Updated the doxygen file.

doc/doxy.config.in

@@ -1,4 +1,4 @@
-# Doxyfile 1.5.8
+# Doxyfile 1.5.6
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project
@@ -57,8 +57,8 @@ CREATE_SUBDIRS         = NO
 # Croatian, Czech, Danish, Dutch, Farsi, Finnish, French, German, Greek, 
 # Hungarian, Italian, Japanese, Japanese-en (Japanese with English messages), 
 # Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian, Polish, 
-# Portuguese, Romanian, Russian, Serbian, Serbian-Cyrilic, Slovak, Slovene, 
+# Portuguese, Romanian, Russian, Serbian, Slovak, Slovene, Spanish, Swedish, 
-# Spanish, Swedish, and Ukrainian.
+# and Ukrainian.
 
 OUTPUT_LANGUAGE        = English
 
@@ -165,6 +165,13 @@ QT_AUTOBRIEF           = NO
 
 MULTILINE_CPP_IS_BRIEF = NO
 
+# If the DETAILS_AT_TOP tag is set to YES then Doxygen 
+# will output the detailed description near the top, like JavaDoc.
+# If set to NO, the detailed description appears after the member 
+# documentation.
+
+DETAILS_AT_TOP         = YES
+
 # If the INHERIT_DOCS tag is set to YES (the default) then an undocumented 
 # member inherits the documentation from any documented member that it 
 # re-implements.
@@ -217,17 +224,6 @@ OPTIMIZE_FOR_FORTRAN   = NO
 
 OPTIMIZE_OUTPUT_VHDL   = NO
 
-# Doxygen selects the parser to use depending on the extension of the files it parses. 
-# With this tag you can assign which parser to use for a given extension. 
-# Doxygen has a built-in mapping, but you can override or extend it using this tag. 
-# The format is ext=language, where ext is a file extension, and language is one of 
-# the parsers supported by doxygen: IDL, Java, Javascript, C#, C, C++, D, PHP, 
-# Objective-C, Python, Fortran, VHDL, C, C++. For instance to make doxygen treat 
-# .inc files as Fortran files (default is PHP), and .f files as C (default is Fortran), 
-# use: inc=Fortran f=C
-
-EXTENSION_MAPPING      = 
-
 # If you use STL classes (i.e. std::string, std::vector, etc.) but do not want 
 # to include (a tag file for) the STL sources as input, then you should 
 # set this tag to YES in order to let doxygen match functions declarations and 
@@ -280,23 +276,7 @@ SUBGROUPING            = YES
 # be useful for C code in case the coding convention dictates that all compound 
 # types are typedef'ed and only the typedef is referenced, never the tag name.
 
-TYPEDEF_HIDES_STRUCT   = NO
+TYPEDEF_HIDES_STRUCT   = YES
-
-# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to 
-# determine which symbols to keep in memory and which to flush to disk. 
-# When the cache is full, less often used symbols will be written to disk. 
-# For small to medium size projects (<1000 input files) the default value is 
-# probably good enough. For larger projects a too small cache size can cause 
-# doxygen to be busy swapping symbols to and from disk most of the time 
-# causing a significant performance penality. 
-# If the system has enough physical memory increasing the cache will improve the 
-# performance by keeping more symbols in memory. Note that the value works on 
-# a logarithmic scale so increasing the size by one will rougly double the 
-# memory usage. The cache size is given by this formula: 
-# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0, 
-# corresponding to a cache size of 2^16 = 65536 symbols
-
-SYMBOL_CACHE_SIZE      = 0
 
 #---------------------------------------------------------------------------
 # Build related configuration options
@@ -489,8 +469,7 @@ SHOW_DIRECTORIES       = NO
 SHOW_FILES             = YES
 
 # Set the SHOW_NAMESPACES tag to NO to disable the generation of the 
-# Namespaces page. 
+# Namespaces page.  This will remove the Namespaces entry from the Quick Index
-# This will remove the Namespaces entry from the Quick Index 
 # and from the Folder Tree View (if specified). The default is YES.
 
