Release-1.3.9.1-20041114

39 files changed, 1208 insertions, 263 deletions

diff --git a/INSTALL b/INSTALL
index 13f7a6f..dedc493 100644
--- a/INSTALL
+++ b/INSTALL
@@ -1,7 +1,7 @@
-DOXYGEN Version 1.3.9.1
+DOXYGEN Version 1.3.9.1-20041114
 
 Please read the installation section of the manual 
 (http://www.doxygen.org/install.html) for instructions.
 
 --------
-Dimitri van Heesch (28 October 2004)
+Dimitri van Heesch (14 November 2004)
diff --git a/README b/README
index 18edef9..355709e 100644
--- a/README
+++ b/README
@@ -1,4 +1,4 @@
-DOXYGEN Version 1.3.9.1
+DOXYGEN Version 1.3.9.1_20041114
 
 Please read INSTALL for compilation instructions.
 
@@ -17,4 +17,4 @@ to subscribe to the lists or to visit the archives.
 
 Enjoy,
 
-Dimitri van Heesch (dimitri@stack.nl) (28 October 2004)
+Dimitri van Heesch (dimitri@stack.nl) (14 November 2004)
diff --git a/VERSION b/VERSION
index c4d3ba9..c330fa6 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-1.3.9.1
+1.3.9.1-20041114
diff --git a/doc/commands.doc b/doc/commands.doc
index b3af6d0..26e58ca 100644
--- a/doc/commands.doc
+++ b/doc/commands.doc
@@ -51,6 +51,7 @@ documentation:
 \refitem cmdcategory \\category
 \refitem cmdclass \\class
 \refitem cmdcode \\code
+\refitem cmdcond \\cond
 \refitem cmdcopydoc \\copydoc
 \refitem cmddate \\date
 \refitem cmddef \\def
@@ -65,6 +66,7 @@ documentation:
 \refitem cmdelseif \\elseif
 \refitem cmdem \\em
 \refitem cmdendcode \\endcode
+\refitem cmdendcond \\endcond
 \refitem cmdenddot \\enddot
 \refitem cmdendhtmlonly \\endhtmlonly
 \refitem cmdendif \\endif
@@ -223,6 +225,7 @@ doxygen. Unrecognized commands are treated as normal text.
 
   \sa section \ref cmdclass "\\class".
 
+<hr>
 \section cmdclass \class <name> [<header-file>] [<header-name>]
 
   \addindex \\class
@@ -755,6 +758,72 @@ See section \ref memgroup for an example.
   for an example.
 
 <hr>
+\section cmdcond \cond [<section-label>]
+
+  \addindex \\cond
+  Starts a conditional section that ends with a corresponding 
+  \ref cmdendcond "\\endcond" command, which is typically found in 
+  another comment block. The main purpose of this pair of
+  commands is to (conditionally) exclude part of a file from processing
+  (traditionally this could only be achieved using C processor commands). 
+
+  The section between \\cond and \\endcond commands can be included by
+  adding its section label to the \ref cfg_enabled_sections "ENABLED_SECTIONS"
+  configuration option. If the section label is omitted, the section will
+  be excluded from processing unconditionally.
+
+  For conditional sections within a comment block one should 
+  use a \ref cmdif "\\if" ... \ref cmdendif "\\endif" block.
+
+  Conditional sections can be nested. In this case a nested section will only
+  be shown if it and its containing section are included.
+
+  Here is an example showing the commands in action:
+
+\verbatim
+/** An interface */
+class Intf
+{
+  public:
+    /** A method */
+    virtual void func() = 0;
+
+    /// @cond TEST
+
+    /** A method used for testing */
+    virtual void test() = 0;
+
+    /// @endcond
+};
+
+/// @cond DEV
+/*
+ *  The implementation of the interface 
+ */
+class Implementation : public Intf
+{
+  public:
+    void func();
+
+    /// @cond TEST
+    void test();
+    /// @endcond
+
+    /// @cond
+    /** This method is obsolete and does
+     *  not show up in the documentation.
+     */
+    void obsolete();
+    /// @endcond
+};
+
+/// @endcond 
+\endverbatim
+
+The output will be different depending on whether \c ENABLED_SECTIONS
+is empty, \c TEST, \c DEV, or \c DEV \c TEST.
+
+<hr>
 \section cmddate \date { date description }
 
   \addindex \\date
@@ -804,10 +873,18 @@ See section \ref memgroup for an example.
               \ref cmdelse "\\else", and \ref cmdelseif "\\elseif".
 
 <hr>
+\section cmdendcond \endcond
+
+  \addindex \\endcond
+  Ends a conditional section that was started by \ref cmdcond "\\cond".
+
+  \sa \ref cmdcond "\\cond".
+
+<hr>
 \section cmdendif \endif 
 
   \addindex \\endif
-  Ends a conditional section that was started with \c \\if or \c \\ifnot
+  Ends a conditional section that was started by \c \\if or \c \\ifnot
   For each \c \\if or \c \\ifnot one and only one matching \c \\endif must follow.
 
   \sa \ref cmdif "\\if", and \ref cmdifnot "\\ifnot".
diff --git a/doc/config.doc b/doc/config.doc
index af065ec..e1e9472 100644
--- a/doc/config.doc
+++ b/doc/config.doc
@@ -73,6 +73,7 @@ followed by the descriptions of the tags grouped by category.
 \refitem cfg_compact_rtf COMPACT_RTF
 \refitem cfg_create_subdirs CREATE_SUBDIRS
 \refitem cfg_details_at_top DETAILS_AT_TOP 
+\refitem cfg_directory_graph DIRECTORY_GRAPH
 \refitem cfg_disable_index DISABLE_INDEX 
 \refitem cfg_distribute_group_doc DISTRIBUTE_GROUP_DOC
 \refitem cfg_dot_image_format DOT_IMAGE_FORMAT
@@ -609,7 +610,8 @@ function's detailed documentation block.
  \addindex ENABLED_SECTIONS
  The \c ENABLED_SECTIONS tag can be used to enable conditional
  documentation sections, marked by \ref cmdif "\\if" \<section-label\> ... 
- \ref cmdendif "\\endif" blocks.
+ \ref cmdendif "\\endif" and \ref cmdcond "\\cond" \<section-label\> ...
+ \ref cmdendcond "\\endcond" blocks.
 
 \anchor cfg_max_initializer_lines
 <dt>\c MAX_INITIALIZER_LINES <dd>
@@ -1583,10 +1585,18 @@ TAGFILES = file1=loc1 "file2 = loc2" ... </pre>
  If the \c GRAPHICAL_HIERARCHY and \c HAVE_DOT tags are set to \c YES then 
  doxygen will graphical hierarchy of all classes instead of a textual one.
 
+\anchor cfg_directory_graph
+<dt>\c DIRECTORY_GRAPH <dd>
+ \addindex DIRECTORY_GRAPH		    
+ If the \c DIRECTORY_GRAPH, \c SHOW_DIRECTORIES and \c HAVE_DOT options are set 
+ to \c YES then doxygen will show the dependencies a directory has on other directories
+ in a graphical way. The dependency relations are determined by the #include
+ relations between the files in the directories.
+
 \anchor cfg_dot_image_format
 <dt>\c DOT_IMAGE_FORMAT <dd>
  \addindex DOT_IMAGE_FORMAT
- The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
+ The \c DOT_IMAGE_FORMAT tag can be used to set the image format of the images
  generated by dot. Possible values are gif, jpg, and png.
  If left blank png will be used.
 
diff --git a/doc/faq.doc b/doc/faq.doc
index fb8bb0b..8cd217d 100644
--- a/doc/faq.doc
+++ b/doc/faq.doc
@@ -79,7 +79,13 @@ document either the class or namespace.
  
 <li><b>How can I make doxygen ignore some code fragment?</b>
 <p>
-You can use Doxygen's preprocessor for this: 
+
+The new and easiest way is to add one comment block 
+with a \ref cmdcond "\\cond" command at the start and one comment block 
+with a \ref cmdendcond "\\endcond" command at the end of the piece of
+code that should be ignored. This should be within the same file of course.
+
+But you can also use Doxygen's preprocessor for this: 
 If you put
 \verbatim
 #ifndef DOXYGEN_SHOULD_SKIP_THIS
@@ -97,7 +103,10 @@ as <code>PREPROCESSING = YES</code>.
 
 <li><b>How can I change what is after the <code>\#include</code> in the class documentation?</b>
 
-You can document your class like
+In most cases you can use STRIP_FROM_INC_PATH to strip a user defined
+part of a path.
+
+You can also document your class as follows
 
 \verbatim
 /*! \class MyClassName include.h path/include.h
diff --git a/doc/infoflow.gif b/doc/infoflow.gif
index f26763e..7b4468b 100644
--- a/doc/infoflow.gif
+++ b/doc/infoflow.gif
diff --git a/doc/install.doc b/doc/install.doc
index 8546efe..3c9a74b 100644
--- a/doc/install.doc
+++ b/doc/install.doc
@@ -385,7 +385,9 @@ Currently, I have only compiled doxygen for Windows using Microsoft's
 Visual C++ (version 6.0). For other compilers you may need to edit the 
 perl script in <code>wintools/make.pl</code> a bit. 
 Let me know what you had to change if you got Doxygen working with another 
-compiler. 
+compiler. If you have Visual Studio you can also use the .dsw file found in
+the <code>wintools</code> directory. Note that this file is not maintained
+by me, so it might be outdated a little.
 
 If you have Visual C++ 6.0, and the source distribution, you can easily
 build doxygen using the project files in the \c wintools directory. If
@@ -462,57 +464,16 @@ Here is what is required:
     commerical version of Qt. 
 
     For doxywizard, a complete Qt library is 
-    still a requirement however. You can download the non-commercial version
-    from Troll-Tech web-site. See doxygen download page for a link.
+    still a requirement however. A commercial license to build
+    doxywizard with the latest Qt library was kindly donated to me
+    by the nice people at <a href="http://www.trolltech.com">TrollTech</a>. 
+    See doxygen download page for a link.
    
-<li>To generate LaTeX documentation or formulas in HTML you need the tools:
-    <code>latex</code>, <code>dvips</code> and <code>gswin32</code>. 
-    To get these working under Windows
-    install the fpTeX distribution. You can find more info at:
-    http://www.fptex.org/ and download it from CTAN or one of its mirrors.
-    In the Netherlands for example this would be: 
-    ftp://ftp.easynet.nl/mirror/CTAN/systems/win32/fptex/
-
-    Make sure the tools are available from a dos box, by adding the 
-    directory they are in to the search path.
-
-    For your information, the LaTeX is freely available set of so
-    called macros and styles on the top of the famous TeX program
-    (by famous Donald Knuth) and the accompanied utilities (all
-    available for free). It is used for high quality
-    typesetting. The result -- in the form of so called
-    <code>DVI</code> (DeVice Independent) file -- can be printed or
-    displayed on various devices preserving exactly the same look up
-    to the capability of the device. The <code>dvips</code> allows you
-    to convert the <code>dvi</code> to the high quality PostScript
-    (i.e. PostScript that can be processed by utilities like 
-    <code>psnup</code>, <code>psbook</code>, <code>psselect</code>,
-    and others). The derived version of TeX (the pdfTeX) can be used
-    to produce PDF output instead of DVI, or the PDF can be produced
-    from PostScript using the utility <code>ps2pdf</code>.
-
-    If you want to use MikTeX then you need to select at least the 
-    medium size installation. For really old versions of MikTex or minimal 
-    installations, you may need to download the fancyhdr package separately. 
-    You can find it at:
-    ftp://ftp.tex.ac.uk/tex-archive/macros/latex/contrib/supported/fancyhdr/
-
-<li>If you want to generate compressed HTML help 
-    (see \ref cfg_generate_htmlhelp "GENERATE_HTMLHELP") in the 
-    config file, then you need the Microsoft HTML help workshop. 
-    You can download it at: 
-    http://msdn.microsoft.com/library/default.asp?url=/library/en-us/htmlhelp/html/vsconHH1Start.asp
-
 <li>If you used WinZip to extract the tar archive it will (apparently) not 
     create empty folders, so you have to add the folders
     <code>objects</code> and <code>bin</code> manually in the root of the 
     distribution before compiling.
 
