)
           {
@@ -1303,8 +1343,8 @@ static void writeNamespaceTree(NamespaceSDict *nsDict,FTVHelp *ftv,
     NamespaceDef *nd;
     for (nli.toFirst();(nd=nli.current());++nli)
     {
-      if (!rootOnly || (nd->isLinkableInProject() && 
-                        nd->getOuterScope()==Doxygen::globalScope))
+      if (/*nd->isLinkableInProject() && */
+          (!rootOnly || nd->getOuterScope()==Doxygen::globalScope))
       {
         int count=0;
         if (nd->getNamespaceSDict())
@@ -1337,30 +1377,29 @@ static void writeNamespaceTree(NamespaceSDict *nsDict,FTVHelp *ftv,
           count+=classCount;
         }
 
-        if (nd->getLanguage()==SrcLangExt_VHDL)
+        
+        QCString ref; 
+        QCString file; 
+        if (nd->isLinkableInProject())
         {
-          QCString q=nd->getOutputFileBase().replace(0,strlen("namespace"),"class");
-          ftv->addContentsItem(count>0,nd->localName(),nd->getReference(),q,0,FALSE,TRUE,nd);
-        }
-        else
-        {
-          ftv->addContentsItem(count>0,nd->localName(),nd->getReference(),
-              nd->getOutputFileBase(),0,FALSE,TRUE,nd); 
+          ref = nd->getReference();
+          file = nd->getOutputFileBase();
+          if (nd->getLanguage()==SrcLangExt_VHDL) // UGLY HACK
+          {
+            file=file.replace(0,strlen("namespace"),"class");
+          }
         }
 
+        ftv->addContentsItem(count>0,nd->localName(),ref,file,0,FALSE,TRUE,nd); 
+
         if (addToIndex)
         {
-          if (nd->getLanguage()==SrcLangExt_VHDL) // UGLY HACK
-          {
-            QCString q=nd->getOutputFileBase().replace(0,strlen("namespace"),"class");
-            Doxygen::indexList.addContentsItem(count>0,nd->localName(),nd->getReference(),q,QCString(),count>0,showClasses);
-          }
-          else
-          {
-            Doxygen::indexList.addContentsItem(count>0,nd->localName(),nd->getReference(),nd->getOutputFileBase(),QCString(),count>0,showClasses);
-          }
+          Doxygen::indexList.addContentsItem(count>0,nd->localName(),ref,file,QCString(),
+                                             count>0 && !file.isEmpty(),addToIndex);
         }
 
+        //printf("*** writeNamespaceTree count=%d addToIndex=%d showClasses=%d classCount=%d\n",
+        //    count,addToIndex,showClasses,classCount);
         if (count>0)
         {
           if (addToIndex) Doxygen::indexList.incContentsDepth();
@@ -1594,6 +1633,7 @@ static QCString letterToLabel(char startLetter)
 
 //----------------------------------------------------------------------------
 
+/** Special class list where sorting takes IGNORE_PREFIX into account. */
 class PrefixIgnoreClassList : public ClassList
 {
 public:
@@ -1608,6 +1648,7 @@ public:
   }
 };
 
+/** Class representing a cell in the alphabetical class index. */
 class AlphaIndexTableCell
 {
   public:
@@ -1629,12 +1670,14 @@ class AlphaIndexTableCell
     int m_col;
 };
 
+/** Class representing a row in the alphabetical class index. */
 class AlphaIndexTableRows : public QList<AlphaIndexTableCell>
 {
   public:
     AlphaIndexTableRows() { setAutoDelete(TRUE); }
 };
 
+/** Iterator for the cells in a row of the alphabetical class index. */
 class AlphaIndexTableRowsIterator : public QListIterator<AlphaIndexTableCell>
 {
   public:
@@ -1642,6 +1685,7 @@ class AlphaIndexTableRowsIterator : public QListIterator<AlphaIndexTableCell>
       QListIterator<AlphaIndexTableCell>(list) {}
 };
 
