doc support

C/arith0.c

@@ -21,6 +21,11 @@ static char     SccsId[] = "%W% %G%";
 /**
    @file arith0.c
 
+*/
+
+//! @{
+
+/**
    @defgroup arithmetic_operators Arithmetic Functions
    @ingroup arithmetic
 

C/arrays.c

@@ -17,7 +17,7 @@
 
 
 /** @defgroup YAPArrays Named Arrays
-@ingroup YAPExtensions
+@ingroup extensions
 @{
 
 The YAP system includes experimental support for arrays. The
@@ -1050,7 +1050,6 @@ must be an atom (named array). The  _Size_ must evaluate to an
 integer.  The  _Type_ must be bound to one of types mentioned
 previously.
 */
-/// @memberof static_array/3
 p_create_static_array( USES_REGS1 )
 {
   Term ti = Deref(ARG2);
@@ -1267,7 +1266,6 @@ Reset static array with name  _Name_ to its initial value.
 
 
 */
-/// @memberof reset_static_array/1
 static Int 
 p_clear_static_array( USES_REGS1 )
 {
@@ -1307,7 +1305,6 @@ further accesses to the array will return an error.
 
 
 */
-/// @memberof close_static_array/1
 static Int 
 p_close_static_array( USES_REGS1 )
 {
@@ -1370,7 +1367,6 @@ terms (type `term`).
 
 
 */
-/// @memberof mmapped_array/4
 static Int 
 p_create_mmapped_array( USES_REGS1 )
 {
@@ -1684,7 +1680,6 @@ to use the operations on mutable terms.
 
 
 */
-/// @memberof update_array/3
 static Int 
 p_assign_static( USES_REGS1 )
 {
@@ -2179,7 +2174,6 @@ terms.
 
 
  */
-/// @memberof add_to_array_element/4
 
 static Int 
 p_add_to_array_element( USES_REGS1 )
@@ -2413,7 +2407,6 @@ that name.
 
 
 */
-/// @memberof static_array_to_term/2
 static Int
 p_static_array_to_term( USES_REGS1 )
 {
@@ -2583,7 +2576,6 @@ p_static_array_to_term( USES_REGS1 )
 Give the location or memory address for  a static array with name
  _Name_. The result is observed as an integer.
 */
-/// @memberof static_array_location/2
 static Int
 p_static_array_location( USES_REGS1 )
 {

C/atomic.c

@@ -18,8 +18,8 @@
 static char     SccsId[] = "%W% %G%";
 #endif
 
-/** @defgroup Predicates_on_Atoms Predicates on Atoms
+/** @addgroup Predicates_on_Atoms Predicates on Atoms
-@ingroup YAPBuiltins
+    @ingroup YAPChars
 @{
 
 The following predicates are used to manipulate atoms:

C/attvar.c

@@ -28,6 +28,12 @@ static char SccsId[]="%W% %G%";
 #define NULL (void *)0
 #endif
 
+/** @{ */
+
+/** @defgroup Attribute_Variables_Builtins Implementation of Attribute Declarations
+    @ingroup Attributed_Variables
+*/
+
 #ifdef COROUTINING
 
 #define TermVoidAtt TermFoundVar
@@ -995,6 +1001,14 @@ p_all_attvars( USES_REGS1 )
   } while (TRUE);
 }
 
+/** @pred attvar( _-Var_) 
+
+
+    Succeed if  _Var_ is an attributed variable.
+
+
+
+*/
 static Int
 p_is_attvar( USES_REGS1 )
 {
@@ -1104,16 +1118,10 @@ void Yap_InitAttVarPreds(void)
   Yap_InitCPred("all_attvars", 1, p_all_attvars, 0);
   CurrentModule = OldCurrentModule;
   Yap_InitCPred("attvar", 1, p_is_attvar, SafePredFlag|TestPredFlag);
-/** @pred attvar( _-Var_) 
-
-
-Succeed if  _Var_ is an attributed variable.
-
-
-
- */
   Yap_InitCPred("$att_bound", 1, p_attvar_bound, SafePredFlag|TestPredFlag);
 }
 
 
 
+/** @} */
+

C/bb.c

@@ -20,7 +20,7 @@ static char     SccsId[] = "%W% %G%";
 
 
 /** @defgroup BlackBoard The Blackboard
-@ingroup YAPBuiltins
+@ingroup builtins
 @{
 
 YAP implements a blackboard in the style of the SICStus Prolog

C/cmppreds.c

@@ -19,7 +19,7 @@
 
 
 /** @defgroup Comparing_Terms Comparing Terms
-@ingroup YAPBuiltins
+@ingroup builtins
 
 The following predicates are used to compare and order terms, using the
 standard ordering:

C/dbase.c

@@ -20,7 +20,7 @@ static char     SccsId[] = "%W% %G%";
 
 
 /** @defgroup Internal_Database Internal Data Base
-@ingroup YAPBuiltins
+@ingroup builtins
 @{
 
 Some programs need global information for, e.g. counting or collecting 

C/eval.c

@@ -18,13 +18,14 @@
 static char     SccsId[] = "%W% %G%";
 #endif
 
-/**
+//! @file eval.c
-   @file eval.c
 
+//! @{   
+
+/**
    @defgroup arithmetic_preds Arithmetic Predicates
    @ingroup arithmetic
 
-   @{
 */
 
 
@@ -200,7 +201,6 @@ BEAM_is(void)
 #endif
 
 /**
-@{
    @pred is( X:number, + Y:ground) is det
 
    This predicate succeeds iff the result of evaluating the expression
@@ -246,8 +246,6 @@ p_is( USES_REGS1 )
   return Yap_unify_constant(ARG1,out);
 }
 
-//@}
-
 /**
  @pred isnan(? X:float) is det
 
@@ -319,7 +317,7 @@ p_isinf( USES_REGS1 )
 }
 
 /**
-@{   @pred logsum(+ Log1:float, + Log2:float, - Out:float ) is det
+   @pred logsum(+ Log1:float, + Log2:float, - Out:float ) is det
 
 True if  _Log1_ is the logarithm of the positive number  _A1_,
  _Log2_ is the logarithm of the positive number  _A2_, and
@@ -400,7 +398,6 @@ p_logsum( USES_REGS1 )
   }
 }
 
-// @}
 
 Int
 Yap_ArithError(yap_error_number type, Term where, char *format,...)
@@ -458,9 +455,7 @@ Yap_EvalError(yap_error_number type, Term where, char *format,...)
 