-<li><a href="http://www.research.att.com/sw/tools/graphviz/">
-    the Graph visualization toolkit version 1.8.10</a><br>
-    \latexonly(see {\tt http://www.research.att.com/sw/tools/graphviz/})\endlatexonly.
-    Needed for the include dependency graphs, the graphical inheritance graphs,
-    and the collaboration graphs.
 </ul>
 
 
@@ -577,23 +538,66 @@ To install doxygen, just copy the binaries from the <code>bin</code> directory
 to a location somewhere in the path. Alternatively, you can include 
 the <code>bin</code> directory of the distribution to the path.
 
-<!--
-For running doxywizard you need to install the non-commercial version of
-the Qt library first. This library can be downloaded from 
-http://www.trolltech.com/products/download/qt-win-noncomm.html
--->
+There are a couple of tools you may want to install to use all of doxygen's
+features:
+
+<ul>
+<li>To generate LaTeX documentation or formulas in HTML you need the tools:
+    <code>latex</code>, <code>dvips</code> and <code>gswin32</code>. 
+    To get these working under Windows
+    install the fpTeX distribution. You can find more info at:
+    http://www.fptex.org/ and download it from CTAN or one of its mirrors.
+    In the Netherlands for example this would be: 
+    ftp://ftp.easynet.nl/mirror/CTAN/systems/win32/fptex/
+
+    Make sure the tools are available from a dos box, by adding the 
+    directory they are in to the search path.
+
+    For your information, the LaTeX is freely available set of so
+    called macros and styles on the top of the famous TeX program
+    (by famous Donald Knuth) and the accompanied utilities (all
+    available for free). It is used for high quality
+    typesetting. The result -- in the form of so called
+    <code>DVI</code> (DeVice Independent) file -- can be printed or
+    displayed on various devices preserving exactly the same look up
+    to the capability of the device. The <code>dvips</code> allows you
+    to convert the <code>dvi</code> to the high quality PostScript
+    (i.e. PostScript that can be processed by utilities like 
+    <code>psnup</code>, <code>psbook</code>, <code>psselect</code>,
+    and others). The derived version of TeX (the pdfTeX) can be used
+    to produce PDF output instead of DVI, or the PDF can be produced
+    from PostScript using the utility <code>ps2pdf</code>.
+
+    If you want to use MikTeX then you need to select at least the 
+    medium size installation. For really old versions of MikTex or minimal 
+    installations, you may need to download the fancyhdr package separately. 
+    You can find it at:
+    ftp://ftp.tex.ac.uk/tex-archive/macros/latex/contrib/supported/fancyhdr/
+
+<li>If you want to generate compressed HTML help 
+    (see \ref cfg_generate_htmlhelp "GENERATE_HTMLHELP") in the 
+    config file, then you need the Microsoft HTML help workshop. 
+    You can download it at: 
+    http://msdn.microsoft.com/library/default.asp?url=/library/en-us/htmlhelp/html/vsconHH1Start.asp
+
+<li><a href="http://www.research.att.com/sw/tools/graphviz/">
+    the Graph visualization toolkit version 1.8.10</a><br>
+    \latexonly(see {\tt http://www.research.att.com/sw/tools/graphviz/})\endlatexonly.
+    Needed for the include dependency graphs, the graphical inheritance graphs,
+    and the collaboration graphs.
+</ul>
 
 \section build_tools Tools used to develop doxygen
 
 Doxygen was developed and tested under Linux using the following 
 open-source tools:
 <ul>
-<li>GCC version 2.95.3
+<li>GCC version 3.3.1
 <li>GNU flex version 2.5.4
-<li>GNU bison version 1.35
-<li>GNU make version 3.79.1
-<li>Perl version 5.005_03 
-<li>VIM version 5.8
+<li>GNU bison version 1.75
+<li>GNU make version 3.80
+<li>Perl version 5.8.1
+<li>VIM version 6.2
 <li>Mozilla 1.0
 <li>Troll Tech's tmake version 1.3 (included in the distribution) 
 <li>teTeX version 1.0
diff --git a/doc/language.doc b/doc/language.doc
index 7281318..ba92211 100644
--- a/doc/language.doc
+++ b/doc/language.doc
@@ -23,7 +23,7 @@ text fragments, generated by doxygen, can be produced in languages other
 than English (the default). The output language is chosen through the
 configuration file (with default name and known as Doxyfile).
 
-Currently (version 1.3.9), 30 languages 
+Currently (version 1.3.9.1), 30 languages 
 are supported (sorted alphabetically):
 Afrikaans, Brazilian Portuguese, Catalan, Chinese, Chinese
 Traditional, Croatian, Czech, Danish, Dutch, English, Finnish, French,
@@ -210,7 +210,7 @@ when the translator was updated.
     <td>Serbian</td>
     <td>Dejan Milosavljevic</td>
     <td>dmilos at email dot com</td>
-    <td>1.3.8</td>
+    <td>up-to-date</td>
   </tr>
   <tr bgcolor="#ffffff">
     <td>Slovak</td>
@@ -318,7 +318,7 @@ when the translator was updated.
   \hline
   Russian & Alexandr Chelpanov & {\tt\tiny cav@cryptopro.ru} & up-to-date \\
   \hline
-  Serbian & Dejan Milosavljevic & {\tt\tiny dmilos@email.com} & 1.3.8 \\
+  Serbian & Dejan Milosavljevic & {\tt\tiny dmilos@email.com} & up-to-date \\
   \hline
   Slovak & Stanislav Kudl\'{a}\v{c} & {\tt\tiny skudlac@pobox.sk} & 1.2.18 \\
   \hline
diff --git a/doc/preprocessing.doc b/doc/preprocessing.doc
index bce601a..883f8d2 100644
--- a/doc/preprocessing.doc
+++ b/doc/preprocessing.doc
@@ -74,8 +74,30 @@ and specify the macro definitions after
 the \ref cfg_predefined "PREDEFINED" or 
 \ref cfg_expand_as_defined "EXPAND_AS_DEFINED" tag.  
 
-As an example, suppose you have the following obfuscated code fragment
-of an abstract base class called \c IUnknown:
+A typically example where some help from the preprocessor is needed is
+when dealing with Microsoft's __declspec language extension. Here is an
+example function.
+
+\verbatim
+extern "C" void __declspec(dllexport) ErrorMsg( String aMessage,...);
+\endverbatim
+
+When nothing is done, doxygen will be confused and see __declspec as
+some sort of function. To help doxygen one typically uses the following
+preprocessor settings:
+
+\verbatim  
+ENABLE_PREPROCESSING   = YES
+MACRO_EXPANSION        = YES
+EXPAND_ONLY_PREDEF     = YES
+PREDEFINED             = __declspec(x)=
+\endverbatim
+
+This will make sure the __declspec(dllexport) is removed before doxygen
+parses the source code.
+
+For a more complex example, suppose you have the following obfuscated 
+code fragment of an abstract base class called \c IUnknown:
 
 \verbatim
 /*! A reference to an IID */
diff --git a/doc/translator_report.txt b/doc/translator_report.txt
index 9a6959f..ab1718b 100644
--- a/doc/translator_report.txt
+++ b/doc/translator_report.txt
@@ -1,4 +1,4 @@
-(1.3.9)
+(1.3.9.1)
 
 Doxygen supports the following 30 languages (sorted alphabetically):
 
@@ -8,7 +8,7 @@ German, Greek, Hungarian, Italian, Japanese (+En), Korean (+En),
 Lithuanian, Norwegian, Polish, Portuguese, Romanian, Russian, Serbian,
 Slovak, Slovene, Spanish, Swedish, and Ukrainian.
 
-Of them, 13 translators are up-to-date, 17 translators are based on
+Of them, 14 translators are up-to-date, 16 translators are based on
 some adapter class, and 2 are English based.
 
 ----------------------------------------------------------------------
@@ -29,6 +29,7 @@ still may be some details listed even for them:
   TranslatorItalian
   TranslatorPolish
   TranslatorRussian
+  TranslatorSerbian
   TranslatorSwedish
 
 ----------------------------------------------------------------------
@@ -42,7 +43,6 @@ must be implemented to become up-to-date:
   TranslatorDanish                1.3.9 	 6 methods to implement
   TranslatorAfrikaans             1.3.9 	 6 methods to implement
   TranslatorSpanish               1.3.8 	 7 methods to implement
-  TranslatorSerbian               1.3.8 	 7 methods to implement
   TranslatorLithuanian            1.3.8 	 7 methods to implement
   TranslatorKorean                1.3.8 	 7 methods to implement
   TranslatorChinesetraditional    1.3.8 	 7 methods to implement
@@ -452,22 +452,6 @@ TranslatorRomanian   (TranslatorAdapter_1_2_16)  22 methods to implement
     virtual QCString trRTFTableOfContents()
 
 
-TranslatorSerbian   (TranslatorAdapter_1_3_8)  7 methods to implement
------------------
-
-  Implements 194 of the required methods.
-
-  Missing methods (should be implemented):
-
-    virtual QCString trDirIndex()
-    virtual QCString trDirDocumentation()
-    virtual QCString trDirectories()
-    virtual QCString trDirDescription()
-    virtual QCString trSourceFile(QCString & filename)
-    virtual QCString trDirReference(const char * dirName)
-    virtual QCString trDir(bool first_capital, bool singular)
-
-
 TranslatorSlovak   (TranslatorAdapter_1_2_18)  20 methods to implement
 ----------------
 
diff --git a/packages/rpm/doxygen.spec b/packages/rpm/doxygen.spec
index 20c6268..58be2e9 100644
--- a/packages/rpm/doxygen.spec
+++ b/packages/rpm/doxygen.spec
@@ -1,6 +1,6 @@
 Summary: A documentation system for C/C++.
 Name: doxygen
-Version: 1.3.9.1
+Version: 1.3.9.1_20041114
 Release: 1
 Epoch: 1
 Source0: ftp://ftp.stack.nl/pub/users/dimitri/%{name}-%{version}.src.tar.gz
diff --git a/src/commentcnv.h b/src/commentcnv.h
index 8d2079e..6b17ccd 100644
--- a/src/commentcnv.h
+++ b/src/commentcnv.h
@@ -20,7 +20,8 @@
 
 class BufStr;
 
-extern void convertCppComments(BufStr *inBuf,BufStr *outBuf);
+extern void convertCppComments(BufStr *inBuf,BufStr *outBuf,
+                               const char *fileName);
 
 #endif
 
diff --git a/src/commentcnv.l b/src/commentcnv.l
index 76c624f..7c182e2 100644
--- a/src/commentcnv.l
+++ b/src/commentcnv.l
@@ -22,19 +22,36 @@
 #include <stdio.h>
 #include <stdlib.h>
 
+#include <qstack.h>
+#include <qregexp.h>
+
 #include "bufstr.h"
 #include "debug.h"
 #include "message.h"
 #include "config.h"
 #include "doxygen.h"
 
-static BufStr *g_inBuf;
-static BufStr *g_outBuf;
-static int     g_inBufPos;
-static int     g_col;
-static int     g_blockHeadCol;
-static bool    g_mlBrief;
-static int     g_readLineCtx;
+struct CondCtx
+{
+  CondCtx(int line,QCString id,bool b) 
+    : lineNr(line),sectionId(id), skip(b) {}
+  int lineNr;
+  QCString sectionId;
+  bool skip;
+};
+  
+static BufStr * g_inBuf;
+static BufStr * g_outBuf;
+static int      g_inBufPos;
+static int      g_col;
+static int      g_blockHeadCol;
+static bool     g_mlBrief;
+static int      g_readLineCtx;
+static bool     g_skip;
+static QCString g_fileName;
+static int      g_lineNr;
+static int      g_condCtx;
+static QStack<CondCtx> g_condStack;
 
 static void replaceCommentMarker(const char *s,int len)
 {
@@ -44,6 +61,7 @@ static void replaceCommentMarker(const char *s,int len)
   while ((c=*p) && (c==' ' || c=='\t' || c=='\n')) 
   {
     g_outBuf->addChar(c);
+    g_lineNr += c=='\n';
     p++;
   }
   // replace start of comment marker by spaces
@@ -82,20 +100,115 @@ static inline int computeIndent(const char *s)
 
 static inline void copyToOutput(const char *s,int len)
 {
-  g_outBuf->addArray(s,len);
   int i;
-  static int tabSize=Config_getInt("TAB_SIZE");
-  for (i=0;i<len;i++) 
+  if (g_skip) // only add newlines.
   {
-    switch (s[i])
+    for (i=0;i<len;i++) 
     {
-      case '\n': g_col=0; break;
-      case '\t': g_col+=tabSize-(g_col%tabSize); break;
-      default:   g_col++; break;
+      if (s[i]=='\n') 
+      {
+	g_outBuf->addChar('\n');
+	g_lineNr++;
+      }
+    }
+  }
+  else
+  {
+    g_outBuf->addArray(s,len);
+    static int tabSize=Config_getInt("TAB_SIZE");
+    for (i=0;i<len;i++) 
+    {
+      switch (s[i])
+      {
+	case '\n': g_col=0; g_lineNr++; break;
+	case '\t': g_col+=tabSize-(g_col%tabSize); break;
+	default:   g_col++; break;
+      }
     }
   }
 }
 