+/** Class representing the columns in the alphabetical class index. */
 class AlphaIndexTableColumns : public QList<AlphaIndexTableRows>
 {
   public:
@@ -1839,10 +1883,6 @@ static void writeAlphabeticalClassList(OutputList &ol)
               {
                 nsDispName=namesp;
               }
-              if (cname.right(2)=="-g" || cname.right(2)=="-p")
-              {
-                cname = cname.left(cname.length()-2);
-              }
 
               ol.writeObjectLink(cd->getReference(),
                   cd->getOutputFileBase(),cd->anchor(),cname);
@@ -1909,7 +1949,7 @@ static void writeAlphabeticalIndex(OutputList &ol)
 
   if (addToIndex)
   {
-    Doxygen::indexList.addContentsItem(TRUE,title,0,"classes",0,TRUE,TRUE); 
+    Doxygen::indexList.addContentsItem(FALSE,title,0,"classes",0,FALSE,TRUE); 
   }
 
   ol.startContents();
@@ -1961,9 +2001,11 @@ static void writeAnnotatedIndex(OutputList &ol)
   // ---------------
   ol.pushGeneratorState();
   ol.disable(OutputGenerator::Html);
+  Doxygen::indexList.disable();
 
   writeAnnotatedClassList(ol);
 
+  Doxygen::indexList.enable();
   ol.popGeneratorState();
 
   // ---------------
@@ -2380,6 +2422,7 @@ static void writeQuickMemberIndex(OutputList &ol,
 
 //----------------------------------------------------------------------------
 
+/** Helper class representing a class member in the navigation menu. */
 struct CmhlInfo
 {
   CmhlInfo(const char *fn,const char *t) : fname(fn), title(t) {}
@@ -2559,6 +2602,7 @@ static void writeClassMemberIndex(OutputList &ol)
 
 //----------------------------------------------------------------------------
 
+/** Helper class representing a file member in the navigation menu. */
 struct FmhlInfo 
 {
   FmhlInfo(const char *fn,const char *t) : fname(fn), title(t) {}
@@ -2729,6 +2773,7 @@ static void writeFileMemberIndex(OutputList &ol)
 
 //----------------------------------------------------------------------------
 
+/** Helper class representing a namespace member in the navigation menu. */
 struct NmhlInfo
 {
   NmhlInfo(const char *fn,const char *t) : fname(fn), title(t) {}
@@ -3418,11 +3463,29 @@ static void writeGroupTreeNode(OutputList &ol, GroupDef *gd, int level, FTVHelp*
           MemberDef *md;
           for (mi.toFirst();(md=mi.current());++mi)
           {
+            LockingPtr<MemberList> enumList = md->enumFieldList();
+            bool isDir = enumList!=0 && md->isEnumerate();
             if (md->isVisible() && md->name().find('@')==-1)
             {
-              Doxygen::indexList.addContentsItem(FALSE,
+              Doxygen::indexList.addContentsItem(isDir,
                   md->name(),md->getReference(),
-                  md->getOutputFileBase(),md->anchor(),FALSE);
+                  md->getOutputFileBase(),md->anchor(),FALSE,addToIndex);
+            }
+            if (isDir)
+            {
+              Doxygen::indexList.incContentsDepth();
+              MemberListIterator emli(*enumList);
+              MemberDef *emd;
+              for (emli.toFirst();(emd=emli.current());++emli)
+              {
+                if (emd->isVisible())
+                {
+                  Doxygen::indexList.addContentsItem(FALSE,
+                      emd->name(),emd->getReference(),emd->getOutputFileBase(),
+                      emd->anchor(),FALSE,addToIndex);
+                }
+              }
+              Doxygen::indexList.decContentsDepth();
             }
           }
         }
@@ -3435,9 +3498,16 @@ static void writeGroupTreeNode(OutputList &ol, GroupDef *gd, int level, FTVHelp*
         {
           if (cd->isVisible())
           {
-            Doxygen::indexList.addContentsItem(FALSE,
+            if (cd->isLinkable() && cd->isEmbeddedInOuterScope())
+            {
+              addMembersToIndex(cd,LayoutDocManager::Class,cd->displayName(FALSE),cd->anchor(),addToIndex,TRUE);
+            }
+            else // only index the class, not its members
+            {
+              Doxygen::indexList.addContentsItem(FALSE,
                 cd->localName(),cd->getReference(),
                 cd->getOutputFileBase(),cd->anchor(),FALSE,FALSE);
+            }
           }
         }
       }
@@ -3634,9 +3704,11 @@ static void writeGroupIndex(OutputList &ol)
   // 2.{
   ol.pushGeneratorState();
   ol.disable(OutputGenerator::Html);
+  Doxygen::indexList.disable();
 
   writeGroupHierarchy(ol,0,FALSE);
 