 /**
 
-   @{
+   @pred between(+ Low:int, + High:int, ? Value:int) is nondet
- 
-  @pred between(+ Low:int, + High:int, ? Value:int) is nondet
 
    _Low_ and  _High_ are integers,  _High_ \>= _Low_. If
    _Value_ is an integer,  _Low_ =\< _Value_
@@ -603,11 +598,6 @@ init_between( USES_REGS1 )
   return cont_between( PASS_REGS1 );
 }
 
-/**
- *
- * @}
-*/
-
 void
 Yap_InitEval(void)
 {

C/globals.c

@@ -24,7 +24,7 @@ static char SccsId[] = "%W% %G%";
 @file globals.c
 
  @defgroup Global_Variables Global Variables
-@ingroup YAPBuiltins
+@ingroup builtins
 @{
 
 Global variables are associations between names (atoms) and

C/inlines.c

@@ -17,7 +17,7 @@
 
 
 /** @defgroup YAP_Terms Predicates on terms
-@ingroup YAPBuiltins
+@ingroup builtins
 @{
 
 

C/mavar.c

@@ -17,7 +17,7 @@
 
 
 /** @defgroup Term_Modification Term Modification
-@ingroup YAPBuiltins
+@ingroup builtins
 @{
 
 It is sometimes useful to change the value of instantiated

C/stdpreds.c

@@ -425,7 +425,32 @@ Int show_time(USES_REGS1) /* MORE PRECISION */
 }
 
 #endif /* BEAM */
+// @{
 
+/**
+   @defgroup YAPSetVal
+   @ingroup Internal_Database
+
+   Maintain a light-weight map where the key is an atom, and the value can be any constant.
+*/
+   
+/** @pred  set_value(+ _A_,+ _C_)
+
+
+    Associate atom  _A_ with constant  _C_.
+
+    The `set_value` and `get_value` built-ins give a fast alternative to
+    the internal data-base. This is a simple form of implementing a global
+    counter.
+
+    ~~~~~
+    read_and_increment_counter(Value) :-
+    get_value(counter, Value),
+    Value1 is Value+1,
+    set_value(counter, Value1).
+    ~~~~~
+    This predicate is YAP specific.
+*/
 static Int p_setval(USES_REGS1) { /* '$set_value'(+Atom,+Atomic) */
   Term t1 = Deref(ARG1), t2 = Deref(ARG2);
   if (!IsVarTerm(t1) && IsAtomTerm(t1) &&
@@ -436,6 +461,13 @@ static Int p_setval(USES_REGS1) { /* '$set_value'(+Atom,+Atomic) */
   return (FALSE);
 }
 
+/** @pred  get_value(+ _A_,- _V_)
+    In YAP, atoms can be associated with constants. If one such
+    association exists for atom  _A_, unify the second argument with the
+    constant. Otherwise, unify  _V_ with `[]`.
+
+    This predicate is YAP specific.
+*/
 static Int p_value(USES_REGS1) { /* '$get_value'(+Atom,?Val) */
   Term t1 = Deref(ARG1);
   if (IsVarTerm(t1)) {
@@ -453,7 +485,7 @@ static Int p_values(USES_REGS1) { /* '$values'(Atom,Old,New) */
   Term t1 = Deref(ARG1), t3 = Deref(ARG3);
 
   if (IsVarTerm(t1)) {
-    Yap_Error(INSTANTIATION_ERROR, t1, "set_value/2");
+    Yap_Error(INSTANTIATION_ERROR, t1, "set_value/2");
     return (FALSE);
   }
   if (!IsAtomTerm(t1)) {
@@ -472,6 +504,9 @@ static Int p_values(USES_REGS1) { /* '$values'(Atom,Old,New) */
   return (TRUE);
 }
 
+//@}
+
+
 static Int p_opdec(USES_REGS1) { /* '$opdec'(p,type,atom)		 */
   /* we know the arguments are integer, atom, atom */
   Term p = Deref(ARG1), t = Deref(ARG2), at = Deref(ARG3);
@@ -1914,42 +1949,9 @@ static Int p_yapor_workers(USES_REGS1) { return FALSE; }
 void Yap_InitCPreds(void) {
   /* numerical comparison */
   Yap_InitCPred("set_value", 2, p_setval, SafePredFlag | SyncPredFlag);
-  /** @pred  set_value(+ _A_,+ _C_)
+    Yap_InitCPred("get_value", 2, p_value,
-
-
-  Associate atom  _A_ with constant  _C_.
-
-  The `set_value` and `get_value` built-ins give a fast alternative to
-  the internal data-base. This is a simple form of implementing a global
-  counter.
-
-  ~~~~~
-  read_and_increment_counter(Value) :-
-  get_value(counter, Value),
-  Value1 is Value+1,
-  set_value(counter, Value1).
-  ~~~~~
-  This predicate is YAP specific.
-
-
-
-
-
-  */
-  Yap_InitCPred("get_value", 2, p_value,
                 TestPredFlag | SafePredFlag | SyncPredFlag);
-  /** @pred  get_value(+ _A_,- _V_)
+    Yap_InitCPred("$values", 3, p_values, SafePredFlag | SyncPredFlag);
-
-
-  In YAP, atoms can be associated with constants. If one such
-  association exists for atom  _A_, unify the second argument with the
-  constant. Otherwise, unify  _V_ with `[]`.
-
-  This predicate is YAP specific.
-
-
-  */
-  Yap_InitCPred("$values", 3, p_values, SafePredFlag | SyncPredFlag);
   /* general purpose */
   Yap_InitCPred("$opdec", 4, p_opdec, SafePredFlag | SyncPredFlag);
   Yap_InitCPred("=..", 2, p_univ, 0);

C/sysbits.c

@@ -18,6 +18,8 @@
 static char SccsId[] = "%W% %G%";
 #endif
 
+// @{
+
 /**
    @addtogroup YAPOS
 */
@@ -3258,3 +3260,5 @@ rw_lock_voodoo(void) {
 
 
 #endif /* YAPOR || THREADS */
+
+//@

C/unify.c

@@ -15,7 +15,7 @@
 *									 *
 *************************************************************************/
 /** @defgroup Rational_Trees Rational Trees
-@ingroup YAPExtensions
+@ingroup extensions
 @{
 
 Prolog unification is not a complete implementation. For efficiency
@@ -998,7 +998,7 @@ Yap_InitUnify(void)
   CACHE_REGS
   Term cm = CurrentModule;
   Yap_InitCPred("unify_with_occurs_check", 2, p_ocunify, SafePredFlag);
-/** @pred  unify_with_occurs_check(?T1,?T2) is iso 
+  /** @pred  unify_with_occurs_check(?T1,?T2) is iso 
 
 
 Obtain the most general unifier of terms  _T1_ and  _T2_, if there
@@ -1064,3 +1064,5 @@ Yap_TrimTrail(void)
 
 #include "trim_trail.h"
 }
+
+//! @}

H/eval.h

@@ -19,7 +19,7 @@
 
     @defgroup arithmetic Arithmetic in YAP 
 
-@ingroup YAPBuiltins
+@ingroup builtins
 
 + See @ref arithmetic_preds for the predicates that implement arithment
 

OPTYap/or.structs.h

@@ -15,7 +15,7 @@
 /** 
 
 @defgroup Parallelism Parallelism in YAP
-@ingroup YAPExtensions
+@ingroup extensions
 @{
 
 There has been a sizeable amount of work on an or-parallel

library/apply.yap

@@ -1,5 +1,5 @@
 /** @defgroup Apply Apply Macros
-@ingroup YAPLibrary
+@ingroup library
 @{
 
 This library provides a SWI-compatible set of utilities for applying a

library/assoc.yap

@@ -5,7 +5,7 @@
 %   Note   : the keys should be bound, the associated values need not be.
 