+static void startCondSection(const char *sectId)
+{
+  g_condStack.push(new CondCtx(g_lineNr,sectId,g_skip));
+  if (Config_getList("ENABLED_SECTIONS").find(sectId)!=-1)
+  {
+    //printf("*** Section is enabled!\n");
+  }
+  else
+  {
+    //printf("*** Section is disabled!\n");
+    g_skip=TRUE;
+  }
+}
+
+static void endCondSection()
+{
+  if (g_condStack.isEmpty())
+  {
+    warn(g_fileName,g_lineNr,"Found \\endcond command without matching \\cond");
+    g_skip=FALSE;
+  }
+  else
+  {
+    CondCtx *ctx = g_condStack.pop();
+    g_skip=ctx->skip;
+  }
+}
+
+/** remove and executes \\cond and \\endcond commands in \a s */
+static QCString handleCondCmdInAliases(const QCString &s)
+{
+  QCString result;
+  //printf("handleCondCmdInAliases(%s)\n",s.data());
+  static QRegExp cmdPat("[\\\\@][a-z_A-Z][a-z_A-Z0-9]*");
+  int p=0,i,l;
+  while ((i=cmdPat.match(s,p,&l))!=-1)
+  {
+    result+=s.mid(p,i-p);
+    QCString cmd = s.mid(i+1,l-1);
+    //printf("Found command %s\n",cmd.data());
+    if (cmd=="cond")
+    {
+      int sp=i+l,ep;
+      const char *arg=s.data()+sp;
+      char c;
+      // skip spaces
+      while ((c=*arg) && (c==' ' || c=='\t')) arg++,sp++;
+      // read argument
+      if (*arg=='\n') // no arg
+      {
+	startCondSection(" ");
+	ep=sp;
+      }
+      else // get argument
+      {
+	while ((c=*arg) && isId(c)) arg++,ep++;
+	if (ep>sp)
+	{
+	  QCString id = s.mid(sp,ep-sp);
+	  //printf("Found conditional section id %s\n",id.data());
+	  startCondSection(id);
+	}
+      }
+      p=ep;
+    }
+    else if (cmd=="endcond")
+    {
+      endCondSection();
+      p=i+l;
+    }
+    else
+    {
+      result+=s.mid(i,l);
+      p=i+l;
+    }
+  }
+  result+=s.right(s.length()-p);
+  return result;
+}
+
+
 #undef  YY_INPUT
 #define YY_INPUT(buf,result,max_size) result=yyread(buf,max_size);
 
@@ -122,6 +235,7 @@ CHARLIT   (("'"\\[0-7]{1,3}"'")|("'"\\."'")|("'"[^' \\\n]{1,4}"'"))
 %x CComment
 %x Verbatim
 %x ReadLine
+%x CondLine
 
 %%
 
@@ -213,17 +327,6 @@ CHARLIT   (("'"\\[0-7]{1,3}"'")|("'"\\."'")|("'"[^' \\\n]{1,4}"'"))
                                      copyToOutput(yytext,yyleng); 
 				     BEGIN(Scan); 
                                    }
-<CComment>[\\@][a-z_A-Z][a-z_A-Z0-9]*   { // expand alias
-  				      QCString *pValue=Doxygen::aliasDict[yytext+1];
-				      if (pValue)
-				      {    
-					copyToOutput(pValue->data(),pValue->length());
-				      }
-				      else
-				      {
-					copyToOutput(yytext,yyleng);
-				      }
-  				   }
 <CComment>.			   {
                                      copyToOutput(yytext,yyleng); 
   				   }
@@ -276,11 +379,47 @@ CHARLIT   (("'"\\[0-7]{1,3}"'")|("'"\\."'")|("'"[^' \\\n]{1,4}"'"))
   				     copyToOutput(yytext,yyleng);
                                      BEGIN(g_readLineCtx);
   				   }
-<ReadLine>[\\@][a-z_A-Z][a-z_A-Z0-9]*   { // expand alias
+<CComment,ReadLine>("\\\\"|"@@")[a-z_A-Z][a-z_A-Z0-9]*[ \t]* { // escaped command
+				     copyToOutput(yytext,yyleng);
+  				   }
+<CComment,ReadLine>[\\@]"cond"[ \t]+	   { // conditional section
+  				     g_condCtx = YY_START; 
+  				     BEGIN(CondLine);
+  				   }
+<CComment,ReadLine>[\\@]"endcond"/[^a-z_A-Z0-9] { // end of conditional section
+  				     bool oldSkip=g_skip;
+  				     endCondSection();
+				     if (YY_START==CComment && oldSkip && !g_skip) 
+    			             {
+				       //printf("** Adding start of comment!\n");
+ 				       g_outBuf->addChar('/');
+     				       g_outBuf->addChar('*');
+    				     }
+				    }
+<CondLine>[a-z_A-Z][a-z_A-Z0-9.\-]* {
+  				     bool oldSkip=g_skip;
+                                     startCondSection(yytext);
+				     if (g_condCtx==CComment && !oldSkip && g_skip) 
+    			             {
+				       //printf("** Adding terminator for comment!\n");
+ 				       g_outBuf->addChar('*');
+     				       g_outBuf->addChar('/');
+    				     }
+  				     BEGIN(g_condCtx);
+  				   }
+<CondLine>[ \t]*
+<CComment,ReadLine>[\\@]"cond"[ \t]*\n |
+<CondLine>.			   { // forgot section id?
+  				     startCondSection(" "); // fake section id causing the section to be hidden unconditionally
+				     if (*yytext=='\n') g_lineNr++;
+				     if (YY_START==CondLine) BEGIN(g_condCtx);
+  				   }
+<CComment,ReadLine>[\\@][a-z_A-Z][a-z_A-Z0-9]*   { // expand alias
   				      QCString *pValue=Doxygen::aliasDict[yytext+1];
 				      if (pValue)
 				      {    
-					copyToOutput(pValue->data(),pValue->length());
+					QCString val = handleCondCmdInAliases(*pValue);
+					copyToOutput(val.data(),val.length());
 				      }
 				      else
 				      {
@@ -320,16 +459,28 @@ void replaceComment(int offset)
  *  -# It converts multi-line C++ style comment blocks (that are aligned)
  *     to C style comment blocks (if MULTILINE_CPP_IS_BRIEF is set to NO).
  *  -# It replaces aliases with their definition (see ALIASES)
+ *  -# It handles conditional sections (\cond...\endcond blocks)
  */
-void convertCppComments(BufStr *inBuf,BufStr *outBuf)
+void convertCppComments(BufStr *inBuf,BufStr *outBuf,const char *fileName)
 {
   g_inBuf    = inBuf;
   g_outBuf   = outBuf;
   g_inBufPos = 0;
   g_col      = 0;
   g_mlBrief = Config_getBool("MULTILINE_CPP_IS_BRIEF");
+  g_skip     = FALSE;
+  g_fileName = fileName;
+  g_lineNr   = 0;
+  g_condStack.clear();
+  g_condStack.setAutoDelete(TRUE);
   BEGIN(Scan);
   yylex();
+  while (!g_condStack.isEmpty())
+  {
+    CondCtx *ctx = g_condStack.pop();
+    warn(g_fileName,ctx->lineNr,"Conditional section with %s does not have "
+	"a corresponding \\endcond command within this file.",ctx->sectionId.data());
+  }
   if (Debug::isFlagSet(Debug::CommentCnv))
   {
     msg("-------------\n%s\n-------------\n",g_outBuf->data());
diff --git a/src/config.l b/src/config.l
index 1b73bbd..be17859 100644
--- a/src/config.l
+++ b/src/config.l
@@ -2697,6 +2697,15 @@ void Config::create()
                     TRUE
                  );
   cb->addDependency("HAVE_DOT");
+  cb = addBool(    
+                    "DIRECTORY_GRAPH",
+		    "If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES \n"
+		    "then doxygen will show the dependencies a directory has on other directories \n"
+		    "in a graphical way. The dependency relations are determined by the #include\n"
+		    "relations between the files in the directories.\n",
+                    TRUE
+               );
+  cb->addDependency("HAVE_DOT");
   ce = addEnum(
                     "DOT_IMAGE_FORMAT",
                     "The DOT_IMAGE_FORMAT tag can be used to set the image format of the images \n"
diff --git a/src/debug.cpp b/src/debug.cpp
index 7a0739e..ef79ee5 100644
--- a/src/debug.cpp
+++ b/src/debug.cpp
@@ -57,6 +57,8 @@ static int labelToEnumValue(const char *l)
     return Debug::PrintTree;
   else if (label=="time")
     return Debug::Time;
+  else if (label=="extcmd")
+    return Debug::ExtCmd;
   else
     return 0;
 }
diff --git a/src/debug.h b/src/debug.h
index ef2792d..40d4c5a 100644
--- a/src/debug.h
+++ b/src/debug.h
@@ -31,7 +31,8 @@ class Debug
                      CommentCnv   = 0x00000020,
                      Validate     = 0x00000040,
                      PrintTree    = 0x00000080,
-                     Time         = 0x00000100
+                     Time         = 0x00000100,
+                     ExtCmd       = 0x00000200
                    };
     static void print(DebugMask mask,int prio,const char *fmt,...);
     static void setFlag(const char *label);
diff --git a/src/dirdef.cpp b/src/dirdef.cpp
index 34743ea..b7959e2 100644
--- a/src/dirdef.cpp
+++ b/src/dirdef.cpp
@@ -5,6 +5,7 @@
 #include "outputlist.h"
 #include "language.h"
 #include "message.h"
+#include "dot.h"
 
 //----------------------------------------------------------------------
 // method implementation
@@ -27,7 +28,6 @@ DirDef::DirDef(const char *path) : Definition(path,1,path)
     m_shortName = m_shortName.mid(pi+1);
   }
   
-  m_subdirs.setAutoDelete(TRUE);
   m_fileList   = new FileList;
   m_classSDict = new ClassSDict(17);
   m_usedDirs   = new QDict<UsedDir>(257);
@@ -141,6 +141,21 @@ void DirDef::writeDocumentation(OutputList &ol)
     Doxygen::tagFile << "    <filename>" << convertToXML(getOutputFileBase()) << Doxygen::htmlFileExtension << "</filename>" << endl;
   }
   
+  // write graph dependency graph
+  if (Config_getBool("DIRECTORY_GRAPH") && Config_getBool("HAVE_DOT"))
+  {
+    DotDirDeps dirDep(this);
+    if (!dirDep.isTrivial())
+    {
+      msg("Generating dependency graph for directory %s\n",displayName().data());
+      ol.disable(OutputGenerator::Man);
+      ol.newParagraph();
+      ol.startDirDepGraph();
+      //TODO: ol.parseText(theTranslator->trDirDepGraph());
+      ol.endDirDepGraph(dirDep);
+      ol.enableAll();
+    }
+  }
 
   ol.startMemberSections();
   // write subdir list
@@ -154,7 +169,7 @@ void DirDef::writeDocumentation(OutputList &ol)
     while (dd)
     {
       ol.startMemberItem(0);
-      ol.parseText(theTranslator->trDir(FALSE,TRUE));
+      ol.parseText(theTranslator->trDir(FALSE,TRUE)+" ");
       ol.insertMemberAlign();
       ol.writeObjectLink(dd->getReference(),dd->getOutputFileBase(),0,dd->shortName());
       ol.endMemberItem();
@@ -232,13 +247,11 @@ void DirDef::writeDocumentation(OutputList &ol)
   ol.popGeneratorState();
 }
 