+  Doxygen::indexList.enable();
   ol.popGeneratorState();
   // 2.}
 
diff --git a/src/index.h b/src/index.h
index 9bb98b6..050350f 100644
--- a/src/index.h
+++ b/src/index.h
@@ -107,10 +107,16 @@ class IndexList : public IndexIntf
 
   public:
     /** Creates a list of indexes */
-    IndexList() { m_intfs.setAutoDelete(TRUE); }
+    IndexList() { m_intfs.setAutoDelete(TRUE); m_enabled=TRUE; }
     /** Add an index generator to the list */
     void addIndex(IndexIntf *intf) 
     { m_intfs.append(intf); }
+    void disable()
+    { m_enabled = FALSE; }
+    void enable()
+    { m_enabled = TRUE; }
+    bool isEnabled() const
+    { return m_enabled; }
 
     // IndexIntf implementation
     void initialize() 
@@ -118,24 +124,26 @@ class IndexList : public IndexIntf
     void finalize() 
     { foreach(&IndexIntf::finalize); }
     void incContentsDepth()
-    { foreach(&IndexIntf::incContentsDepth); }
+    { if (m_enabled) foreach(&IndexIntf::incContentsDepth); }
     void decContentsDepth()
-    { foreach(&IndexIntf::decContentsDepth); }
+    { if (m_enabled) foreach(&IndexIntf::decContentsDepth); }
     void addContentsItem(bool isDir, const char *name, const char *ref, 
                          const char *file, const char *anchor,bool separateIndex=FALSE,bool addToNavIndex=FALSE,
                          Definition *def=0)
-    { foreach<bool,const char *,const char *,const char *,const char*,bool,bool,Definition *>
+    { if (m_enabled) foreach<bool,const char *,const char *,const char *,const char*,bool,bool,Definition *>
              (&IndexIntf::addContentsItem,isDir,name,ref,file,anchor,separateIndex,addToNavIndex,def); }
     void addIndexItem(Definition *context,MemberDef *md,const char *title=0)
-    { foreach<Definition *,MemberDef *>
+    { if (m_enabled) foreach<Definition *,MemberDef *>
              (&IndexIntf::addIndexItem,context,md,title); }
     void addIndexFile(const char *name) 
-    { foreach<const char *>(&IndexIntf::addIndexFile,name); }
+    { if (m_enabled) foreach<const char *>(&IndexIntf::addIndexFile,name); }
     void addImageFile(const char *name) 
-    { foreach<const char *>(&IndexIntf::addImageFile,name); }
+    { if (m_enabled) foreach<const char *>(&IndexIntf::addImageFile,name); }
     void addStyleSheetFile(const char *name) 
-    { foreach<const char *>(&IndexIntf::addStyleSheetFile,name); }
+    { if (m_enabled) foreach<const char *>(&IndexIntf::addStyleSheetFile,name); }
 
+  private:
+    bool m_enabled;
 };
 
 
diff --git a/src/latexdocvisitor.cpp b/src/latexdocvisitor.cpp
index d86b5fc..7d326cb 100644
--- a/src/latexdocvisitor.cpp
+++ b/src/latexdocvisitor.cpp
@@ -60,121 +60,6 @@ static const char *getSectionName(int level)
   return secLabels[QMIN(maxLevels-1,l)];
 }
 