 /** @defgroup Association_Lists Association Lists
-@ingroup YAPLibrary
+@ingroup library
 @{
 
 The following association list manipulation predicates are available

library/atts.yap

@@ -17,11 +17,12 @@
 
 :- module(attributes, [op(1150, fx, attribute)]).
 
+%% @{  
 
-/** @defgroup Old_Style_Attribute_Declarations SICStus Prolog style Attribute Declarations
+/**
-@ingroup Attributed_Variables
+  @defgroup Old_Style_Attribute_Declarations SICStus Prolog style Attribute Declarations
-@{
+  @ingroup Attributed_Variables
-
+  
 Old style attribute declarations are activated through loading the
 library <tt>atts</tt> . The command
 
@@ -50,12 +51,17 @@ variable. Unification will resume after this call.
 <tt>project_attributes/2</tt> is used from a set of variables into a set of
 constraints or goals. One application of <tt>project_attributes/2</tt> is in
 the top-level, where it is used to output the set of
-floundered constraints at the end of a query.
+  floundered constraints at the end of a query.
+*/
+
+%% @}
+
+
+%% @{
 
 /** @defgroup Attribute_Declarations Attribute Declarations
 @ingroup Old_Style_Attribute_Declarations
-@{
+  
-
 Attributes are compound terms associated with a variable. Each attribute
 has a <em>name</em> which is <em>private</em> to the module in which the
 attribute was defined. Variables may have at most one attribute with a
@@ -498,5 +504,5 @@ do_verify_attributes([_|Mods], AttVar, Binding, Goals) :-
 	do_verify_attributes(Mods, AttVar, Binding, Goals).
 
 /**
-@}
+  @}
 */

library/avl.yap

@@ -17,7 +17,7 @@
 
 
 /** @defgroup AVL_Trees AVL Trees
-@ingroup YAPLibrary
+@ingroup library
 @{
 
 AVL trees are balanced search binary trees. They are named after their

library/bhash.yap

@@ -39,14 +39,14 @@ It relies on dynamic array code.
 
 array_default_size(2048).
 
-/** is_b_hash( +Hash )
+/** @pred is_b_hash( +Hash )
 
 Term _Hash_ is a hash table.
 */
 is_b_hash(V) :- var(V), !, fail.
 is_b_hash(hash(_,_,_,_,_)).
 
-/** b_hash_new( -NewHash )
+/** @pred b_hash_new( -NewHash )
 
 Create a empty hash table _NewHash_, with size 2048 entries.
 */
@@ -56,7 +56,7 @@ b_hash_new(hash(Keys, Vals, Size, N, _, _)) :-
 	array(Vals, Size),
 	create_mutable(0, N).
 
-/** b_hash_new( -_NewHash_, +_Size_ )
+/** @pred b_hash_new( -_NewHash_, +_Size_ )
 
 Create a empty hash table, with size _Size_ entries.
 */
@@ -65,7 +65,7 @@ b_hash_new(hash(Keys, Vals, Size, N, _, _), Size) :-
 	array(Vals, Size),
 	create_mutable(0, N).
 
-/** b_hash_new( -_NewHash_, +_Size_, :_Hash_, :_Cmp_ )
+/** @pred b_hash_new( -_NewHash_, +_Size_, :_Hash_, :_Cmp_ )
 
 Create a empty hash table, with size _Size_ entries.
 _Hash_ defines a partition function, and _Cmp_ defined a comparison function.
@@ -75,13 +75,15 @@ b_hash_new(hash(Keys,Vals, Size, N, HashF, CmpF), Size, HashF, CmpF) :-
 	array(Vals, Size),
 	create_mutable(0, N).
 
-/** b_hash_size( +_Hash_, -_Size_ )
+/**
+  @pred  b_hash_size( +_Hash_, -_Size_ )
 
 _Size_ unifies with the size of the hash table _Hash_.
 */
 b_hash_size(hash(_, _, Size, _, _, _), Size).
 
-/** b_hash_size_lookup( +_Key_, ?_Val_, +_Hash_ )
+/**
+  @pred b_hash_lookup( +_Key_, ?_Val_, +_Hash_ )
 
 Search the ground term _Key_ in table _Hash_ and unify _Val_ with the associated entry.
 */
@@ -103,7 +105,8 @@ fetch_key(Keys, Index, Size, Key, CmpF, ActualIndex) :-
 	    fetch_key(Keys, I1, Size, Key, CmpF, ActualIndex)
 	).
 
-/** b_hash_update( +_Key_, +_Hash_, +NewVal )
+/**
+  @pred b_hash_update( +_Key_, +_Hash_, +NewVal )
 
 Update to the value associated with the ground term _Key_ in table _Hash_ to _NewVal_.
 */
@@ -114,7 +117,8 @@ b_hash_update(Hash, Key, NewVal):-
 	array_element(Vals, ActualIndex, Mutable),
 	update_mutable(NewVal, Mutable).
 
-/** b_hash_update( +_Key_, -_OldVal_, +_Hash_, +NewVal )
+/**
+  @pred b_hash_update( +_Key_, -_OldVal_, +_Hash_, +NewVal )
 
 Update to the value associated with the ground term _Key_ in table _Hash_ to _NewVal_, and unify _OldVal_ with the current value.
 */
@@ -153,7 +157,8 @@ find_or_insert(Keys, Index, Size, N, CmpF, Vals, Key, NewVal, Hash, NewHash) :-
 	    find_or_insert(Keys, I1, Size, N, CmpF, Vals, Key, NewVal, Hash, NewHash)
 	).
 
-/** b_hash_insert_new(+_Hash_, +_Key_, _Val_, +_NewHash_ )
+/**
+  @pred b_hash_insert_new(+_Hash_, +_Key_, _Val_, +_NewHash_ )
 
 Insert the term _Key_-_Val_ in table _Hash_ and unify _NewHash_ with the result. If ground term _Key_ exists, fail.
 */
@@ -259,7 +264,8 @@ cmp_f(F, A, B) :-
 cmp_f(F, A, B) :-
 	call(F, A, B).
 
-/** b_hash_to_list(+_Hash_, -_KeyValList_ )
+/**
+  @pred b_hash_to_list(+_Hash_, -_KeyValList_ )
 
 The term _KeyValList_ unifies with a list containing all terms _Key_-_Val_ in the hash table.
 */
@@ -268,7 +274,8 @@ b_hash_to_list(hash(Keys, Vals, _, _, _, _), LKeyVals) :-
 	Vals =.. (_.LVs),
 	mklistpairs(LKs, LVs, LKeyVals).
 
-/** b_key_to_list(+_Hash_, -_KeyList_ )
+/**
+  @pred b_key_to_list(+_Hash_, -_KeyList_ )
 
 The term _KeyList_ unifies with a list containing all keys in the hash table.
 */
@@ -276,7 +283,8 @@ b_hash_keys_to_list(hash(Keys, _, _, _, _, _), LKeys) :-
 	Keys =.. (_.LKs),
 	mklistels(LKs, LKeys).
 