-void DirDef::writePathFragment(OutputList &ol)
+void DirDef::writePathFragment(OutputList &ol) const
 {
-  if (getOuterScope()!=Doxygen::globalScope && 
-      getOuterScope()->definitionType()==Definition::TypeDir)
+  if (m_parent)
   {
-    //printf("getOuterScope %s\n",getOuterScope()->name().data());
-    ((DirDef*)getOuterScope())->writePathFragment(ol);
+    m_parent->writePathFragment(ol);
     ol.writeString("&nbsp;/&nbsp;");
   }
   ol.writeObjectLink(getReference(),getOutputFileBase(),0,shortName());
@@ -276,7 +289,8 @@ void DirDef::setLevel()
 /** Add as "uses" dependency between \a this dir and \a dir,
  *  that was caused by a dependency on file \a fd.
  */ 
-void DirDef::addUsesDependency(DirDef *dir,FileDef *fd,bool inherited)
+void DirDef::addUsesDependency(DirDef *dir,FileDef *srcFd,
+                               FileDef *dstFd,bool inherited)
 {
   if (this==dir) return; // do not add self-dependencies
   //printf("  > add dependency %s->%s due to %s\n",shortName().data(),
@@ -287,11 +301,12 @@ void DirDef::addUsesDependency(DirDef *dir,FileDef *fd,bool inherited)
   UsedDir *usedDir = m_usedDirs->find(dir->getOutputFileBase());
   if (usedDir) // dir dependency already present
   {
-     FileDef *usedFd = usedDir->findFile(fd->getOutputFileBase());
-     if (usedFd==0) // new file dependency
+     FilePair *usedPair = usedDir->findFilePair(
+         srcFd->getOutputFileBase()+dstFd->getOutputFileBase());
+     if (usedPair==0) // new file dependency
      {
        //printf("  => new file\n");
-       usedDir->addFile(fd); 
+       usedDir->addFileDep(srcFd,dstFd); 
        added=TRUE;
      }
      else
@@ -303,19 +318,19 @@ void DirDef::addUsesDependency(DirDef *dir,FileDef *fd,bool inherited)
   {
     //printf("  => new file\n");
     usedDir = new UsedDir(dir,inherited);
-    usedDir->addFile(fd); 
+    usedDir->addFileDep(srcFd,dstFd); 
     m_usedDirs->insert(dir->getOutputFileBase(),usedDir);
     added=TRUE;
   }
   if (added && dir->parent())
   {
     // add relation to parent of used dir
-    addUsesDependency(dir->parent(),fd,inherited);
+    addUsesDependency(dir->parent(),srcFd,dstFd,inherited);
   }
   if (parent())
   {
     // add relation for the parent of this dir as well
-    parent()->addUsesDependency(dir,fd,TRUE);
+    parent()->addUsesDependency(dir,srcFd,dstFd,TRUE);
   }
 }
 
@@ -345,7 +360,7 @@ void DirDef::computeDependencies()
             if (usedDir)
             {
               // add dependency: thisDir->usedDir
-              addUsesDependency(usedDir,ii->fileDef,FALSE);
+              addUsesDependency(usedDir,fd,ii->fileDef,FALSE);
             }
           } 
         }
@@ -364,31 +379,46 @@ bool DirDef::isParentOf(DirDef *dir) const
     return FALSE;
 }
 
+bool DirDef::depGraphIsTrivial() const
+{
+  return FALSE;
+}
+
+//----------------------------------------------------------------------
+
+int FilePairDict::compareItems(GCI item1,GCI item2)
+{
+  FilePair *left  = (FilePair*)item1;
+  FilePair *right = (FilePair*)item2;
+  int orderHi = stricmp(left->source()->name(),right->source()->name());
+  int orderLo = stricmp(left->destination()->name(),right->destination()->name());
+  return orderHi==0 ? orderLo : orderHi;
+}
+
 //----------------------------------------------------------------------
 
 UsedDir::UsedDir(DirDef *dir,bool inherited) :
-   m_dir(dir), m_inherited(inherited)
+   m_dir(dir), m_filePairs(7), m_inherited(inherited)
 {
+  m_filePairs.setAutoDelete(TRUE);
 }
 
 UsedDir::~UsedDir()
 {
 }
 
-void UsedDir::addFile(FileDef *fd)
+void UsedDir::addFileDep(FileDef *srcFd,FileDef *dstFd)
 {
-  m_files.insert(fd->getOutputFileBase(),fd);
+  m_filePairs.inSort(srcFd->getOutputFileBase()+dstFd->getOutputFileBase(),
+                     new FilePair(srcFd,dstFd));
 }
 
-FileDef *UsedDir::findFile(const char *name)
+FilePair *UsedDir::findFilePair(const char *name)
 {
   QCString n=name;
-  return n.isEmpty() ? 0 : m_files.find(n);
+  return n.isEmpty() ? 0 : m_filePairs.find(n);
 }
 
-//----------------------------------------------------------------------
-// helper functions
-
 DirDef *DirDef::createNewDir(const char *path)
 {
   ASSERT(path!=0);
@@ -442,13 +472,27 @@ void DirDef::writeDepGraph(QTextStream &t)
 {
     t << "digraph G {\n";
     t << "  compound=true\n";
+    t << "  node [ fontsize=10, fontname=\"Helvetica\"];\n";
+    t << "  edge [ labelfontsize=9, labelfontname=\"Helvetica\"];\n";
 
     QDict<DirDef> dirsInGraph(257);
     
     dirsInGraph.insert(getOutputFileBase(),this);
+    if (parent())
+    {
+      t << "  subgraph cluster" << parent()->getOutputFileBase() << " {\n";
+      t << "    graph [ bgcolor=\"#ddddee\", pencolor=\"black\", label=\"" 
+        << parent()->shortName() 
+        << "\" fontname=\"Helvetica\", fontsize=10, URL=\"";
+      t << parent()->getOutputFileBase() << Doxygen::htmlFileExtension;
+      t << "\"]\n";
+    }
     if (isCluster())
     {
       t << "  subgraph cluster" << getOutputFileBase() << " {\n";
+      t << "    graph [ bgcolor=\"#eeeeff\", pencolor=\"black\", label=\"\""
+        << " URL=\"" << getOutputFileBase() << Doxygen::htmlFileExtension 
+        << "\"];\n";
       t << "    " << getOutputFileBase() << " [shape=plaintext label=\"" 
         << shortName() << "\"];\n";
 
@@ -461,8 +505,15 @@ void DirDef::writeDepGraph(QTextStream &t)
           << sdir->shortName() << "\"";
         if (sdir->isCluster())
         {
-          t << " color=\"red\" fillcolor=\"white\" style=\"filled\"";
+          t << " color=\"red\"";
+        }
+        else
+        {
+          t << " color=\"black\"";
         }
+        t << " fillcolor=\"white\" style=\"filled\"";
+        t << " URL=\"" << sdir->getOutputFileBase() 
+          << Doxygen::htmlFileExtension << "\"";
         t << "];\n";
         dirsInGraph.insert(sdir->getOutputFileBase(),sdir);
       }
@@ -470,7 +521,14 @@ void DirDef::writeDepGraph(QTextStream &t)
     }
     else
     {
-      t << getOutputFileBase() << " [shape=box label=\"" << shortName() << "\"];\n";
+      t << "  " << getOutputFileBase() << " [shape=box, label=\"" 
+        << shortName() << "\", style=\"filled\", fillcolor=\"#eeeeff\","
+        << " pencolor=\"black\", URL=\"" << getOutputFileBase() 
+        << Doxygen::htmlFileExtension << "\"];\n";
+    }
+    if (parent())
+    {
+      t << "  }\n";
     }
 
     // add nodes for other used directories
@@ -500,7 +558,8 @@ void DirDef::writeDepGraph(QTextStream &t)
           {
             t << " color=\"red\" fillcolor=\"white\" style=\"filled\"";
           }
-          t << "];\n";
+          t << " URL=\"" << usedDir->getOutputFileBase() 
+            << Doxygen::htmlFileExtension << "\"];\n";
           dirsInGraph.insert(usedDir->getOutputFileBase(),usedDir);
           break;
         }
@@ -523,11 +582,20 @@ void DirDef::writeDepGraph(QTextStream &t)
             !usedDir->isParentOf(dir) &&             // don't point to own parent
             dirsInGraph.find(usedDir->getOutputFileBase())) // only point to nodes that are in the graph
         {
-          int nrefs = udir->files().count();
+          QCString relationName;
+          relationName.sprintf("dir_%06d_%06d",dir->m_dirCount,usedDir->m_dirCount);
+          if (Doxygen::dirRelations.find(relationName)==0)
+          {
+            // new relation
+            Doxygen::dirRelations.append(relationName,
+                new DirRelation(relationName,dir,udir));
+          }
+          int nrefs = udir->filePairs().count();
           t << "  " << dir->getOutputFileBase() << "->" 
-            << usedDir->getOutputFileBase();
-          t << " [headlabel=\"" << nrefs << "\" headhref=\"http://www.doxygen.org\"]";
-          t << ";\n";
+                    << usedDir->getOutputFileBase();
+          t << " [headlabel=\"" << nrefs << "\", labeldistance=1.5";
+          t << " headhref=\"" << relationName << Doxygen::htmlFileExtension 
+            << "\"];\n";
         }
       }
     }
@@ -536,6 +604,85 @@ void DirDef::writeDepGraph(QTextStream &t)
 }
 
 //----------------------------------------------------------------------
+
+static void writePartialDirPath(OutputList &ol,const DirDef *root,const DirDef *target)
+{
+  if (target->parent()!=root) 
+  {
+    writePartialDirPath(ol,root,target->parent());
+    ol.writeString("&nbsp;/&nbsp;");
+  }
+  ol.writeObjectLink(target->getReference(),target->getOutputFileBase(),0,target->shortName());
+}
+
+static void writePartialFilePath(OutputList &ol,const DirDef *root,const FileDef *fd)
+{
+  if (fd->getDirDef() && fd->getDirDef()!=root)
+  {
+    writePartialDirPath(ol,root,fd->getDirDef());
+    ol.writeString("&nbsp;/&nbsp;");
+  }
+  if (fd->isLinkable())
+  {
+    ol.writeObjectLink(fd->getReference(),fd->getOutputFileBase(),0,fd->name());
+  }
+  else
+  {
+    ol.startBold();
+    ol.docify(fd->name());
+    ol.endBold();
+  }
+}
+
+void DirRelation::writeDocumentation(OutputList &ol)
+{
+  ol.pushGeneratorState();
+  ol.disableAllBut(OutputGenerator::Html);
+
+  QCString shortTitle=m_src->shortName()+" &rarr; "+
+                      m_dst->dir()->shortName()+" Relation";//theTranslator->trDirRelation(m_shortName);
+  QCString title=m_src->displayName()+" -> "+
+                 m_dst->dir()->shortName()+" Relation";//theTranslator->trDirRelation(m_dispName);
+  startFile(ol,getOutputFileBase(),getOutputFileBase(),title);
+
+  // write navigation path
+  m_src->writeNavigationPath(ol);
+
+  //startTitle(ol,getOutputFileBase());
+  //  ol.parseText(shortTitle);
+  //endTitle(ol,getOutputFileBase(),title);
+  ol.writeString("<h3>"+shortTitle+"</h3>");
+  
+  ol.writeString("<table class=\"dirtab\">");
+  ol.writeString("<tr class=\"dirtab\">");
+  ol.writeString("<th class=\"dirtab\">File in ");
+  m_src->writePathFragment(ol);
+  ol.writeString("</th>");
+  ol.writeString("<th class=\"dirtab\">Includes file in ");
+  m_dst->dir()->writePathFragment(ol);
+  ol.writeString("</th>");
+  ol.writeString("</tr>");
+
+  SDict<FilePair>::Iterator fpi(m_dst->filePairs());
+  FilePair *fp;
+  for (fpi.toFirst();(fp=fpi.current());++fpi)
+  {
+    ol.writeString("<tr class=\"dirtab\">");
+    ol.writeString("<td class=\"dirtab\">");
+    writePartialFilePath(ol,m_src,fp->source());
+    ol.writeString("</td>");
+    ol.writeString("<td class=\"dirtab\">");
+    writePartialFilePath(ol,m_dst->dir(),fp->destination());
+    ol.writeString("</td>");
+    ol.writeString("</tr>");
+  }
+  ol.writeString("</table>");
+  
+  endFile(ol); 
+  ol.popGeneratorState();
+}
+
+//----------------------------------------------------------------------
 // external functions
 
 void buildDirectories()
@@ -678,5 +825,14 @@ void generateDirDocs(OutputList &ol)
   {
     dir->writeDocumentation(ol);
   }
+  if (Config_getBool("DIRECTORY_GRAPH"))
+  {
+    SDict<DirRelation>::Iterator rdi(Doxygen::dirRelations);
+    DirRelation *dr;
+    for (rdi.toFirst();(dr=rdi.current());++rdi)
+    {
+      dr->writeDocumentation(ol);
+    }
+  }
 }
 
diff --git a/src/dirdef.h b/src/dirdef.h
index 09034a2..e331405 100644
--- a/src/dirdef.h
+++ b/src/dirdef.h
@@ -34,12 +34,14 @@ class QTextStream;
 
 class DirDef;
 