-#if 0
-static int rowspan(DocHtmlCell *cell)
-{
-  int retval = 0;
-  HtmlAttribList attrs = cell->attribs();
-  uint i;
-  for (i=0; i<attrs.count(); ++i) 
-  {
-    if (attrs.at(i)->name.lower()=="rowspan")
-    {
-      retval = attrs.at(i)->value.toInt();
-      break;
-    }
-  }
-  return retval;
-}
-
-static int colspan(DocHtmlCell *cell)
-{
-  int retval = 1;
-  HtmlAttribList attrs = cell->attribs();
-  uint i;
-  for (i=0; i<attrs.count(); ++i) 
-  {
-    if (attrs.at(i)->name.lower()=="colspan")
-    {
-      retval = QMAX(1,attrs.at(i)->value.toInt());
-      break;
-    }
-  }
-  return retval;
-}
-
-static int align(DocHtmlCell *cell)
-{
-  HtmlAttribList attrs = cell->attribs();
-  uint i;
-  for (i=0; i<attrs.count(); ++i) 
-  {
-    if (attrs.at(i)->name.lower()=="align")
-    {
-      if (attrs.at(i)->value.lower()=="center") 
-        return 1;
-      else if (attrs.at(i)->value.lower()=="right") 
-        return 2;
-      else return 0;
-    }
-  }
-  return 0;
-}
-
-struct ActiveRowSpan
-{
-  ActiveRowSpan(int rows,int col) : rowsLeft(rows), column(col) {}
-  int rowsLeft;
-  int column;
-};
-
-typedef QList<ActiveRowSpan> RowSpanList;
-
-static int determineNumCols(DocHtmlTable *table)
-{
-  RowSpanList rowSpans;
-  rowSpans.setAutoDelete(TRUE);
-  int maxCols=0;
-  int rowIdx=1;
-  QListIterator<DocNode> li(table->children());
-  DocNode *rowNode;
-  for (li.toFirst();(rowNode=li.current());++li)
-  {
-    int colIdx=1;
-    int cells=0;
-    if (rowNode->kind()==DocNode::Kind_HtmlRow)
-    {
-      uint i;
-      DocHtmlRow *row = (DocHtmlRow*)rowNode;
-      QListIterator<DocNode> rli(row->children());
-      DocNode *cellNode;
-      for (rli.toFirst();(cellNode=rli.current());++rli)
-      {
-        if (cellNode->kind()==DocNode::Kind_HtmlCell)
-        {
-          DocHtmlCell *cell = (DocHtmlCell*)cellNode;
-          int rs = rowspan(cell);
-          int cs = colspan(cell);
-
-          for (i=0;i<rowSpans.count();i++)
-          {
-            if (rowSpans.at(i)->rowsLeft>0 && 
-                rowSpans.at(i)->column==colIdx) 
-            {
-              colIdx=rowSpans.at(i)->column+1;
-              cells++;
-            }
-          }
-          if (rs>0) rowSpans.append(new ActiveRowSpan(rs,colIdx));
-          cell->setRowIndex(rowIdx);
-          cell->setColumnIndex(colIdx);
-          colIdx+=cs; 
-          cells++;
-        }
-      }
-      for (i=0;i<rowSpans.count();i++)
-      {
-        if (rowSpans.at(i)->rowsLeft>0) rowSpans.at(i)->rowsLeft--;
-      }
-      row->setVisibleCells(cells);
-      rowIdx++;
-    }
-    if (colIdx-1>maxCols) maxCols=colIdx-1;
-  }
-  return maxCols;
-}
-#endif
-
 QCString LatexDocVisitor::escapeMakeIndexChars(const char *s)
 {
   QCString result;
@@ -1363,25 +1248,6 @@ void LatexDocVisitor::visitPost(DocSecRefList *)
   m_t << "\\normalsize" << endl;
 }
 