-/** b_key_to_list(+_Hash_, -_ValList_ )
+/**
+  @pred b_key_to_list(+_Hash_, -_ValList_ )
 
 The term _`valList_ unifies with a list containing all values in the hash table.
 */

library/block_diagram.yap

@@ -202,7 +202,7 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 /** @defgroup Block_Diagram Block Diagram
-@ingroup YAPLibrary
+@ingroup library
 @{
 
 This library provides a way of visualizing a prolog program using
@@ -232,7 +232,7 @@ parameter(texts((+inf))).
 parameter(depth((+inf))).
 parameter(default_ext('.yap')).
 
-/** @pred make_diagram(+inputfilename, +ouputfilename) 
+/** @pred make_diagram(+Inputfilename, +Ouputfilename) 
 
 
 
@@ -252,7 +252,7 @@ make_diagram(InputFile, OutputFile):-
   write('}'), nl,
   told.
 
-/** @pred make_diagram(+inputfilename, +ouputfilename, +predicate, +depth, +extension)
+/** @pred make_diagram(+Inputfilename, +Ouputfilename, +Predicate, +Depth, +Extension)
 
 
 The same as make_diagram/2 but you can define how many of the imported/exporeted predicates will be shown with predicate, and how deep the crawler is allowed to go with depth. The extension is used if the file use module directives do not include a file extension.

library/c_alarms.yap

@@ -211,7 +211,7 @@
                      timer_pause/2]).
 
 /** @defgroup CAlarms Concurrent Alarms
-@ingroup YAPLibrary
+@ingroup library
 @{
 
 This library provides a concurrent signals.  To use it use:

library/charsio.yap

@@ -33,7 +33,7 @@
     ]).
 
 /** @defgroup CharsIO Operations on Sequences of Codes.
-@ingroup YAPLibrary
+@ingroup library
 
 Term to sequence of codes conversion, mostly replaced by engine code.
 */

library/cleanup.yap

@@ -9,7 +9,7 @@
 		    ]).
 
 %% @defgroup Cleanup Call Cleanup
-% @ingroup YAPLibrary
+% @ingroup library
 % @{
 %
 % <tt>call_cleanup/1</tt> and <tt>call_cleanup/2</tt> allow predicates to register

library/clp/clpfd.pl

@@ -67,7 +67,7 @@
 
 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
 
-
+/**
    To make the predicate terminate if any argument is instantiated, add
    the (implied) constraint F #\= 0 before the recursive call. Otherwise,
    the query fac(N, 0) is the only non-terminating case of this kind.

library/coinduction.yap

@@ -31,7 +31,7 @@
 :- use_module(library(error)).
 
 /** <module> Co-Logic Programming
-  @ingroup YAPLibrary
+  @ingroup library
 
 This simple module implements the   directive coinductive/1 as described
 in "Co-Logic Programming: Extending Logic  Programming with Coinduction"

library/dbqueues.yap

@@ -1,6 +1,6 @@
 /**
   @defgroup DBQUeue Non-baacktrackable queues in YAP.
-  @ingroup YAPLibrary
+  @ingroup library
   @{
   
 A library to implement queues of NB Terms

library/dbusage.yap

@@ -1,7 +1,7 @@
 
 /**
   @defgroup DBUsage Memory Usage in Prolog Data-Base
-  @ingroup YAPLibrary
+  @ingroup library
   @{
 
   This library provides a set of utilities for studying memory usage in YAP.

library/dgraphs.yap

@@ -5,7 +5,7 @@
 
 
 /** @defgroup DGraphs Directed Graphs
-@ingroup YAPLibrary
+@ingroup library
 @{
 
 The following graph manipulation routines use the red-black tree library

library/dialect/swi.yap

@@ -2,7 +2,7 @@
 % SWI emulation.
 % written in an on-demand basis.
 
-%% @defgroup SWILibrary Compatibility with SWI-Prolog and Other Prolog systems
+%% @defgroup swi Compatibility with SWI-Prolog and Other Prolog systems
 
 /** 
 
@@ -148,21 +148,9 @@ that concatenated give  _A12_.
 
  
 */
+
 goal_expansion(atom_concat(A,B,C),atomic_concat(A,B,C)).
 %goal_expansion(arg(A,_,_),_) :- nonvar(A), !, fail.
-/** @pred  arg(+ _N_,+ _T_, _A_) is iso 
-
-
-Succeeds if the argument  _N_ of the term  _T_ unifies with
- _A_. The arguments are numbered from 1 to the arity of the term.
-
-The current version will generate an error if  _T_ or  _N_ are
-unbound, if  _T_ is not a compound term, of if  _N_ is not a positive
-integer. Note that previous versions of YAP would fail silently
-under these errors.
-
-@} 
-*/
 goal_expansion(arg(A,B,C),genarg(A,B,C)).
 
 % make sure we also use 

library/dialect/swi/fli/blobs.c

@@ -16,11 +16,11 @@
 *************************************************************************/
 /**
  *
- *   @file blobs.c
+ * @{ 
+*   @file blobs.c
  *
  *   @addtogroup swi-c-interface
  *
- * @{
  */
 
 #include	<Yap.h>
@@ -250,7 +250,7 @@ PL_unregister_blob_type(PL_blob_t *type)
 {
   fprintf(stderr,"PL_unregister_blob_type not implemented yet\n");
   return FALSE;
-}
+xs}
 
 void
 Yap_install_blobs(void)

library/dialect/swi/fli/swi.c

@@ -140,9 +140,10 @@ UserCPredicate(char *a, CPredicate def, unsigned long int arity, Term mod, int f
   CurrentModule = cm;
 } 
 
+//!  @{ 
+
 /** @defgroup swi-ATOMS Atom Construction
  *  @ingroup swi-c-interface
- *  @{
  *  */
 
 
@@ -177,11 +178,12 @@ X_API char* PL_atom_nchars(atom_t a, size_t *len)	 /* SAM check type */
   return s;
 }
 
-/** @}
+//!  @}
+
+/** @{
  *
  * @defgroup swi-term_references Term References
  *  @ingroup swi-c-interface
- *  @{
  *  */
 
 /** @brief duplicate a term reference
@@ -226,14 +228,17 @@ X_API void PL_reset_term_refs(term_t after)
 }
 
 /** @}
- *  @defgroup swi-term_manipulation Term Manipulation
+ */
+
+//!  @{
+
+/**  @defgroup swi-term_manipulation Term Manipulation
  *  @ingroup swi-c-interface
  *  */
 
 /**
  *  @defgroup swi-get-operations Reading Terms
  *  @ingroup swi-term_manipulation
- *  @{
  *  */
 
 /** @brief *name is assigned the name and *arity the arity if term ts, or the operaton fails.
@@ -647,10 +652,11 @@ X_API int PL_get_string(term_t t, char **s, size_t *len)
  *  @}
  *  */
 
+//!  @{
 /**
  *  @defgroup swi-unify-operations Unifying Terms
  *  @ingroup swi-term_manipulation
- *  @{
+
  *  */
 
 

library/dialect/swi/fli/swi.h

@@ -9,7 +9,10 @@
 *************************************************************************/
 
 /** 
-  @file swi.h
+
+    @{
+  
+    @file swi.h
 
   @defgroup swi-c-interface SWI-Prolog Foreign Language Interface
   @ingroup ChYInterface
@@ -30,8 +33,6 @@
  * Prolog has all the information necessary to perform its memory management without special precautions
  *  from the C programmer.
 