+/** A list of directories */
 class DirList : public QList<DirDef>
 {
   public:
    int compareItems(GCI item1,GCI item2);
 };
 
+/** A directory */
 class DirDef : public Definition
 {
   public:
@@ -63,23 +65,25 @@ class DirDef : public Definition
     DirDef *parent() const { return m_parent; }
     const QDict<UsedDir> *usedDirs() const { return m_usedDirs; }
     bool isParentOf(DirDef *dir) const;
+    bool depGraphIsTrivial() const;
 
     // generate output
     void writeDetailedDocumentation(OutputList &ol);
     void writeDocumentation(OutputList &ol);
     void writeNavigationPath(OutputList &ol);
     void writeDepGraph(QTextStream &t);
+    void writePathFragment(OutputList &ol) const;
 
     static DirDef *mergeDirectoryInTree(const QCString &path);
     bool visited;
 
   private:
     friend void computeDirDependencies();
-    void writePathFragment(OutputList &ol);
     void setLevel();
     static DirDef *createNewDir(const char *path);
     static bool matchPath(const QCString &path,QStrList &l);
-    void addUsesDependency(DirDef *usedDir,FileDef *fd,bool inherited);
+    void addUsesDependency(DirDef *usedDir,FileDef *srcFd,
+                           FileDef *dstFd,bool inherited);
     void computeDependencies();
 
     DirList m_subdirs;
@@ -93,23 +97,59 @@ class DirDef : public Definition
     QDict<UsedDir> *m_usedDirs;
 };
 
+class FilePair 
+{
+  public:
+    FilePair(FileDef *src,FileDef *dst) : m_src(src), m_dst(dst) {}
+    const FileDef *source() const { return m_src; }
+    const FileDef *destination() const { return m_dst; }
+  private:
+    FileDef *m_src;
+    FileDef *m_dst;
+};
+
+class FilePairDict : public SDict<FilePair>
+{
+  public:
+    FilePairDict(int size) : SDict<FilePair>(size) {}
+    int compareItems(GCI item1,GCI item2);
+};
+
+/** Usage information of a directory . */
 class UsedDir
 {
   public:
     UsedDir(DirDef *dir,bool inherited);
     virtual ~UsedDir();
-    void addFile(FileDef *fd);
-    FileDef *findFile(const char *name);
-    const QDict<FileDef> &files() const { return m_files; }
+    void addFileDep(FileDef *srcFd,FileDef *dstFd);
+    FilePair *findFilePair(const char *name);
+    const FilePairDict &filePairs() const { return m_filePairs; }
     const DirDef *dir() const { return m_dir; }
     bool inherited() const { return m_inherited; }
 
   private:
     DirDef *m_dir;
-    QDict<FileDef> m_files;
+    FilePairDict m_filePairs;
     bool m_inherited;
 };
 
+/** A usage relation between two direction. */
+class DirRelation
+{
+  public:
+    DirRelation(const QCString &name,DirDef *src,UsedDir *dst) 
+      : m_name(name), m_src(src), m_dst(dst) {}
+    DirDef  *source() const      { return m_src; }
+    UsedDir *destination() const { return m_dst; }
+    void writeDocumentation(OutputList &ol);
+    QCString getOutputFileBase() const { return m_name; }
+
+  private:
+    QCString m_name;
+    DirDef  *m_src;
+    UsedDir *m_dst;
+};
+
 inline int DirList::compareItems(GCI item1,GCI item2)
 {
   return stricmp(((DirDef *)item1)->shortName(),((DirDef *)item2)->shortName());
diff --git a/src/docparser.cpp b/src/docparser.cpp
index b69c98a..420a79d 100644
--- a/src/docparser.cpp
+++ b/src/docparser.cpp
@@ -4367,7 +4367,7 @@ reparsetoken:
                k!=DocNode::Kind_SimpleSect &&
                k!=DocNode::Kind_AutoList &&
                k!=DocNode::Kind_SimpleList &&
-               k!=DocNode::Kind_Verbatim &&
+               /*k!=DocNode::Kind_Verbatim &&*/
                k!=DocNode::Kind_HtmlHeader &&
                k!=DocNode::Kind_ParamSect &&
                k!=DocNode::Kind_XRefItem
@@ -4518,7 +4518,7 @@ reparsetoken:
 	  }
 	  else if (retval==RetVal_OK) 
 	  {
-	    // the command ended normally, keep scanner for new tokens.
+	    // the command ended normally, keep scanning for new tokens.
 	    retval = 0;
 	  }
           else if (retval==TK_LISTITEM || retval==TK_ENDLIST || retval==TK_WORD)
diff --git a/src/dot.cpp b/src/dot.cpp
index 4627a8f..41d6901 100644
--- a/src/dot.cpp
+++ b/src/dot.cpp
@@ -27,6 +27,7 @@
 #include "scanner.h"
 #include "defargs.h"
 #include "docparser.h"
+#include "debug.h"
 
 #include <qdir.h>
 #include <qfile.h>
@@ -1927,7 +1928,7 @@ DotInclDepGraph::DotInclDepGraph(FileDef *fd,int maxRecursionDepth,bool inverse)
   m_diskName  = fd->getFileBase().copy();
   QCString tmp_url=fd->getReference()+"$"+fd->getFileBase();
   m_startNode = new DotNode(m_curNodeNumber++,
-                            fd->name(),
+                            fd->docName(),
                             tmp_url.data(),
                             0,       // distance
                             TRUE     // root node
@@ -1965,7 +1966,7 @@ QCString DotInclDepGraph::writeGraph(QTextStream &out,
     err("Error: Output dir %s does not exist!\n",path); exit(1);
   }
   QCString oldDir = convertToQCString(QDir::currentDirPath());
-  // go to the output directory (i.e. path)
+  // go to the html output directory (i.e. path)
   QDir::setCurrent(d.absPath());
   QDir thisDir;
 
@@ -1978,27 +1979,27 @@ QCString DotInclDepGraph::writeGraph(QTextStream &out,
   QCString imgExt = Config_getEnum("DOT_IMAGE_FORMAT");
 
   QCString md5 = computeMd5Signature(m_startNode,         // root
-                                     DotNode::Dependency, // gt
+                                     DotNode::CallGraph,  // gt
                                      format,              // format
-                                     FALSE,               // lrRank
+                                     TRUE,                // lrRank
                                      FALSE,               // renderParents
                                      QMIN(m_recDepth,m_maxDistance), // maxDist
-                                     !m_inverse           // backArrows
+                                     FALSE                // backArrows
                                     );
   if (checkAndUpdateMd5Signature(baseName,md5) ||
       !QFileInfo(baseName+".map").exists()
      )
   {
-    findMaximalDotGraph(m_startNode,                     // root
-                        QMIN(m_recDepth,m_maxDistance),  // maxDist
-                        baseName,                        // baseName
-                        thisDir,                         // thisDir
-                        DotNode::Dependency,             // gt
-                        format,                          // format
-                        FALSE,                           // lrRank
-                        FALSE,                           // renderParents
-                        !m_inverse                       // backArrows
-    );
+    findMaximalDotGraph(m_startNode,                      // root
+                        QMIN(m_recDepth,m_maxDistance),   // maxDist
+                        baseName,                         // baseName
+                        thisDir,                          // thisDir
+                        DotNode::CallGraph,               // gt
+                        format,                           // format
+                        TRUE,                             // lrRank
+                        FALSE,                            // renderParents
+                        FALSE                             // backArrows
+                       );
     if (format==BITMAP)
     {
       // run dot to create a bitmap image
@@ -2045,16 +2046,13 @@ QCString DotInclDepGraph::writeGraph(QTextStream &out,
         }
       }
     }
-
-    if (Config_getBool("DOT_CLEANUP")) thisDir.remove(baseName+".dot");
   }
 
   if (format==BITMAP && generateImageMap)
   {
     out << "<p><center><img src=\"" << relPath << baseName << "." 
-      << imgExt << "\" border=\"0\" usemap=\"#"
-      << mapName << "_map\" alt=\"";
-    if (m_inverse) out << "Included by dependency graph"; else out << "Include dependency graph";
+        << imgExt << "\" border=\"0\" usemap=\"#"
+        << mapName << "_map\" alt=\"";
     out << "\">";
     out << "</center>" << endl;
     QString tmpstr;
@@ -2066,6 +2064,7 @@ QCString DotInclDepGraph::writeGraph(QTextStream &out,
       out << tmpstr;
       out << "</map>" << endl;
     }
+    //thisDir.remove(baseName+".map");
   }
   else if (format==EPS)
   {
@@ -2076,18 +2075,19 @@ QCString DotInclDepGraph::writeGraph(QTextStream &out,
       QDir::setCurrent(oldDir);
       return baseName;
     }
-
     int maxWidth = 420; /* approx. page width in points */
-
+   
     out << "\\begin{figure}[H]\n"
-      "\\begin{center}\n"
-      "\\leavevmode\n"
-      "\\includegraphics[width=" << QMIN(width/2,maxWidth) 
-      << "pt]{" << baseName << "}\n"
-      "\\end{center}\n"
-      "\\end{figure}\n";
+           "\\begin{center}\n"
+           "\\leavevmode\n"
+           "\\includegraphics[width=" << QMIN(width/2,maxWidth) 
+                                      << "pt]{" << baseName << "}\n"
+           "\\end{center}\n"
+           "\\end{figure}\n";
   }
 
+  if (Config_getBool("DOT_CLEANUP")) thisDir.remove(baseName+".dot");
+
   QDir::setCurrent(oldDir);
   return baseName;
 }
@@ -2338,7 +2338,7 @@ bool DotCallGraph::isTrivial() const
 
 //-------------------------------------------------------------
 
-DotDirDeps::DotDirDeps(DirDef *)
+DotDirDeps::DotDirDeps(DirDef *dir) : m_dir(dir)
 {
 }
 