-//void LatexDocVisitor::visitPre(DocLanguage *l)
-//{
-//  QCString langId = Config_getEnum("OUTPUT_LANGUAGE");
-//  if (l->id().lower()!=langId.lower())
-//  {
-//    pushEnabled();
-//    m_hide = TRUE;
-//  }
-//}
-//
-//void LatexDocVisitor::visitPost(DocLanguage *l) 
-//{
-//  QCString langId = Config_getEnum("OUTPUT_LANGUAGE");
-//  if (l->id().lower()!=langId.lower())
-//  {
-//    popEnabled();
-//  }
-//}
-
 void LatexDocVisitor::visitPre(DocParamSect *s)
 {
   if (m_hide) return;
diff --git a/src/latexgen.h b/src/latexgen.h
index 254632f..cd47ac3 100644
--- a/src/latexgen.h
+++ b/src/latexgen.h
@@ -22,6 +22,7 @@
 
 class QFile;
 
+/** Generator for LaTeX output. */
 class LatexGenerator : public OutputGenerator
 {
   public:
@@ -164,7 +165,7 @@ class LatexGenerator : public OutputGenerator
     void endSmall()         { t << "\\normalsize "; }
     void startMemberDescription(const char *,const char *);
     void endMemberDescription();
-    void writeInheritedSectionTitle(const char *,const char *,
+    void writeInheritedSectionTitle(const char *,const char *,const char *,
                       const char *,const char *,const char *) {}
     void startDescList(SectionTypes)     { t << "\\begin{Desc}\n\\item["; }
     void endDescList()       { t << "\\end{Desc}" << endl; }
@@ -187,6 +188,7 @@ class LatexGenerator : public OutputGenerator
     void startQuickIndices() {}
     void endQuickIndices() {}
     void writeSplitBar(const char *) {}
+    void writeNavigationPath(const char *) {}
     void writeLogo() {}
     void writeQuickLinks(bool,HighlightedItem,const char*) {}
     void startContents() {}
diff --git a/src/mangen.h b/src/mangen.h
index 7187e5d..fe951ad 100644
--- a/src/mangen.h
+++ b/src/mangen.h
@@ -22,6 +22,7 @@
 
 class QFile;
 
+/** Generator for Man page output. */
 class ManGenerator : public OutputGenerator
 {
   public:
@@ -160,7 +161,7 @@ class ManGenerator : public OutputGenerator
     void endSmall()           {}
     void startMemberDescription(const char *,const char *) { t << "\n.RI \"\\fI"; firstCol=FALSE; }
     void endMemberDescription()   { t << "\\fP\""; firstCol=FALSE; }
-    void writeInheritedSectionTitle(const char *,const char *,
+    void writeInheritedSectionTitle(const char *,const char *,const char *,
                       const char *,const char *,const char *) {}
     void startDescList(SectionTypes);
     void endDescList()        {}
@@ -184,6 +185,7 @@ class ManGenerator : public OutputGenerator
     void startQuickIndices() {}
     void endQuickIndices() {}
     void writeSplitBar(const char *) {}
+    void writeNavigationPath(const char *) {}
     void writeLogo() {}
     void writeQuickLinks(bool,HighlightedItem,const char *) {}
     void startContents() {}
diff --git a/src/markdown.cpp b/src/markdown.cpp
index bb1a5a3..559828f 100644
--- a/src/markdown.cpp
+++ b/src/markdown.cpp
@@ -1339,6 +1339,11 @@ static bool isCodeBlock(const char *data,int offset,int size,int &indent)
     //printf(">isCodeBlock: line is not indented enough %d<4\n",indent0);
     return FALSE;
   }
+  if (indent0>=size || data[indent0]=='\n') // empty line does not start a code block
+  {
+    //printf("only spaces at the end of a comment block\n");
+    return FALSE;
+  }
     
   i=offset;
   int nl=0;
@@ -1382,8 +1387,8 @@ static bool isCodeBlock(const char *data,int offset,int size,int &indent)
     {
       return FALSE;
     }
-    //printf(">isCodeBlock global indent %d>=%d+4=%d\n",
-    //    indent0,indent,indent0>=indent+4);
+    //printf(">isCodeBlock global indent %d>=%d+4=%d nl=%d\n",
+    //    indent0,indent,indent0>=indent+4,nl);
     return indent0>=indent+codeBlockIndent;
   }
 }
@@ -2121,6 +2126,7 @@ static QCString detab(const QCString &s,int &refIndent)
   }
   if (minIndent!=maxIndent) refIndent=minIndent; else refIndent=0;
   out.addChar(0);
+  //printf("detab refIndent=%d\n",refIndent);
   return out.get();
 }
 