-  @{
-  
  */
 void Yap_swi_install(void);
 void Yap_install_blobs(void);

library/exo_interval.yap

@@ -8,7 +8,7 @@
 
 
 /** @defgroup Exo_Intervals Exo Intervals
-@ingroup YAPLibrary
+@ingroup library
 @{
 
 This package assumes you use exo-compilation, that is, that you loaded

library/heaps.yap

@@ -18,7 +18,7 @@
 
 
 /** @defgroup Heaps Heaps
-@ingroup YAPLibrary
+@ingroup library
 @{
 
 A heap is a labelled binary tree where the key of each node is less than

library/lam_mpi.yap

@@ -4,7 +4,7 @@
 
 
 /** @defgroup LAM LAM
-@ingroup YAPLibrary
+@ingroup library
 @{
 
 This library provides a set of utilities for interfacing with LAM MPI.

library/lambda.pl

@@ -41,7 +41,7 @@ official policies, either expressed or implied, of Ulrich Neumerkel.
 		   op(201,xfx,+\)]).
 
 /** <module> Lambda expressions
-@ingroup YAPLibrary
+@ingroup library
 
 This library provides lambda expressions to simplify higher order
 programming based on call/N.

library/lineutils.yap

@@ -20,7 +20,7 @@
 	  ]).
 
 /** @defgroup LineUtilities Line Manipulation Utilities
-@ingroup YAPLibrary
+@ingroup library
 @{
 
 This package provides a set of useful predicates to manipulate

library/lists.yap

@@ -5,7 +5,7 @@
 %
 
 /** @defgroup Lists List Manipulation
-@ingroup YAPLibrary
+@ingroup library
 @{
 
 The following list manipulation routines are available once included

library/maplist.yap

@@ -1,6 +1,7 @@
 /**
 
-@defgroup YAPControl Meta- and Control Predicates
+  @defgroup YAPMapList Meta- and Control Predicates
+  @ingroup library
 @{
 
 */
@@ -22,7 +23,7 @@
   * @file maplist.yap
   *
   * @defgroup maplist Map List and Term Operations
-  * @ingroup YAPLibrary
+  * @ingroup library
   *
   * This library provides a set of utilities for applying a predicate to
   * all elements of a list. They allow one to easily perform the most common do-loop constructs in Prolog.

library/matlab.yap

@@ -1,6 +1,6 @@
 
 /** @defgroup MATLAB MATLAB Package Interface
-@ingroup YAPLibrary
+@ingroup library
 @{
 
 The MathWorks MATLAB is a widely used package for array

library/matrix.yap

@@ -16,7 +16,7 @@
 *************************************************************************/
 
 /** @defgroup matrix Matrix Library
-@ingroup YAPLibrary
+@ingroup library
 @{
 
 This package provides a fast implementation of multi-dimensional

library/nb.yap

@@ -16,7 +16,7 @@
 *************************************************************************/
 
 /** @defgroup NonhYBacktrackable_Data_Structures Non-Backtrackable Data Structures
-@ingroup YAPLibrary
+@ingroup library
 @{
 
 The following routines implement well-known data-structures using global

library/ordsets.yap

@@ -19,7 +19,7 @@
 
 
 /** @defgroup Ordered_Sets Ordered Sets
-@ingroup YAPLibrary
+@ingroup library
 @{
 
 The following ordered set manipulation routines are available once

library/prandom.yap

@@ -17,7 +17,7 @@
 
 /**
  @groupdef PseudoRandom Van Gelder Random Number Generator
- @ingroup YAPBuiltins
+ @ingroup builtins
  @{
 */
 

library/queues.yap

@@ -7,7 +7,7 @@
 %   Needs  : lib(lists) for append/3.
 
 /** @defgroup Queues Queues
-@ingroup YAPLibrary
+@ingroup library
 @{
 
 The following queue manipulation routines are available once

library/random.yap

@@ -23,7 +23,7 @@
 %   arithmetic.
  
 /** @defgroup Pseudo_Random Random Number Generator
-@ingroup YAPLibrary
+@ingroup library
 @{
 
 The following random number operations are included with the
@@ -55,7 +55,7 @@ integers then  _NUMBER_ will also be an integer, otherwise
 
 
 /** @defgroup Pseudo_Random Pseudo Random Number Integer Generator
-@ingroup YAPLibrary
+@ingroup library
 @{
 
 The following routines produce random non-negative integers in the range

library/rbtrees.yap

@@ -50,10 +50,13 @@
 	   rb_in/3
        ]).
 
-/** @defgroup RedhYBlack_Trees Red-Black Trees
+%%! @{
-@ingroup YAPLibrary
-@{
 
+/**
+  @file rbtrees.yap
+  @defgroup rbtrees Red-Black Trees
+  @ingroup library
+  
 Red-Black trees are balanced search binary trees. They are named because
 nodes can be classified as either red or   black. The code we include is
 based on "Introduction  to  Algorithms",   second  edition,  by  Cormen,
@@ -109,7 +112,6 @@ rb_new(K,V,t(Nil,black(Nil,K,V,Nil))) :- Nil = black('',_,_,'').
 %%	rb_empty(?T) is semidet.
 %
 %	Succeeds if T is an empty Red-Black tree.
-
 rb_empty(t(Nil,Nil)) :- Nil = black('',_,_,'').
 
 %%	rb_lookup(+Key, -Value, +T) is semidet.
@@ -1036,7 +1038,6 @@ list_to_rbtree(List, T) :-
 %
 %	T is the red-black tree corresponding  to the mapping in ordered
 %	list L.
-
 ord_list_to_rbtree([], t(Nil,Nil)) :- !,
 	Nil = black('', _, _, '').
 ord_list_to_rbtree([K-V], t(Nil,black(Nil,K,V,Nil))) :- !,
@@ -1085,10 +1086,9 @@ size(black(L,_,_,R),Sz0,Szf) :-
 
 %%	is_rbtree(?Term) is semidet.
 %
-%	True if Term is a valide Red-Black tree.
+%	True if Term is a valid Red-Black tree.
 %	
 %	@tbd	Catch variables.
-
 is_rbtree(X) :-
 	var(X), !, fail.
 is_rbtree(t(Nil,Nil)) :- !.
@@ -1231,26 +1231,11 @@ build_ntree(X1,X,T0,TF) :-
 
 
 
-/** @pred is_rbtree(+ _T_) 
 
-
-Check whether  _T_ is a valid red-black tree.
-
- 
-*/
-/** @pred ord_list_to_rbtree(+ _L_, - _T_) 
-
-
- _T_ is the red-black tree corresponding to the mapping in ordered
-list  _L_.
-
-
-
- */
 /** @pred rb_apply(+ _T_,+ _Key_,+ _G_,- _TN_) 
 
 
-If the value associated with key  _Key_ is  _Val0_ in  _T_, and
+  If the value associated with key  _Key_ is  _Val0_ in  _T_, and
 if `call(G,Val0,ValF)` holds, then  _TN_ differs from
  _T_ only in that  _Key_ is associated with value  _ValF_ in
 tree  _TN_. Fails if it cannot find  _Key_ in  _T_, or if
@@ -1448,7 +1433,8 @@ with  _NewVal_. Fails if it cannot find  _Key_ in  _T_.
  _Pairs_ is an infix visit of tree  _T_, where each element of
  _Pairs_ is of the form   _K_- _Val_.
 
