documentation support

docs/Doxyfile.in

@@ -1153,8 +1153,10 @@ HTML_STYLESHEET        =
 # list). For an example see the documentation.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_EXTRA_STYLESHEET  = @CMAKE_SOURCE_DIR@/docs/custom/customdoxygen.css \
-                         @CMAKE_SOURCE_DIR@/docs/solarized-light.css
+HTML_EXTRA_STYLESHEET  = @CMAKE_SOURCE_DIR@/docs/custom/customdoxygen.css
+
+
+#                            @CMAKE_SOURCE_DIR@/docs/solarized-light.css
 
 # The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
 # other source files which should be copied to the HTML output directory. Note
@@ -1582,7 +1584,7 @@ SERVER_BASED_SEARCH    = YES
 # The default value is: NO.
 # This tag requires that the tag SEARCHENGINE is set to YES.
 
-EXTERNAL_SEARCH        = YAP
+EXTERNAL_SEARCH        = NO
 
 # The SEARCHENGINE_URL should point to a search engine hosted by a web server
 # which will return the search results when EXTERNAL_SEARCH is enabled.
@@ -2223,7 +2225,7 @@ DOT_FONTPATH           =
 # The default value is: YES.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-CLASS_GRAPH            = YES
+CLASS_GRAPH            = NO
 
 # If the COLLABORATION_GRAPH tag is set to YES then doxygen will generate a
 # graph for each documented class showing the direct and indirect implementation
@@ -2277,16 +2279,16 @@ TEMPLATE_RELATIONS     = NO
 # The default value is: YES.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-INCLUDE_GRAPH          = YES
+INCLUDE_GRAPH          = NO
 
-							# If the INCLUDED_BY_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are
+# If the INCLUDED_BY_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are
 # set to YES then doxygen will generate a graph for each documented file showing
 # the direct and indirect include dependencies of the file with other documented
 # files.
 # The default value is: YES.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-INCLUDED_BY_GRAPH      = YES
+INCLUDED_BY_GRAPH      = NO
 
 # If the CALL_GRAPH tag is set to YES then doxygen will generate a call
 # dependency graph for every global function or class method.

docs/md/builtins.md

@@ -0,0 +1,15 @@
+@defgroup  builtins  YAP Core Built-ins                  
+
+@brief This chapter describes the core built-in predicates  that control the execution of
+Prolog programs, provide fundamental functionality such as termm manipulation or arithmetic, and support interaction with external
+resources,
+
+Many of the predicates described here have been standardised by the International Standard Organization.
+ The corresponding standartised subset of Prolog also known as ISO-Prolog.                                                                                             
+In the description of the arguments of predicates the following
+notation will be used:
+
++ a preceding plus sign will denote an argument as an "input
+argument" - the argument is read, not written, and it cannot be a free variable at the time of the call;
++ a preceding minus sign will denote an "output argument";
++ an argument with no preceding symbol can be used in both ways.

docs/md/extensions.md

@@ -0,0 +1,21 @@
+Extensions to core Prolog.			{#extensions}
+=========================
+
+YAP includes a number of extensions over the original Prolog
+language. Next, we discuss how to use the most important ones.
+
+  + @ref Rational_Trees
+
+  + @ref AttributedVariables
+
+  + @ref  DepthLimited
+
+  + @ref  Tabling
+
+  + @ref Threads
+
+  + @ref Profiling
+
+  + @ref YAPArrays
+
+  + @ref Parallelism

docs/md/load_files.md

@@ -1,15 +1,12 @@
-Loading and Organising YAP Programs           {#load_files}
-===================================
+@defgroup load_files Loading and Organising YAP Programs    
 
-  Next, we present the main predicates and directives available to load
-  files and to control the Prolog environment.
+  @brief Next, we present the main predicates and directives available to load
+  files and to control the Prolog environment. They include
+
+  + @subpage YAPConsulting
 
   + @subpage YAPModules
 
-  + @ref YAPConsulting
+  + @subpage YAPBigLoad
 
-  +  @ref QLY
-
-  + @ref YAPBigLoad
-
-  
+  

docs/md/packages.md

@@ -1,13 +1,13 @@
 YAP packages              {#packages}
 ============
 
-  + @subpage real
+  + @subpage realxplxc
 
   + @subpage BDDs
 
   + @subpage  gecode
 
-  + @subpage  myddas
+  + @subpage  myddas_dbms
 
   + @ref PFL
 

docs/md/programming.md

@@ -0,0 +1,10 @@
+Programming in YAP            {#YAPProgramming}
+====================
+
+  + @ref Syntax
+
+  + @ref YAPCompilerSettings
+
+  + @ref Indexing
+
+  + @ref Deb_Interaction

docs/md/yap.md

@@ -5,7 +5,7 @@
 ![The YAP Logo](docs/icons/yap_128x128x32.png)
 </center>
 
-NOTE: this version of YAP is still experimental, documentation may be out of date.
+NOTE: this version of YAP is still experimental, documentation may be missing or brout of date.
 
 ## Introduction
 
@@ -25,7 +25,7 @@ The manual is organised as follows:
 
 + @subpage builtins
 
-+ @subpage Extensions
++ @subpage extensions
 
 + @subpage library
 
@@ -59,21 +59,6 @@ from
 Jan Wielemaker. We would also like to gratefully
 acknowledge the contributions from Ashwin Srinivasian.
 
-@page builtins YAP Core Built-ins
-
-
-This chapter describes the core predicates  that control the execution of
-Prolog programs, provide fundamental functionality such as termm manipulation or arithmetic, and support interaction with external
-resources, Many of the predicates described here have been standardised by the ISO. The standartised subset of Prolog also known as ISO-Prolog.                                                                                                                                                                                              
-
-In the description of the arguments of predicates the following
-notation will be used:
-
-+ a preceding plus sign will denote an argument as an "input
-argument" - it cannot be a free variable at the time of the call;
-+ a preceding minus sign will denote an "output argument";
-+ an argument with no preceding symbol can be used in both ways.
-
 
 @page Library YAP Library
 
@@ -89,7 +74,26 @@ argument" - it cannot be a free variable at the time of the call;
 YAP includes a number of extensions over the original Prolog
 language.
 
-         @subpage atts
+  + @subpage atts
+
+  + @ref Rational_Trees
+  
+  + @ref CohYroutining
+
+  + @ref Attributed_Variables
+
+  + @ref  DepthLimited
+
+  + @ref  Tabling
+
+  + @ref Threads
+
+  + @ref Profiling
+
+  + @ref YAPArrays
+
+  + @ref Parallelism
+
 
 @page YAPProgramming Programming in YAP