@@ -2346,6 +2346,142 @@ DotDirDeps::~DotDirDeps()
 {
 }
 
+QCString DotDirDeps::writeGraph(QTextStream &out,
+                            GraphOutputFormat format,
+                            const char *path,
+                            const char *relPath,
+                            bool generateImageMap)
+{
+  QDir d(path);
+  // store the original directory
+  if (!d.exists()) 
+  { 
+    err("Error: Output dir %s does not exist!\n",path); exit(1);
+  }
+  QCString oldDir = convertToQCString(QDir::currentDirPath());
+  // go to the html output directory (i.e. path)
+  QDir::setCurrent(d.absPath());
+  QDir thisDir;
+
+  QCString baseName=m_dir->getOutputFileBase()+"_dep";
+  QCString mapName=baseName;
+  QCString imgExt = Config_getEnum("DOT_IMAGE_FORMAT");
+
+  // todo: create check, update md5 checksum
+  {
+    QFile f(baseName+".dot");
+    if (!f.open(IO_WriteOnly))
+    {
+      err("Cannot create file %s.dot for writing!\n",baseName.data());
+    }
+    QTextStream t(&f);
+    m_dir->writeDepGraph(t);
+    f.close();
+    
+    if (format==BITMAP)
+    {
+      // run dot to create a bitmap image
+      QCString dotArgs(maxCmdLine);
+      QCString imgName=baseName+"."+imgExt;
+      dotArgs.sprintf("\"%s.dot\" -T%s -o \"%s\"",
+          baseName.data(),imgExt.data(),imgName.data());
+      if (generateImageMap)
+      {
+        // run dot also to create an image map
+        dotArgs+=QCString(maxCmdLine).sprintf(" -Timap -o \"%s.map\"",
+            baseName.data());
+      }
+      if (iSystem(Config_getString("DOT_PATH")+"dot",dotArgs)!=0)
+      {
+        err("Problems running dot. Check your installation!\n");
+        QDir::setCurrent(oldDir);
+        return baseName;
+      }
+      checkDotResult(imgName);
+    }
+    else if (format==EPS)
+    {
+      // run dot to create a .eps image
+      QCString dotArgs(maxCmdLine);
+      dotArgs.sprintf("-Tps \"%s.dot\" -o \"%s.eps\"",
+          baseName.data(),baseName.data());
+      if (iSystem(Config_getString("DOT_PATH")+"dot",dotArgs)!=0)
+      {
+        err("Problems running dot. Check your installation!\n");
+        QDir::setCurrent(oldDir);
+        return baseName;
+      }
+      if (Config_getBool("USE_PDFLATEX"))
+      {
+        QCString epstopdfArgs(maxCmdLine);
+        epstopdfArgs.sprintf("\"%s.eps\" --outfile=\"%s.pdf\"",
+            baseName.data(),baseName.data());
+        if (iSystem("epstopdf",epstopdfArgs,TRUE)!=0)
+        {
+          err("Error: Problems running epstopdf. Check your TeX installation!\n");
+          QDir::setCurrent(oldDir);
+          return baseName;
+        }
+      }
+    }
+  }
+
+  if (format==BITMAP && generateImageMap)
+  {
+    out << "<p><center><img src=\"" << relPath << baseName << "." 
+        << imgExt << "\" border=\"0\" usemap=\"#"
+        << mapName << "_map\" alt=\"";
+    out << m_dir->displayName();
+    out << "\">";
+    out << "</center>" << endl;
+    QString tmpstr;
+    QTextOStream tmpout(&tmpstr);
+    convertMapFile(tmpout,baseName+".map",relPath,TRUE);
+    if (!tmpstr.isEmpty())
+    {
+      out << "<map name=\"" << mapName << "_map\">" << endl;
+      out << tmpstr;
+      out << "</map>" << endl;
+    }
+    else
+    {
+      //printf("Map is empty!\n");
+    }
+    //thisDir.remove(baseName+".map");
+  }
+  else if (format==EPS)
+  {
+    int width,height;
+    if (!readBoundingBoxEPS(baseName+".eps",&width,&height))
+    {
+      err("Error: Could not extract bounding box from .eps!\n");
+      QDir::setCurrent(oldDir);
+      return baseName;
+    }
+    int maxWidth = 420; /* approx. page width in points */
+   
+    out << "\\begin{figure}[H]\n"
+           "\\begin{center}\n"
+           "\\leavevmode\n"
+           "\\includegraphics[width=" << QMIN(width/2,maxWidth) 
+                                      << "pt]{" << baseName << "}\n"
+           "\\end{center}\n"
+           "\\end{figure}\n";
+  }
+
+  if (Config_getBool("DOT_CLEANUP")) thisDir.remove(baseName+".dot");
+
+  QDir::setCurrent(oldDir);
+  return baseName;
+
+
+}
+
+bool DotDirDeps::isTrivial() const
+{
+  return m_dir->depGraphIsTrivial();
+}
+
 //-------------------------------------------------------------
 
 void generateGraphLegend(const char *path)
diff --git a/src/dot.h b/src/dot.h
index 5c5ed22..477eba4 100644
--- a/src/dot.h
+++ b/src/dot.h
@@ -207,6 +207,14 @@ class DotDirDeps
   public:
     DotDirDeps(DirDef *dir);
    ~DotDirDeps();
+    bool isTrivial() const;
+    QCString writeGraph(QTextStream &out,
+                        GraphOutputFormat format,
+                        const char *path,
+                        const char *relPath,
+                        bool writeImageMap=TRUE);
+  private:
+    DirDef *m_dir;
 };
 
 void generateGraphLegend(const char *path);
diff --git a/src/doxygen.cpp b/src/doxygen.cpp
index 0e57ce1..607ff85 100644
--- a/src/doxygen.cpp
+++ b/src/doxygen.cpp
@@ -122,6 +122,7 @@ bool           Doxygen::outputToWizard=FALSE;
 QDict<int> *   Doxygen::htmlDirMap = 0;
 QCache<LookupInfo> Doxygen::lookupCache(20000,20000);
 DirSDict       Doxygen::directories(17);
+SDict<DirRelation> Doxygen::dirRelations(257);
 
 static StringList     inputFiles;         
 static StringDict     excludeNameDict(1009);   // sections
@@ -4738,6 +4739,7 @@ static void findMember(Entry *root,
                   NamespaceSDict::Iterator nsdi(*nnl);
                   for (nsdi.toFirst();(nnd=nsdi.current());++nsdi)
                   {
+                    Debug::print(Debug::FindMembers,0,"   adding used namespace %s\n",nnd->qualifiedName().data());
                     nl->append(nnd->qualifiedName(),nnd);
                   }
                 }
@@ -4751,6 +4753,7 @@ static void findMember(Entry *root,
                   NamespaceSDict::Iterator nsdi(*fnl);
                   for (nsdi.toFirst();(fnd=nsdi.current());++nsdi)
                   {
+                    Debug::print(Debug::FindMembers,0,"   adding used namespace %s\n",fnd->qualifiedName().data());
                     nl->append(fnd->qualifiedName(),fnd);
                   }
                 }
@@ -4766,6 +4769,7 @@ static void findMember(Entry *root,
                   Definition *ncd;
                   for (csdi.toFirst();(ncd=csdi.current());++csdi)
                   {
+                    Debug::print(Debug::FindMembers,0,"   adding used class %s\n",ncd->qualifiedName().data());
                     cl->append(ncd->qualifiedName(),ncd);
                   }
                 }
@@ -4779,6 +4783,7 @@ static void findMember(Entry *root,
                   Definition *fcd;
                   for (csdi.toFirst();(fcd=csdi.current());++csdi)
                   {
+                    Debug::print(Debug::FindMembers,0,"   adding used class %s\n",fcd->qualifiedName().data());
                     cl->append(fcd->qualifiedName(),fcd);
                   }
                 }
@@ -7330,10 +7335,7 @@ static void readFiles(BufStr &output)
 
     bufPtr->addChar('\n'); /* to prevent problems under Windows ? */
 
-    //if (!multiLineIsBrief)
-    //{
-      convertCppComments(&tempBuf,&output);
-    //}
+    convertCppComments(&tempBuf,&output,fileName);
 
     s=inputFiles.next();
     //printf("-------> adding new line\n");
@@ -7553,6 +7555,126 @@ static void readFormulaRepository()
 }
 
 //----------------------------------------------------------------------------
+
+static QDict<void> aliasesProcessed;
+
+static QCString expandAliasesRec(const QCString s)
+{
+  QCString result;
+  static QRegExp cmdPat("[\\\\@][a-z_A-Z][a-z_A-Z0-9]*");
+  QCString value=s;
+  int i,p=0,l;
+  while ((i=cmdPat.match(value,p,&l))!=-1)
+  {
+    result+=value.mid(p,i-p);
+    QCString cmd=value.mid(i+1,l-1);
+    //printf("Found command '%s'\n",cmd.data());
+    QCString *aliasText=Doxygen::aliasDict.find(cmd);
+    if (aliasesProcessed.find(cmd)==0 && aliasText) // expand the alias
+    {
+      aliasesProcessed.insert(cmd,(void *)0x8);
+      result+=expandAliasesRec(*aliasText);
+      aliasesProcessed.remove(cmd);
+    }
+    else // command is not an alias
+    {
+      result+=value.mid(i,l);
+    }
+    p=i+l;
+  }
+  result+=value.right(value.length()-p);
+
+  //printf("expandAliases '%s'->'%s'\n",s.data(),result.data());
+  return result;
+}
+
+static void expandAliases()
+{
+  QDictIterator<QCString> adi(Doxygen::aliasDict);
+  QCString *s;
+  for (adi.toFirst();(s=adi.current());++adi)
+  {
+    aliasesProcessed.clear();
+    *s = expandAliasesRec(*s);
+  }
+}
+
+//----------------------------------------------------------------------------
+
+static void escapeAliases()
+{
+  QDictIterator<QCString> adi(Doxygen::aliasDict);
+  QCString *s;
+  for (adi.toFirst();(s=adi.current());++adi)
+  {
+    QCString value=*s,newValue;
+    int in,p=0;
+    // for each \n in the alias command value
+    while ((in=value.find("\\n",p))!=-1)
+    {
+      newValue+=value.mid(p,in-p);
+      // expand \n's except if \n is part of a built-in command.
+      if (value.mid(in,5)!="\\note" && 
+          value.mid(in,5)!="\\name" && 
+          value.mid(in,10)!="\\namespace" && 
+          value.mid(in,14)!="\\nosubgrouping"
+         ) 
+      {
+        newValue+="\\_linebr ";
+      }
+      else 
+      {
+        newValue+="\\n";
+      }
+      p=in+2;
+    }
+    newValue+=value.mid(p,value.length()-p);
+    *s=newValue;
+    //printf("Alias %s has value %s\n",adi.currentKey().data(),s->data());
+  }
+}
+
+//----------------------------------------------------------------------------
+
+static void readAliases()
+{ 
+  // add aliases to a dictionary
+  Doxygen::aliasDict.setAutoDelete(TRUE);
+  QStrList &aliasList = Config_getList("ALIASES");
+  const char *s=aliasList.first();
+  while (s)
+  {
+    if (Doxygen::aliasDict[s]==0)
+    {
+      QCString alias=s;
+      int i=alias.find('=');
+      if (i>0)
+      {
+        QCString name=alias.left(i).stripWhiteSpace();
+        QCString value=alias.right(alias.length()-i-1);
+        //printf("Alias: found name=`%s' value=`%s'\n",name.data(),value.data()); 
+        if (!name.isEmpty())
+        {
+          QCString *dn=Doxygen::aliasDict[name];
+          if (dn==0) // insert new alias
+          {
+            Doxygen::aliasDict.insert(name,new QCString(value));
+          }
+          else // overwrite previous alias
+          {
+            *dn=value;
+          }
+        }
+      }
+    }
+    s=aliasList.next();
+  }
+  expandAliases();
+  escapeAliases();
+  aliasesProcessed.clear();
+}
+
+//----------------------------------------------------------------------------
 // print the usage of doxygen
 
 static void usage(const char *name)
@@ -7620,6 +7742,8 @@ void initDoxygen()
   Doxygen::memGrpInfoDict.setAutoDelete(TRUE);
   Doxygen::tagDestinationDict.setAutoDelete(TRUE);
   Doxygen::lookupCache.setAutoDelete(TRUE);
+  Doxygen::directories.setAutoDelete(TRUE);
+  Doxygen::dirRelations.setAutoDelete(TRUE);
 }
 
 void cleanUpDoxygen()
@@ -8088,60 +8212,8 @@ void parseInput()
     s=expandAsDefinedList.next();
   }
 