-@}
+  
- 
 */
 
+%%! @}  
+

library/regexp.yap

@@ -16,7 +16,7 @@
 *************************************************************************/
 
 /** @defgroup RegExp Regular Expressions
-@ingroup YAPLibrary
+@ingroup library
 @{
 
 This library includes routines to determine whether a regular expression

library/sockets.yap

@@ -2,7 +2,7 @@
 
 <module> SICStus compatible socket library
 
-@ingroup YAPBuiltins
+@ingroup builtins
 
 YAP includes a SICStus Prolog compatible socket interface. In YAP-6.3
 this uses the `clib` package to emulate the old low level interface that

library/splay.yap

@@ -16,7 +16,7 @@
 *************************************************************************/
 
 /** @defgroup Splay_Trees Splay Trees
-@ingroup YAPLibrary
+@ingroup library
 @{
 
 Splay trees are explained in the paper "Self-adjusting Binary Search

library/system.yap

@@ -16,7 +16,7 @@
 *************************************************************************/
 
 /** @defgroup System Calling The Operating System from YAP
-@ingroup YAPLibrary
+@ingroup library
 @{
 
 YAP now provides a library of system utilities compatible with the

library/terms.yap

@@ -15,7 +15,7 @@
 *									 *
 *************************************************************************/
 /** @defgroup Terms Utilities On Terms
-@ingroup YAPLibrary
+@ingroup library
 @{
 
 The next routines provide a set of commonly used utilities to manipulate

library/timeout.yap

@@ -21,7 +21,7 @@
 
 
 /** @defgroup Timeout Calls With Timeout
-@ingroup YAPLibrary
+@ingroup library
 @{
 
 The <tt>time_out/3</tt> command relies on the <tt>alarm/3</tt> built-in to

library/trees.yap

@@ -25,7 +25,7 @@
 
 
 /** @defgroup Trees Updatable Binary Trees
-@ingroup YAPLibrary
+@ingroup library
 @{
 
 The following queue manipulation routines are available once

library/tries.yap

@@ -7,7 +7,7 @@
 
 
 /** @defgroup Tries Trie DataStructure
-@ingroup YAPLibrary
+@ingroup library
 @{
 
 The next routines provide a set of utilities to create and manipulate

library/ugraphs.yap

@@ -10,7 +10,7 @@
  
 
 /** @defgroup UGraphs Unweighted Graphs
-@ingroup YAPLibrary
+@ingroup library
 @{
 
 The following graph manipulation routines are based in code originally

library/undgraphs.yap

@@ -20,7 +20,7 @@
 	    undgraph_min_tree/2]).
 
 /** @defgroup UnDGraphs Undirected Graphs
-@ingroup YAPLibrary
+@ingroup library
 @{
 
 The following graph manipulation routines use the red-black tree graph

misc/sysgraph

@@ -1053,30 +1053,44 @@ always_strip_module(M0:A, M0, A).
 
 c_links :-
     open('tmp/foreigns.yap', write, S),
-    clinks(S).
+    clinks(S),
+    fail.
+c_links :-
+    open('tmp/foreigns.c', write, S),
+    cclinks(S),
+    fail.
 
 clinks(S) :-
 	module_file( F, NM ),
-	format( S, 'mod( ~q , ~q ). ~n', [NM, F] ),
+	format( S, 'mod( ~q , ~q ).~n', [NM, F] ),
+	fail.
+clinks(S) :-
+        system_predicate(C),
+	functor(C, N, A),
+	format( S, 'sys ~q/~d.~n', [N, A] ),
 	fail.
 clinks(S) :-
     exported( ( Fi0-M:F/A :- Fi1-M1:F1/A ) ),
     ( M \= M1 -> M \= prolog ; F \= F1 ),
-    functor(S0, F, A),
+%    functor(S0, F, A),
-    S0 =.. [F| Args],
+%    S0 =.. [F| Args],
-    S1 =.. [F1| Args],
+%    S1 =.. [F1| Args],
-    numbervars(Args, 0, _),
+%    numbervars(Args, 0, _),
-    format( S, '% ~q <- ~q.~n~q:~q :- ~q:~q. ~n', [Fi0, Fi1, M,S0, M1,S1] ),
+    format( S, '% ~q <- ~q.~n~q:~q imports ~q:~q. ~n', [Fi0, Fi1, M,F/A, M1,F1/A] ),
-    fail.
+			fail.
 clinks(S) :-
-    node( M, F/A, File-Line, c(F)),
+    close(S).
-    functor( S0, F, A),
+
-    S0 =.. [F| Args],
+cclinks(S) :-
-    S1 =.. [foreign, F| Args],
+    node( M, F/A, File-_Line, c(F)),
-    numbervars(Args, 0, _),
+%    functor( S0, F, A),
-    format( S, ' ~a:~d~nforeign(~q , ~q , ~q, ~q ).~n', [File, Line, M:S0, S1, File, Line] ),
+%    S0 =.. [F| Args],
+%    S1 =.. [foreign, F| Args],
+%    numbervars(Args, 0, _),
+    format( S, '/// @file ~a~n', [File] ),
+    format( S, '/// @memberof ~a ~a:~a/~d~n', [F, M, F, A] ),
     fail.
-clinks(S) :-
+cclinks(S) :-
     close(S).
 
 warn_singletons(_Vars, _Pos).
@@ -1088,9 +1102,9 @@ warn_singletons(_Vars, _Pos).
 %
 comment( _Pos - Comment) :-
     skip_blanks(1, Comment, N),
-    doc( Comment, N ), !,
+    doc( Comment, N ),
     format( "%s\n", [Comment] ),
-    verif
+    !.
 comment( _Pos - _Comment).
 
 skip_blanks(I, Comment, N) :-
@@ -1491,9 +1505,9 @@ add_comments :-
 add_comments :-
   listing( open_comment ).
 
-check_comment( Comment, CN, _Line, File ) :-
+check_comment( Comment, CN, _Line, _qFile ) :-
     string_codes( Comment, [_,_,_|C]),
-    check_groups(0,C,[]),
+    check_groups(0,_C,[]),
     check_quotes(0,C,[]),
     (
         append(C0,[0'@,0'},0' ,0'*,0'/,10], C) -> %'
@@ -1505,7 +1519,8 @@ check_comment( Comment, CN, _Line, File ) :-
 check_comment( Comment, Comment,  Line, File ) :-
     format(user_error,'*** bad comment ~a ~d~n~n~s~n~', [File,Line,Comment]).
 