diff --git a/src/memberdef.cpp b/src/memberdef.cpp
index 539b621..8591ca3 100644
--- a/src/memberdef.cpp
+++ b/src/memberdef.cpp
@@ -1837,9 +1837,16 @@ void MemberDef::_getLabels(QStrList &sl,Definition *container) const
         if      (isNew())                 sl.append("new");
         if      (isOptional())            sl.append("optional");
         if      (isRequired())            sl.append("required");
+
+        if      (isNonAtomic())           sl.append("nonatomic");
+        else if (isObjCProperty())        sl.append("atomic");
+
+        // mutual exclusive Objective 2.0 property attributes
         if      (isAssign())              sl.append("assign");
         else if (isCopy())                sl.append("copy");
         else if (isRetain())              sl.append("retain");
+        else if (isWeak())                sl.append("weak");
+        else if (isStrong())              sl.append("strong");
 
         if (!isObjCMethod())
         {
@@ -2774,8 +2781,9 @@ void MemberDef::warnIfUndocumented()
   //       name().data(),prot);
   if ((!hasUserDocumentation() && !extractAll) &&
       !isFriendClass() && 
-      name().find('@')==-1 && d->name().find('@')==-1 &&
-      protectionLevelVisible(m_impl->prot)
+      name().find('@')==-1 && d && d->name().find('@')==-1 &&
+      protectionLevelVisible(m_impl->prot) &&
+      !isReference()
      )
   {
     warn_undoc(getDefFileName(),getDefLine(),"warning: Member %s%s (%s) of %s %s is not documented.",
@@ -3854,6 +3862,17 @@ bool MemberDef::isRetain() const
   return (m_impl->memSpec&Entry::Retain)!=0; 
 }
 
+bool MemberDef::isWeak() const
+{
+  makeResident();
+  return (m_impl->memSpec&Entry::Weak)!=0; 
+}
+
+bool MemberDef::isStrong() const
+{
+  makeResident();
+  return (m_impl->memSpec&Entry::Strong)!=0; 
+}
 
 bool MemberDef::isImplementation() const
 { 
@@ -4613,3 +4632,7 @@ void MemberDef::unlock() const
   }
 }
 
+QCString MemberDef::displayName(bool) const 
+{ 
+  return Definition::name(); 
+}
diff --git a/src/memberdef.h b/src/memberdef.h
index 8c916cb..3658ac3 100644
--- a/src/memberdef.h
+++ b/src/memberdef.h
@@ -40,12 +40,7 @@ class QTextStream;
 class ArgumentList;
 class MemberDefImpl;
 
-struct SourceReference
-{
-  FileDef *fd;
-  QCString anchor;
-};
-
+/** A model of a class/file/namespace member symbol. */
 class MemberDef : public Definition
 {
   public:
@@ -157,6 +152,8 @@ class MemberDef : public Definition
     bool isCopy() const;
     bool isAssign() const;
     bool isRetain() const;
+    bool isWeak() const;
+    bool isStrong() const;
     bool isNew() const;
     bool isSealed() const;
     bool isImplementation() const;
@@ -238,7 +235,7 @@ class MemberDef : public Definition
 
     ClassDef *category() const;
 
-    QCString displayName() const { return Definition::name(); }
+    QCString displayName(bool=TRUE) const;
 
     //-----------------------------------------------------------------------------------
     // ----  setters -----
diff --git a/src/membergroup.h b/src/membergroup.h
index fdd219b..6f0aa43 100644
--- a/src/membergroup.h
+++ b/src/membergroup.h
@@ -36,6 +36,7 @@ class Definition;
 class StorageIntf;
 struct ListItemInfo;
 
+/** A class representing a group of members. */
 class MemberGroup 
 {
   public:
@@ -106,10 +107,12 @@ class MemberGroup
     QList<ListItemInfo> *m_xrefListItems;
 };
 
+/** A list of MemberGroup objects. */
 class MemberGroupList : public QList<MemberGroup>
 {
 };
 