 SHOW_NAMESPACES        = YES
@@ -505,15 +484,6 @@ SHOW_NAMESPACES        = YES
 
 FILE_VERSION_FILTER    = 
 
-# 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 that represents 
-# doxygen'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.
-
-LAYOUT_FILE            = 
-
 #---------------------------------------------------------------------------
 # configuration options related to warning and progress messages
 #---------------------------------------------------------------------------
@@ -563,7 +533,7 @@ WARN_FORMAT            = "$file:$line: $text"
 # and error messages should be written. If left blank the output is written 
 # to stderr.
 
-#WARN_LOGFILE           = @CMAKE_CURRENT_BINARY_DIR@/doxy.log
+WARN_LOGFILE           = 
 
 #---------------------------------------------------------------------------
 # configuration options related to the input files
@@ -578,7 +548,6 @@ INPUT                  = @CMAKE_SOURCE_DIR@/include \
                          @CMAKE_SOURCE_DIR@/libssh \
                          @CMAKE_SOURCE_DIR@/doc
 
-
 # This tag can be used to specify the character encoding of the source files 
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is 
 # also the default input encoding. Doxygen uses libiconv (or the iconv built 
@@ -643,18 +612,15 @@ EXCLUDE_SYMBOLS        =
 # directories that contain example code fragments that are included (see 
 # the \include command).
 
-EXAMPLE_PATH           = @CMAKE_SOURCE_DIR@/tests \
+EXAMPLE_PATH           = @CMAKE_SOURCE_DIR@/examples
-                         @CMAKE_SOURCE_DIR@
 
 # If the value of the EXAMPLE_PATH tag contains directories, you can use the 
 # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp 
 # and *.h) to filter out the source-files in the directories. If left 
 # blank all files are included.
 
-EXAMPLE_PATTERNS       = *.cpp \
+EXAMPLE_PATTERNS       = *.c \
-                         *.cc \
                          *.h \
-                         *.hh \
                          INSTALL \
                          DEPENDENCIES \
                          CHANGELOG \
@@ -679,17 +645,14 @@ IMAGE_PATH             =
 # by executing (via popen()) the command <filter> <input-file>, where <filter> 
 # is the value of the INPUT_FILTER tag, and <input-file> is the name of an 
 # input file. Doxygen will then use the output that the filter program writes 
-# to standard output. 
+# to standard output.  If FILTER_PATTERNS is specified, this tag will be 
-# If FILTER_PATTERNS is specified, this tag will be 
 # ignored.
 
 INPUT_FILTER           = 
 
 # The FILTER_PATTERNS tag can be used to specify filters on a per file pattern 
-# basis. 
+# basis.  Doxygen will compare the file name with each pattern and apply the 
-# Doxygen will compare the file name with each pattern and apply the 
+# filter if there is a match.  The filters are a list of the form: 
-# filter if there is a match. 
-# The filters are a list of the form: 
 # pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further 
 # info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER 
 # is applied to all files.
@@ -739,8 +702,7 @@ REFERENCES_RELATION    = YES
 # If the REFERENCES_LINK_SOURCE tag is set to YES (the default)
 # and SOURCE_BROWSER tag is set to YES, then the hyperlinks from
 # functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will
-# link to the source code. 
+# link to the source code.  Otherwise they will link to the documentstion.
-# Otherwise they will link to the documentation.
 
 REFERENCES_LINK_SOURCE = YES
 
@@ -829,13 +791,12 @@ HTML_STYLESHEET        =
 
 HTML_ALIGN_MEMBERS     = YES
 
-# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML 
+# If the GENERATE_HTMLHELP tag is set to YES, additional index files 
-# documentation will contain sections that can be hidden and shown after the 
+# will be generated that can be used as input for tools like the 
-# page has loaded. For this to work a browser that supports 
+# Microsoft HTML help workshop to generate a compiled HTML help file (.chm) 
-# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox 
+# of the generated HTML documentation.
-# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari).
 