-  // add aliases to a dictionary
-  Doxygen::aliasDict.setAutoDelete(TRUE);
-  QStrList &aliasList = Config_getList("ALIASES");
-  s=aliasList.first();
-  while (s)
-  {
-    if (Doxygen::aliasDict[s]==0)
-    {
-      QCString alias=s;
-      int i=alias.find('=');
-      if (i>0)
-      {
-        QCString name=alias.left(i).stripWhiteSpace();
-        QCString value=alias.right(alias.length()-i-1);
-        QCString newValue;
-        int in,p=0;
-        // for each \n in the alias command value
-        while ((in=value.find("\\n",p))!=-1)
-        {
-          newValue+=value.mid(p,in-p);
-          // expand \n's except if \n is part of a built-in command.
-          if (value.mid(in,5)!="\\note" && 
-              value.mid(in,5)!="\\name" && 
-              value.mid(in,10)!="\\namespace" && 
-              value.mid(in,14)!="\\nosubgrouping"
-             ) 
-          {
-            newValue+="\n";
-          }
-          else 
-          {
-            newValue+="\\n";
-          }
-          p=in+2;
-        }
-        newValue+=value.mid(p,value.length()-p);
-        value=newValue;
-        //printf("Alias: found name=`%s' value=`%s'\n",name.data(),value.data()); 
-        if (!name.isEmpty())
-        {
-          QCString *dn=Doxygen::aliasDict[name];
-          if (dn==0) // insert new alias
-          {
-            Doxygen::aliasDict.insert(name,new QCString(value));
-          }
-          else // overwrite previous alias
-          {
-            *dn=value;
-          }
-        }
-      }
-    }
-    s=aliasList.next();
-  }
+  // read aliases and store them in a dictionary
+  readAliases();
 
   /**************************************************************************
    *             Handle Tag Files                                           *
@@ -8448,8 +8520,11 @@ void parseInput()
   msg("Adding todo/test/bug list items...\n");
   addListReferences();
 
-  msg("Computing dependencies between directories...\n");
-  computeDirDependencies();
+  if (Config_getBool("SHOW_DIRECTORIES"))
+  {
+    msg("Computing dependencies between directories...\n");
+    computeDirDependencies();
+  }
 }
 
 void generateOutput()
diff --git a/src/doxygen.h b/src/doxygen.h
index a196432..0257fb2 100644
--- a/src/doxygen.h
+++ b/src/doxygen.h
@@ -115,6 +115,7 @@ class Doxygen
     static QDict<int>               *htmlDirMap;
     static QCache<LookupInfo>        lookupCache;
     static DirSDict                  directories;
+    static SDict<DirRelation>        dirRelations;
 };
 
 void initDoxygen();
diff --git a/src/htmlgen.cpp b/src/htmlgen.cpp
index 8223562..757c72c 100644
--- a/src/htmlgen.cpp
+++ b/src/htmlgen.cpp
@@ -319,8 +319,16 @@ static const char *defaultStyleSheet =
 "}\n"
 "a:visited {\n"
 "	color: #3D2185;\n"
+"}\n"
+".dirtab { padding: 4px;\n"
+"          border-collapse: collapse;\n"
+"          border: 1px solid #b0b0b0;\n"
+"}\n"
+"TH.dirtab { background: #eeeeff;\n"
+"            font-weight: bold;\n"
 "}\n";
 
+
 static QCString g_header;
 static QCString g_footer;
 
@@ -1246,6 +1254,15 @@ void HtmlGenerator::endCallGraph(DotCallGraph &g)
   g.writeGraph(t,BITMAP,dir,relPath);
 }
 
+void HtmlGenerator::startDirDepGraph()
+{
+}
+
+void HtmlGenerator::endDirDepGraph(DotDirDeps &g)
+{
+  g.writeGraph(t,BITMAP,dir,relPath);
+}
+
 void HtmlGenerator::writeGraphicalHierarchy(DotGfxHierarchyTable &g)
 {
   g.writeGraph(t,dir);
diff --git a/src/htmlgen.h b/src/htmlgen.h
index ee2112a..ebaf4fa 100644
--- a/src/htmlgen.h
+++ b/src/htmlgen.h
@@ -192,6 +192,8 @@ class HtmlGenerator : public OutputGenerator
     void endInclDepGraph(DotInclDepGraph &g);
     void startCallGraph();
     void endCallGraph(DotCallGraph &g);
+    void startDirDepGraph();
+    void endDirDepGraph(DotDirDeps &g);
     void writeGraphicalHierarchy(DotGfxHierarchyTable &g);
 
     void startTextBlock(bool) {}
diff --git a/src/htmlhelp.cpp b/src/htmlhelp.cpp
index a90a919..0d5b9c8 100644
--- a/src/htmlhelp.cpp
+++ b/src/htmlhelp.cpp
@@ -174,7 +174,27 @@ void HtmlHelpIndex::writeFields(QTextStream &t)
     { // finish old list at level 2
       if (level2Started) t << "  </UL>" << endl;
       level2Started=FALSE;
-    
+
+      // <Antony>
+      // Added this code so that an item with only one subitem is written
+      // without any subitem.
+      // For example:
+      //   a1, b1 -> will create only a1, not separate subitem for b1
+      //   a2, b2
+      //   a2, b3
+      QCString nextLevel1;
+      IndexField* fnext = ++ifli;
+      if (fnext)
+      {
+        nextLevel1 = fnext->name.left(fnext->name.find('?'));
+        --ifli;
+      }
+      if (level1 != nextLevel1)
+      {
+        level2 = "";
+      }
+      // </Antony>
+
       if (level2.isEmpty())
       {
         t << "  <LI><OBJECT type=\"text/sitemap\">";
@@ -189,7 +209,9 @@ void HtmlHelpIndex::writeFields(QTextStream &t)
         if (f->link)
         {
           t << "  <LI><OBJECT type=\"text/sitemap\">";
-          t << "<param name=\"Local\" value=\"" << f->url << Doxygen::htmlFileExtension << "\">";
+          t << "<param name=\"Local\" value=\"" << f->url << Doxygen::htmlFileExtension;
+          if (!f->anchor.isEmpty()) t << "#" << f->anchor;  
+          t << "\">";
           t << "<param name=\"Name\" value=\"" << level1 << "\">"
                "</OBJECT>\n";
         }
@@ -530,6 +552,6 @@ void HtmlHelp::addIndexItem(const char *level1, const char *level2,
                             const char *ref, const char *anchor)
 {
   index->addItem(level1,level2,ref,anchor,TRUE);
-  index->addItem(level2,level1,ref,anchor,FALSE);
+  index->addItem(level2,level1,ref,anchor,TRUE);
 }
 
diff --git a/src/latexgen.cpp b/src/latexgen.cpp
index 87dca72..70630ae 100644
--- a/src/latexgen.cpp
+++ b/src/latexgen.cpp
@@ -1457,6 +1457,15 @@ void LatexGenerator::endCallGraph(DotCallGraph &g)
   g.writeGraph(t,EPS,Config_getString("LATEX_OUTPUT"),relPath);
 }
 
+void LatexGenerator::startDirDepGraph() 
+{
+}
+
+void LatexGenerator::endDirDepGraph(DotDirDeps &g) 
+{
+  g.writeGraph(t,EPS,Config_getString("LATEX_OUTPUT"),relPath);
+}
+
 void LatexGenerator::startDescription() 
 { 
   t << "\\begin{description}" << endl; 
diff --git a/src/latexgen.h b/src/latexgen.h
index faf9f98..237e4f0 100644
--- a/src/latexgen.h
+++ b/src/latexgen.h
@@ -185,6 +185,8 @@ class LatexGenerator : public OutputGenerator
     void endInclDepGraph(DotInclDepGraph &);
     void startCallGraph();
     void endCallGraph(DotCallGraph &);
+    void startDirDepGraph();
+    void endDirDepGraph(DotDirDeps &g);
     void writeGraphicalHierarchy(DotGfxHierarchyTable &) {}
 
     void startTextBlock(bool) {}
diff --git a/src/mangen.h b/src/mangen.h
index ddc5adb..e4a145b 100644
--- a/src/mangen.h
+++ b/src/mangen.h
@@ -231,6 +231,8 @@ class ManGenerator : public OutputGenerator
     void endInclDepGraph(DotInclDepGraph &) {}
     void startCallGraph() {}
     void endCallGraph(DotCallGraph &) {}
+    void startDirDepGraph() {} 
+    void endDirDepGraph(DotDirDeps &) {}
     void writeGraphicalHierarchy(DotGfxHierarchyTable &) {}
 
     void startTextBlock(bool) {}
diff --git a/src/outputgen.h b/src/outputgen.h
index 8d02b82..16e56a8 100644
--- a/src/outputgen.h
+++ b/src/outputgen.h
@@ -30,6 +30,7 @@ class ClassDiagram;
 class DotClassGraph;
 class DotInclDepGraph;
 class DotCallGraph;
+class DotDirDeps;
 class DotGfxHierarchyTable;
 class DocNode;
 class MemberDef;
@@ -339,6 +340,8 @@ class OutputGenerator : public BaseOutputDocInterface
     virtual void endInclDepGraph(DotInclDepGraph &g) = 0;
     virtual void startCallGraph() = 0;
     virtual void endCallGraph(DotCallGraph &g) = 0;
+    virtual void startDirDepGraph() = 0;
+    virtual void endDirDepGraph(DotDirDeps &g) = 0;
     virtual void writeGraphicalHierarchy(DotGfxHierarchyTable &g) = 0;
     //virtual void startQuickIndexItem(const char *s,const char *l) = 0;
     //virtual void endQuickIndexItem() = 0;
diff --git a/src/outputlist.cpp b/src/outputlist.cpp
index 248e9b9..a0878f3 100644
--- a/src/outputlist.cpp
+++ b/src/outputlist.cpp
@@ -266,6 +266,7 @@ FORALL1(int a1,a1)
 FORALL1(DotClassGraph &a1,a1)
 FORALL1(DotInclDepGraph &a1,a1)
 FORALL1(DotCallGraph &a1,a1)
+FORALL1(DotDirDeps &a1,a1)
 FORALL1(DotGfxHierarchyTable &a1,a1)
 FORALL1(SectionTypes a1,a1)
 #if defined(HAS_BOOL_TYPE) || defined(Q_HAS_BOOL_TYPE)
diff --git a/src/outputlist.h b/src/outputlist.h
index a4be838..12c76ff 100644
--- a/src/outputlist.h
+++ b/src/outputlist.h
@@ -34,6 +34,7 @@
   
 class ClassDiagram;
 class DotClassGraph;
+class DotDirDeps;
 class DotInclDepGraph;
 class DotGfxHierarchyTable;
 class SectionDict;
@@ -322,6 +323,10 @@ class OutputList : public OutputDocInterface
     { forall(&OutputGenerator::startCallGraph); }
     void endCallGraph(DotCallGraph &g)
     { forall(&OutputGenerator::endCallGraph,g); }
+    void startDirDepGraph()
+    { forall(&OutputGenerator::startDirDepGraph); }
+    void endDirDepGraph(DotDirDeps &g)
+    { forall(&OutputGenerator::endDirDepGraph,g); }
     void writeGraphicalHierarchy(DotGfxHierarchyTable &g)
     { forall(&OutputGenerator::writeGraphicalHierarchy,g); }
     void startTextBlock(bool dense=FALSE)
@@ -387,6 +392,7 @@ class OutputList : public OutputDocInterface
     FORALLPROTO1(DotClassGraph &);
     FORALLPROTO1(DotInclDepGraph &);
     FORALLPROTO1(DotCallGraph &);
+    FORALLPROTO1(DotDirDeps &);
     FORALLPROTO1(DotGfxHierarchyTable &);
     FORALLPROTO1(SectionTypes);
 #if defined(HAS_BOOL_TYPE) || defined(Q_HAS_BOOL_TYPE)
diff --git a/src/pre.l b/src/pre.l
index 8266c1c..99d581c 100644
--- a/src/pre.l
+++ b/src/pre.l
@@ -1079,7 +1079,7 @@ static void readIncludeFile(const QCString &inc)
         if (g_yyFileDef)
         {
 	  //printf("Adding include dependency %s->%s\n",oldFileDef->name().data(),incFileName.data());
-  	  g_yyFileDef->addIncludedByDependency(oldFileDef,oldFileDef->name(),localInclude,g_isImported);
+  	  g_yyFileDef->addIncludedByDependency(oldFileDef,oldFileDef->docName(),localInclude,g_isImported);
         }
       }
       FileState *fs=new FileState;
@@ -1114,7 +1114,7 @@ static void readIncludeFile(const QCString &inc)
         if (fd)
         {
           //printf("Adding include dependency (2) %s->%s ambig=%d\n",oldFileDef->name().data(),fd->name().data(),ambig);
-  	  fd->addIncludedByDependency(oldFileDef,oldFileDef->name(),localInclude,g_isImported);
+  	  fd->addIncludedByDependency(oldFileDef,oldFileDef->docName(),localInclude,g_isImported);
         }
       }
       if (Debug::isFlagSet(Debug::Preprocessor))
diff --git a/src/rtfgen.cpp b/src/rtfgen.cpp
index f243d1b..ad240f3 100644
--- a/src/rtfgen.cpp
+++ b/src/rtfgen.cpp
@@ -2258,6 +2258,28 @@ void RTFGenerator::endCallGraph(DotCallGraph &g)
   DBG_RTF(t << "{\\comment (endCallGraph)}"    << endl)
 }
 