-check_groups(0,
+check_groups(0) --> [].
+
 
 check_quotes( 0 ) --> [].
 check_quotes( 0 ) -->

os/pl-ctype.c

@@ -27,8 +27,8 @@
 #include <ctype.h>
 #include "pl-ctype.h"
 
-//! @defgroup YAPChars Character Classification and Manipulation
+//! @defgroup YAPCharsC C-code for Character Classification and Manipulation
-//  @ingroup YAPBuiltins
+//  @ingroup YAPChars
 //
 // This module defines routines to manipulate individual characters.
 //

os/pl-os.c

@@ -29,6 +29,8 @@
 #include <os2.h>                /* this has to appear before pl-incl.h */
 #endif
 
+//@{
+
 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 Solaris has asctime_r() with 3 arguments. Using _POSIX_PTHREAD_SEMANTICS
 is supposed to give the POSIX standard one.
@@ -2826,3 +2828,5 @@ Pause(double t)
 BeginPredDefs(system)
   PRED_DEF("shell", 2, shell, 0)
 EndPredDefs
+
+  // @}

packages/ProbLog/problog.yap

@@ -227,7 +227,7 @@
 /**
 
 @defgroup ProbLog1 The Leuven ProbLog1 System
-@ingroup YAPPackages
+@ingroup packages
 
 @brief This document is intended as a user guide for the users of ProbLog. ProbLog is a probabilistic Prolog, a probabilistic logic programming language, which is integrated in YAP-Prolog.
 

packages/bdd/bdd.yap

@@ -1,5 +1,5 @@
 /** @defgroup BDDs Binary Decision Diagrams and Friends
-@ingroup YAPPackages
+@ingroup packages
 @{
 
 This library provides an interface to the BDD package CUDD. It requires
@@ -71,7 +71,7 @@ may include:
 
 + `nand( _X_,  _Y_)`
 
-    negated conjunction@
+    negated conjunction
 
 + `nor( _X_,  _Y_)`
 
@@ -383,3 +383,4 @@ fetch(pp(P,_,_,_)._Tree, -1, N) :- N is 1-P.
 fetch(pn(P,_,_,_)._Tree, 1, P).
 fetch(pn(P,_,_,_)._Tree, -1, N) :- N is 1-P.
 
+%% @}

packages/gecode/clpfd.yap

@@ -186,10 +186,6 @@ larger or equal
 /** @pred _X_ #\=  _Y_ is semidet
 disequality
  
-*/
-/** @pred all_different( _Vs_    )
-
-Verifies whether all elements of a list are different.
 */
 /** @pred labeling( _Opts_,  _Xs_)
 performs labeling, several variable and value selection options are
@@ -464,10 +460,15 @@ boolvars( Xs ) :-
 	maplist(lm(0, 1, Map), Xs, NXs),
 	length(Xs, N),
 	NXs := boolvars( Space, N ).
+
+/** @pred all_different( _Vs_    )
+  Verifies whether all elements of a list are different.
+*/
 all_different( Xs ) :-
 	get_home(Env),
 	check(Xs, NXs),
 	post( all_different( NXs ), Env, _ ).
+
 all_distinct( Xs ) :-
 	get_home(Env),
 	check(Xs, NXs),

packages/gecode/gecode4_yap_hand_written.yap

@@ -18,7 +18,7 @@
 
 /** @defgroup Gecode Gecode Interface
 
-@ingroup YAPPackages
+@ingroup packages
 @{
 
 

packages/python/python.pl

@@ -11,16 +11,6 @@
 %
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-/** <module> python
-
-A C-based  Prolog interface to python.
-
-@author		Vitor Santos Costa
-@version	0:0:5, 2012/10/8
-@license	Perl Artistic License
-
-*/
-
 %%%
 
 :- module(python, [
@@ -35,7 +25,18 @@ A C-based  Prolog interface to python.
      op(950,yfx,:=),
      (:=)/2,
      (:=)/1
-     ]).
+		  ]).
+
+/** <module> python
+
+  A C-based  Prolog interface to python.
+
+  @author               Vitor Santos Costa
+  @version      0:0:5, 2012/10/8
+  @license      Perl Artistic License
+
+*/
+
 
 
 /************************************************************************************************************