-HTML_DYNAMIC_SECTIONS  = NO
+GENERATE_HTMLHELP      = NO
 
 # If the GENERATE_DOCSET tag is set to YES, additional index files 
 # will be generated that can be used as input for Apple's Xcode 3 
@@ -845,7 +806,6 @@ HTML_DYNAMIC_SECTIONS  = NO
 # directory and running "make install" will install the docset in 
 # ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find 
 # it at startup.
-# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html for more information.
 
 GENERATE_DOCSET        = NO
 
@@ -863,12 +823,13 @@ DOCSET_FEEDNAME        = "Doxygen generated docs"
 
 DOCSET_BUNDLE_ID       = org.doxygen.Project
 
-# If the GENERATE_HTMLHELP tag is set to YES, additional index files 
+# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML 
-# will be generated that can be used as input for tools like the 
+# documentation will contain sections that can be hidden and shown after the 
-# Microsoft HTML help workshop to generate a compiled HTML help file (.chm) 
+# page has loaded. For this to work a browser that supports 
-# of the generated HTML documentation.
+# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox 
+# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari).
 
-GENERATE_HTMLHELP      = NO
+HTML_DYNAMIC_SECTIONS  = NO
 
 # If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can 
 # be used to specify the file name of the resulting .chm file. You 
@@ -907,55 +868,6 @@ BINARY_TOC             = NO
 
 TOC_EXPAND             = NO
 
-# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and QHP_VIRTUAL_FOLDER 
-# are set, an additional index file will be generated that can be used as input for 
-# Qt's qhelpgenerator to generate a Qt Compressed Help (.qch) of the generated 
-# HTML documentation.
-
-GENERATE_QHP           = NO
-
-# If the QHG_LOCATION tag is specified, the QCH_FILE tag can 
-# be used to specify the file name of the resulting .qch file. 
-# The path specified is relative to the HTML output folder.
-
-QCH_FILE               = 
-
-# The QHP_NAMESPACE tag specifies the namespace to use when generating 
-# Qt Help Project output. For more information please see 
-# http://doc.trolltech.com/qthelpproject.html#namespace
-
-QHP_NAMESPACE          = 
-
-# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating 
-# Qt Help Project output. For more information please see 
-# http://doc.trolltech.com/qthelpproject.html#virtual-folders
-
-QHP_VIRTUAL_FOLDER     = doc
-
-# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to add. 
-# For more information please see 
-# http://doc.trolltech.com/qthelpproject.html#custom-filters
-
-QHP_CUST_FILTER_NAME   = 
-
-# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the custom filter to add.For more information please see 
-# <a href="http://doc.trolltech.com/qthelpproject.html#custom-filters">Qt Help Project / Custom Filters</a>.
-
-QHP_CUST_FILTER_ATTRS  = 
-
-# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this project's 
-# filter section matches. 
-# <a href="http://doc.trolltech.com/qthelpproject.html#filter-attributes">Qt Help Project / Filter Attributes</a>.
-
-QHP_SECT_FILTER_ATTRS  = 
-
-# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can 
-# be used to specify the location of Qt's qhelpgenerator. 
-# If non-empty doxygen will try to run qhelpgenerator on the generated 
-# .qhp file.
-
-QHG_LOCATION           = 
-
 # The DISABLE_INDEX tag can be used to turn on/off the condensed index at 
 # top of each HTML page. The value NO (the default) enables the index and 
 # the value YES disables it.
@@ -976,7 +888,7 @@ ENUM_VALUES_PER_LINE   = 4
 # Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are 
 # probably better off using the HTML help feature. Other possible values 
 # for this tag are: HIERARCHIES, which will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list; 
+# and Class Hiererachy pages using a tree view instead of an ordered list;
 # ALL, which combines the behavior of FRAME and HIERARCHIES; and NONE, which
 # disables this behavior completely. For backwards compatibility with previous
 # releases of Doxygen, the values YES and NO are equivalent to FRAME and NONE
@@ -1210,10 +1122,8 @@ GENERATE_PERLMOD       = NO
 PERLMOD_LATEX          = NO
 