+/** An iterator for MemberGroup objects in a MemberGroupList. */
 class MemberGroupListIterator : public QListIterator<MemberGroup>
 {
   public:
@@ -117,6 +120,7 @@ class MemberGroupListIterator : public QListIterator<MemberGroup>
       QListIterator<MemberGroup>(l) {}
 };
 
+/** A sorted dictionary of MemberGroup objects. */
 class MemberGroupSDict : public SIntDict<MemberGroup>
 {
   public:
@@ -128,7 +132,7 @@ class MemberGroupSDict : public SIntDict<MemberGroup>
     }
 };
 
-
+/** Data collected for a member group */
 struct MemberGroupInfo
 {
   MemberGroupInfo() : m_sli(0) {}
@@ -141,19 +145,4 @@ struct MemberGroupInfo
   QList<ListItemInfo> *m_sli;
 };
 
-//class MemberGroupDict : public QIntDict<MemberGroup>
-//{
-//  public:
-//    MemberGroupDict(int size) : QIntDict<MemberGroup>(size) {}
-//   ~MemberGroupDict() {}
-//};
-
-//class MemberGroupDictIterator : public QIntDictIterator<MemberGroup>
-//{
-//  public:
-//    MemberGroupDictIterator(const MemberGroupDict &d) : 
-//      QIntDictIterator<MemberGroup>(d) {}
-//   ~MemberGroupDictIterator() {}
-//};
-
 #endif
diff --git a/src/memberlist.cpp b/src/memberlist.cpp
index c11c6b4..0d74cd6 100644
--- a/src/memberlist.cpp
+++ b/src/memberlist.cpp
@@ -491,7 +491,9 @@ void MemberList::writeDeclarations(OutputList &ol,
   int num = numDecMembers();
   if (inheritedFrom)
   {
-    if ( cd && !optimizeVhdl && countInheritableMembers(inheritedFrom)>0 )
+    //if ( cd && !optimizeVhdl && countInheritableMembers(inheritedFrom)>0 )
+    if ( cd && !optimizeVhdl && cd->countMembersIncludingGrouped(
+                                      m_listType,inheritedFrom,TRUE)>0 )
     {
       ol.pushGeneratorState();
       ol.disableAllBut(OutputGenerator::Html);
@@ -499,7 +501,8 @@ void MemberList::writeDeclarations(OutputList &ol,
                   stripPath(cd->getOutputFileBase());
       if (title)
       {
-        ol.writeInheritedSectionTitle(inheritId,cd->getOutputFileBase(),
+        ol.writeInheritedSectionTitle(inheritId,cd->getReference(),
+                                      cd->getOutputFileBase(), 
                                       cd->anchor(),title,cd->displayName());
       }
       ol.popGeneratorState();
diff --git a/src/memberlist.h b/src/memberlist.h
index facf54f..2c46f02 100644
--- a/src/memberlist.h
+++ b/src/memberlist.h
@@ -27,6 +27,7 @@ class MemberGroup;
 class MemberGroupList;
 class StorageIntf;
 
+/** A list of MemberDef objects. */
 class MemberList : public QList<MemberDef> 
 { 
   public:
@@ -180,6 +181,7 @@ class MemberList : public QList<MemberDef>
     bool m_needsSorting;
 };
 
+/** An iterator for MemberDef objects in a MemberList. */
 class MemberListIterator : public QListIterator<MemberDef>
 {
   public:
@@ -187,6 +189,7 @@ class MemberListIterator : public QListIterator<MemberDef>
     virtual ~MemberListIterator() {}
 };
 
+/** An unsorted dictionary of MemberDef objects. */
 class MemberDict : public QDict<MemberDef>
 {
   public:
@@ -194,6 +197,7 @@ class MemberDict : public QDict<MemberDef>
     virtual ~MemberDict() {}
 };
 
+/** A sorted dictionary of MemberDef objects. */
 class MemberSDict : public SDict<MemberDef>
 {
   public:
diff --git a/src/membername.h b/src/membername.h
index e5fbaa3..68a5293 100644
--- a/src/membername.h
+++ b/src/membername.h