+void RTFGenerator::startDirDepGraph()
+{
+  DBG_RTF(t << "{\\comment (startDirDepGraph)}"    << endl)
+}
+
+void RTFGenerator::endDirDepGraph(DotDirDeps &g)
+{
+  newParagraph();
+
+  QCString fileName = g.writeGraph(t,BITMAP,Config_getString("RTF_OUTPUT"),
+                        relPath,FALSE);
+
+  // display the file
+  t << "{" << endl;
+  t << rtf_Style_Reset << endl;
+  t << "\\par\\pard \\qc {\\field\\flddirty {\\*\\fldinst INCLUDEPICTURE \"";
+  t << fileName << "." << Config_getEnum("DOT_IMAGE_FORMAT");
+  t << "\" \\\\d \\\\*MERGEFORMAT}{\\fldrslt IMAGE}}\\par" << endl;
+  t << "}" << endl;
+  DBG_RTF(t << "{\\comment (endDirDepGraph)}"    << endl)
+}
+
 /** Tests the integrity of the result by counting brackets.
  *
  */
diff --git a/src/rtfgen.h b/src/rtfgen.h
index b4c1dac..1c92bee 100644
--- a/src/rtfgen.h
+++ b/src/rtfgen.h
@@ -227,6 +227,8 @@ class RTFGenerator : public OutputGenerator
     void endInclDepGraph(DotInclDepGraph &);
     void startCallGraph();
     void endCallGraph(DotCallGraph &);
+    void startDirDepGraph();
+    void endDirDepGraph(DotDirDeps &g);
     void writeGraphicalHierarchy(DotGfxHierarchyTable &) {}
 
     void startMemberGroupHeader(bool);
diff --git a/src/scanner.l b/src/scanner.l
index 9cd310e..8dbd70c 100644
--- a/src/scanner.l
+++ b/src/scanner.l
@@ -5612,18 +5612,22 @@ PHPKW	  ("require"|"require_once"|"include"|"include_once"|"echo")[^a-zA-Z0-9_;]
 					  unput('/');unput('*');
 					  BEGIN( tmpDocType );
 					}
+<Doc,JavaDoc,LineDoc,ClassDocBrief,AfterDocBrief,AfterDocLine,CopyArgCommentLine,ClassDoc,PageDoc,AfterDoc,CopyArgComment>"\\_linebr " { 
+                                          // used to compensate for misalignments due to \n's inside ALIASES
+  					  current->doc += '\n';
+  					}
 <Doc,JavaDoc,ClassDoc,PageDoc,ReadFormulaShort,ReadFormulaLong,AfterDoc>^{B}*(("//"{B}*)?)"*"+[ \t]*"-"("#")?{B}+ { 
-  				         current->doc += yytext; 
+  				          current->doc += yytext; 
 					}
 <Doc,JavaDoc,ClassDoc,PageDoc,ReadFormulaShort,ReadFormulaLong,AfterDoc>^{B}*(("//"{B}*)?)"*"+[ \t]*"."{B}*\n { 
-  				         current->doc += yytext; 
-					 yyLineNr++;
+  				          current->doc += yytext; 
+					  yyLineNr++;
 					}
 <ClassDocBrief,AfterDocBrief>^{B}*(("//"{B}*)?)"*"+[ \t]*"-"("#")?{B}+ { 
-  				         current->brief += "-"; 
+  				          current->brief += "-"; 
 					}
 <ClassDocBrief,AfterDocBrief>^{B}*(("//"{B}*)?)"*"+[ \t]*"."{B}*\n { 
-  				         current->brief += "."; yyLineNr++; 
+  				          current->brief += "."; yyLineNr++; 
 					}
 <Doc,JavaDoc,ClassDoc,PageDoc,ReadFormulaShort,ReadFormulaLong,ClassDocBrief,AfterDoc,AfterDocBrief>^{B}*(("//"{B}*)?)"*"+/[^/]
 <Doc,JavaDoc,ClassDoc,PageDoc,ReadFormulaShort,ReadFormulaLong,ClassDocBrief,AfterDoc,AfterDocBrief>^{B}*(("//"{B}*)?)"*"+{B}+ { 
diff --git a/src/sortdict.h b/src/sortdict.h
index 3b8be02..5a04a11 100644
--- a/src/sortdict.h
+++ b/src/sortdict.h
@@ -234,7 +234,7 @@ class SDict
     
     /*! Returns the number of items stored in the dictionary
      */
-    int count()
+    int count() const
     {
       return m_list->count();
     }
diff --git a/src/util.cpp b/src/util.cpp
index 6b011bd..1f625c6 100644
--- a/src/util.cpp
+++ b/src/util.cpp
@@ -45,6 +45,7 @@
 #include "groupdef.h"
 #include "reflist.h"
 #include "pagedef.h"
+#include "debug.h"
 
 #if !defined(_WIN32) || defined(__CYGWIN__)
 #include <unistd.h>
@@ -140,7 +141,7 @@ int iSystem(const char *command,const char *args,bool isBatchFile)
   }
   fullCmd += " ";
   fullCmd += args;
-  //printf("iSystem: Executing %s\n",fullCmd.data());
+  Debug::print(Debug::ExtCmd,0,"Executing external command \"%s\"\n",fullCmd.data());
 
 #if !defined(_WIN32) || defined(__CYGWIN__)
   isBatchFile=isBatchFile;
@@ -2597,6 +2598,172 @@ bool matchArguments(ArgumentList *srcAl,ArgumentList *dstAl,
   return TRUE; // all arguments match 
 }
 
+static QCString extractCanonicalType(Definition *d,FileDef *fs,const Argument *arg)
+{
+  QCString type = arg->type;
+  QCString name = arg->name;
+  if ((type=="const" || type=="volatile") && !name.isEmpty()) 
+  { // name is part of type => correct
+    type+=" ";
+    type+=name;
+  } 
+  if (name=="const" || name=="volatile")
+  { // name is part of type => correct
+    if (!type.isEmpty()) type+=" ";
+    type+=name;
+  }
+
+  // strip const and volatile keywords that are not relatevant for the type
+  stripIrrelevantConstVolatile(type);
+  
+  // strip leading keywords
+  if (type.left(6)=="class ")         type=type.right(type.length()-6);
+  else if (type.left(7)=="struct ")   type=type.right(type.length()-7);
+  else if (type.left(6)=="union ")    type=type.right(type.length()-6);
+  else if (type.left(5)=="enum ")     type=type.right(type.length()-5);
+  else if (type.left(9)=="typename ") type=type.right(type.length()-9);
+
+  static QRegExp id("[a-z_A-Z][a-z_A-Z0-9]*");
+
+  
+  QCString canType;
+  int i,p=0,l;
+  while ((i=id.match(type,p,&l))) // foreach identifier in the type
+  {
+    canType += type.mid(p,i-p);
+    QCString word = type.mid(i,l);
+    ClassDef *cd = getResolvedClass(d,fs,word);
+    if (cd)
+    {
+      canType+=cd->qualifiedName();
+    }
+    else
+    {
+      canType+=word;
+    }
+    p=i+l;
+  }
+  canType += type.right(type.length()-p);
+ 
+  return removeRedundantWhiteSpace(canType);
+}
+
+static bool matchArgument2(
+                   Definition *srcScope,FileDef *srcFileScope,const Argument *srcA,
+                   Definition *dstScope,FileDef *dstFileScope,const Argument *dstA
+                  )
+{
+  //printf("match argument start `%s|%s' <-> `%s|%s' using nsp=%p class=%p\n",
+  //    srcA->type.data(),srcA->name.data(),
+  //    dstA->type.data(),dstA->name.data(),
+  //    usingNamespaces,
+  //    usingClasses);
+
+  if (srcA->array!=dstA->array) // nomatch for char[] against char
+  {
+    NOMATCH
+    return FALSE;
+  }
+
+  QCString canonicalSrcType = extractCanonicalType(srcScope,srcFileScope,srcA);
+  QCString canonicalDstType = extractCanonicalType(dstScope,dstFileScope,dstA);
+  
+  if (canonicalSrcType==canonicalDstType)
+  {
+    MATCH
+    return TRUE;
+  }
+  else
+  {
+    NOMATCH
+    return FALSE;
+  }
+}
+
+
+// new algorithm for argument matching
+bool matchArguments2(Definition *srcScope,FileDef *srcFileScope,ArgumentList *srcAl,
+                     Definition *dstScope,FileDef *dstFileScope,ArgumentList *dstAl,
+                     bool checkCV
+                    )
+{
+  ASSERT(srcScope!=0 && dstScope!=0);
+
+  if (srcAl==0 || dstAl==0)
+  {
+    bool match = srcAl==dstAl; // at least one of the members is not a function
+    if (match)
+    {
+      MATCH
+      return TRUE;
+    }
+    else
+    {
+      NOMATCH
+      return FALSE;
+    }
+  }
+  
+  // handle special case with void argument
+  if ( srcAl->count()==0 && dstAl->count()==1 && 
+       dstAl->getFirst()->type=="void" )
+  { // special case for finding match between func() and func(void)
+    Argument *a=new Argument;
+    a->type = "void";
+    srcAl->append(a);
+    MATCH
+    return TRUE;
+  }
+  if ( dstAl->count()==0 && srcAl->count()==1 &&
+       srcAl->getFirst()->type=="void" )
+  { // special case for finding match between func(void) and func()
+    Argument *a=new Argument;
+    a->type = "void";
+    dstAl->append(a);
+    MATCH
+    return TRUE;
+  }
+  
+  if (srcAl->count() != dstAl->count())
+  {
+    NOMATCH
+    return FALSE; // different number of arguments -> no match
+  }
+
+  if (checkCV)
+  {
+    if (srcAl->constSpecifier != dstAl->constSpecifier) 
+    {
+      NOMATCH
+      return FALSE; // one member is const, the other not -> no match
+    }
+    if (srcAl->volatileSpecifier != dstAl->volatileSpecifier)
+    {
+      NOMATCH
+      return FALSE; // one member is volatile, the other not -> no match
+    }
+  }
+
+  // so far the argument list could match, so we need to compare the types of
+  // all arguments.
+  ArgumentListIterator srcAli(*srcAl),dstAli(*dstAl);
+  Argument *srcA,*dstA;
+  for (;(srcA=srcAli.current(),dstA=dstAli.current());++srcAli,++dstAli)
+  { 
+    if (!matchArgument2(srcScope,srcFileScope,srcA,
+                        dstScope,dstFileScope,dstA)
+       )
+    {
+      NOMATCH
+      return FALSE;
+    }
+  }
+  MATCH
+  return TRUE; // all arguments match 
+}
+
+
+
 // merges the initializer of two argument lists
 // pre:  the types of the arguments in the list should match.
 void mergeArguments(ArgumentList *srcAl,ArgumentList *dstAl,bool forceNameOverwrite)
@@ -2934,7 +3101,7 @@ bool getDefs(const QCString &scName,const QCString &memberName,
           { // namespace is found
             bool match=TRUE;
             ArgumentList *argList=0;
-            if (args)
+            if (args && strcmp(args,"()")!=0)
             {
               argList=new ArgumentList;
               stringToArgumentList(args,argList);
@@ -3001,10 +3168,10 @@ bool getDefs(const QCString &scName,const QCString &memberName,
                 (gd && gd->isLinkable()) || (fd && fd->isLinkable()) 
                )
             {
-              //printf("fd=%p gd=%p inGroup=`%d' args=`%s'\n",fd,gd,inGroup,args);
+              //printf("    fd=%p gd=%p args=`%s'\n",fd,gd,args);
               bool match=TRUE;
               ArgumentList *argList=0;
-              if (args && !md->isDefine())
+              if (args && !md->isDefine() && strcmp(args,"()")!=0)
               {
                 argList=new ArgumentList;
                 stringToArgumentList(args,argList);