 # If the PERLMOD_PRETTY tag is set to YES the Perl module output will be 
-# nicely formatted so it can be parsed by a human reader. 
+# nicely formatted so it can be parsed by a human reader.  This is useful 
-# This is useful 
+# if you want to understand what is going on.  On the other hand, if this 
-# if you want to understand what is going on. 
-# On the other hand, if this 
 # tag is set to NO the size of the Perl module output will be much smaller 
 # and Perl will parse it just the same.
 
@@ -1300,11 +1210,9 @@ SKIP_FUNCTION_MACROS   = YES
 # Optionally an initial location of the external documentation 
 # can be added for each tagfile. The format of a tag file without 
 # this location is as follows: 
-#  
+#   TAGFILES = file1 file2 ... 
-# TAGFILES = file1 file2 ... 
 # Adding location for the tag files is done as follows: 
-#  
+#   TAGFILES = file1=loc1 "file2 = loc2" ... 
-# TAGFILES = file1=loc1 "file2 = loc2" ... 
 # where "loc1" and "loc2" can be relative or absolute paths or 
 # URLs. If a location is present for each tag, the installdox tool 
 # does not have to be run to correct the links.
@@ -1383,11 +1291,6 @@ HAVE_DOT               = @DOXYGEN_DOT_FOUND@
 
 DOT_FONTNAME           = FreeSans
 
-# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs. 
-# The default size is 10pt.
-
-DOT_FONTSIZE           = 10
-
 # By default doxygen will tell dot to use the output directory to look for the 
 # FreeSans.ttf font (which doxygen will put there itself). If you specify a 
 # different font using DOT_FONTNAME you can set the path where dot 
@@ -1430,7 +1333,7 @@ TEMPLATE_RELATIONS     = YES
 # file showing the direct and indirect include dependencies of the file with 
 # other documented files.
 
-INCLUDE_GRAPH          = YES
+INCLUDE_GRAPH          = NO
 
 # If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and 
 # HAVE_DOT tags are set to YES then doxygen will generate a graph for each 
@@ -1445,7 +1348,7 @@ INCLUDED_BY_GRAPH      = YES
 # the time of a run. So in most cases it will be better to enable call graphs 
 # for selected functions only using the \callgraph command.
 
-CALL_GRAPH             = YES
+CALL_GRAPH             = NO
 
 # If the CALLER_GRAPH and HAVE_DOT tags are set to YES then 
 # doxygen will generate a caller dependency graph for every global function 
@@ -1505,10 +1408,10 @@ DOT_GRAPH_MAX_NODES    = 50
 MAX_DOT_GRAPH_DEPTH    = 0
 
 # Set the DOT_TRANSPARENT tag to YES to generate images with a transparent 
-# background. This is disabled by default, because dot on Windows does not 
+# background. This is enabled by default, which results in a transparent 
-# seem to support this out of the box. Warning: Depending on the platform used, 
+# background. Warning: Depending on the platform used, enabling this option 
-# enabling this option may lead to badly anti-aliased labels on the edges of 
+# may lead to badly anti-aliased labels on the edges of a graph (i.e. they 
-# a graph (i.e. they become hard to read).
+# become hard to read).
 
 DOT_TRANSPARENT        = NO
 
@@ -1532,7 +1435,7 @@ GENERATE_LEGEND        = YES
 DOT_CLEANUP            = YES
 
 #---------------------------------------------------------------------------
-# Options related to the search engine
+# Configuration::additions related to the search engine   
 #---------------------------------------------------------------------------
 
 # The SEARCHENGINE tag specifies whether or not a search engine should be