packages/xml/xml_driver.pl

@@ -1,131 +1,138 @@
-/* xml_driver.pl : Contains xml_parse/[2,3] a bi-directional XML parser written in
+/* xml_driver.pl : Contains xml_parse/[2,3] a bi-directional XML parser written in
- * Prolog.
+ * Prolog.
- *
+ *
- * Copyright (C) 2001-2005 Binding Time Limited
+ * Copyright (C) 2001-2005 Binding Time Limited
- * Copyright (C) 2005-2011 John Fletcher
+ * Copyright (C) 2005-2011 John Fletcher
- *
+ *
- * Current Release: $Revision: 3.3 $
+ * Current Release: $Revision: 3.3 $
- * 
+ * 
- * TERMS AND CONDITIONS:
+ * TERMS AND CONDITIONS:
- *
+ *
- * This program is offered free of charge, as unsupported source code. You may
+ * This program is offered free of charge, as unsupported source code. You may
- * use it, copy it, distribute it, modify it or sell it without restriction,
+ * use it, copy it, distribute it, modify it or sell it without restriction,
- * but entirely at your own risk.
+ * but entirely at your own risk.
- *
+ *
- * xml_parse( {+Controls}, +?Chars, ?+Document ) parses Chars to/from a data
+ * xml_parse( {+Controls}, +?Chars, ?+Document ) parses Chars to/from a data
- * structure of the form xml(<atts>, <content>). <atts> is a list of
+ * structure of the form xml(<atts>, <content>). <atts> is a list of
- * <atom>=<string> attributes from the (possibly implicit) XML signature of the
+ * <atom>=<string> attributes from the (possibly implicit) XML signature of the
- * document. <content> is a (possibly empty) list comprising occurrences of :
+ * document. <content> is a (possibly empty) list comprising occurrences of  * ~~~
- *
+ *    pcdata(<string>)                    :  Text
- *    pcdata(<string>)                    :  Text
+ *    comment(<string>)                   :  An xml comment;
- *    comment(<string>)                   :  An xml comment;
+ *    element(<tag>,<atts>,<content>)     :  <tag>..</tag> encloses <content>
- *    element(<tag>,<atts>,<content>)     :  <tag>..</tag> encloses <content>
+ *                                        :  <tag /> if empty
- *                                        :  <tag /> if empty
+ *    instructions(<atom>, <string>)      :  Processing <? <atom> <params> ?>"
- *    instructions(<atom>, <string>)      :  Processing <? <atom> <params> ?>"
+ *     cdata( <string> )                  :  <![CDATA[ <string> ]]>
- *     cdata( <string> )                  :  <![CDATA[ <string> ]]>
+ *    doctype(<atom>, <doctype id>)       :  DTD <!DOCTYPE .. >
- *    doctype(<atom>, <doctype id>)       :  DTD <!DOCTYPE .. >
+ * ~~~~
- *
+ * The conversions are not completely symmetrical, in that weaker XML is
- * The conversions are not completely symmetrical, in that weaker XML is
+ * accepted than can be generated. Specifically, in-bound (Chars -> Document)
- * accepted than can be generated. Specifically, in-bound (Chars -> Document)
+ * does not  require strictly well-formed XML. Document is instantiated to the
- * does not  require strictly well-formed XML. Document is instantiated to the
+ * term malformed(Attributes, Content) if Chars does not represent well-formed
- * term malformed(Attributes, Content) if Chars does not represent well-formed
+ * XML. The Content of a malformed/2 structure can contain:
- * XML. The Content of a malformed/2 structure can contain:
+ *
- *
+ *    unparsed( <string> )                :  Text which has not been parsed
- *    unparsed( <string> )                :  Text which has not been parsed
+ *    out_of_context( <tag> )             :  <tag> is not closed
- *    out_of_context( <tag> )             :  <tag> is not closed
+ *
- *
+ * in addition to the standard term types.
- * in addition to the standard term types.
+ *
- *
+ * Out-bound (Document -> Chars) parsing _does_ require that Document defines
- * Out-bound (Document -> Chars) parsing _does_ require that Document defines
+ * strictly well-formed XML. If an error is detected a 'domain' exception is
- * strictly well-formed XML. If an error is detected a 'domain' exception is
+ * raised.
- * raised.
+ *
- *
+ * The domain exception will attempt to identify the particular sub-term in
- * The domain exception will attempt to identify the particular sub-term in
+ * error and the message will show a list of its ancestor elements in the form
- * error and the message will show a list of its ancestor elements in the form
+ * <tag>{(id)}* where <id> is the value of any attribute _named_ id.
- * <tag>{(id)}* where <id> is the value of any attribute _named_ id.
+ *
- *
+ * At this release, the Controls applying to in-bound (Chars -> Document)
- * At this release, the Controls applying to in-bound (Chars -> Document)
+ * parsing are:
- * parsing are:
+ *
- *
+ *    extended_characters(<bool>)         :  Use the extended character
- *    extended_characters(<bool>)         :  Use the extended character
+ *                                        :  entities for XHTML (default true)
- *                                        :  entities for XHTML (default true)
+ *
- *
+ *    format(<bool>)                      :  Strip layouts when no character data
- *    format(<bool>)                      :  Strip layouts when no character data
+ *                                        :  appears between elements.
- *                                        :  appears between elements.
+ *                                        :  (default true)
- *                                        :  (default true)
+ *
- *
+ *    remove_attribute_prefixes(<bool>)   :  Remove namespace prefixes from
- *    remove_attribute_prefixes(<bool>)   :  Remove namespace prefixes from
+ *                                        :  attributes when it's the same as the
- *                                        :  attributes when it's the same as the
+ *                                        :  prefix of the parent element
- *                                        :  prefix of the parent element
+ *                                        :  (default false).
- *                                        :  (default false).
+ *
- *
+ *    allow_ampersand(<bool>)             :  Allow unescaped ampersand
- *    allow_ampersand(<bool>)             :  Allow unescaped ampersand
+ *                                        :  characters (&) to occur in PCDATA.
- *                                        :  characters (&) to occur in PCDATA.
+ *                                        :  (default false).
- *                                        :  (default false).
+ *
- *
+ *    [<bool> is one of 'true' or 'false']
- *    [<bool> is one of 'true' or 'false']
+ *
- *
+ * For out-bound (Document -> Chars) parsing, the only available option is:
- * For out-bound (Document -> Chars) parsing, the only available option is:
+ *
- *
+ *    format(<Bool>)                      :  Indent the element content
- *    format(<Bool>)                      :  Indent the element content
+ *                                        :  (default true)
- *                                        :  (default true)
+ *
- *
+ * Different DCGs for input and output are used because input parsing is
- * Different DCGs for input and output are used because input parsing is
+ * more flexible than output parsing. Errors in input are recorded as part
- * more flexible than output parsing. Errors in input are recorded as part
+ * of the data structure. Output parsing throws an exception if the document
- * of the data structure. Output parsing throws an exception if the document
+ * is not well-formed, diagnosis tries to identify the specific culprit term.
- * is not well-formed, diagnosis tries to identify the specific culprit term.
+ */
- */
+
-xml_parse( Chars, Document ) :-
+:- module( xml, [xml_parse/2,
-	xml_parse( [], Chars, Document ).
+		xml_parse/3,
-
+		 document_to_xml/3,
-xml_parse( Controls, Chars, Document ) :-
+		 xml_subterm/2
-	( ground( Chars ) ->
+		]).
-		xml_to_document( Controls, Chars, Document )
+
-	; otherwise ->
+xml_parse( Chars, Document ) :-
-		document_to_xml( Controls, Document, Chars )
+	xml_parse( [], Chars, Document ).
-	).
+
-
+xml_parse( Controls, Chars, Document ) :-
-document_to_xml( Controls, Document, Chars ) :-
+	( ground( Chars ) ->
-	( member( format(false), Controls ) ->
+		xml_to_document( Controls, Chars, Document )
-		Format = false
+	; otherwise ->
-	; otherwise ->
+		document_to_xml( Controls, Document, Chars )
-		Format = true
+	).
-	),
+
-	( ground( Document ),
+document_to_xml( Controls, Document, Chars ) :-
-	  document_generation(Format, Document, Chars0, [] ) ->
+	( member( format(false), Controls ) ->
-			Chars = Chars0
+		Format = false
-	; otherwise ->
+	; otherwise ->
-		xml_fault( Document, [], Culprit, Path, Message ),
+		Format = true
-		xml_exception( Message, Document, Culprit, Path )
+	),
-	).
+	( ground( Document ),
-
+	  document_generation(Format, Document, Chars0, [] ) ->
-/* xml_subterm( +XMLTerm, ?Subterm ) unifies Subterm with a sub-term of Term.
+			Chars = Chars0
- * Note that XMLTerm is a sub-term of itself. 
+	; otherwise ->
- */
+		xml_fault( Document, [], Culprit, Path, Message ),
-xml_subterm( Term, Term ).
+		xml_exception( Message, Document, Culprit, Path )
-xml_subterm( xml(_Attributes, Content), Term ) :-
+	).
-	xml_subterm( Content, Term ).	
+
-xml_subterm( [H|T], Term ) :-
+/** xml_subterm( +XMLTerm, ?Subterm )
-	( xml_subterm( H, Term )
+ * unifies Subterm with a sub-term of Term.
-	; xml_subterm( T, Term )
+ * Note that XMLTerm is a sub-term of itself. 
-	).
+ */
-xml_subterm( element(_Name,_Attributes,Content), Term ) :-
+xml_subterm( Term, Term ).
-	xml_subterm( Content, Term ).
+xml_subterm( xml(_Attributes, Content), Term ) :-
-xml_subterm( namespace(_URI,_Prefix,Content), Term ) :-
+	xml_subterm( Content, Term ).	
-	xml_subterm( Content, Term ).
+xml_subterm( [H|T], Term ) :-
-
+	( xml_subterm( H, Term )
-/* xml is intended to be a rather modular module: it should be easy to
+	; xml_subterm( T, Term )
- * build a program that can output XML, but not read it, or vice versa.
+	).
- * Similarly, you may be happy to dispense with diagnosis once you are
+xml_subterm( element(_Name,_Attributes,Content), Term ) :-
- * sure that your code will only try to make valid calls to xml_parse/2.
+	xml_subterm( Content, Term ).
- *
+xml_subterm( namespace(_URI,_Prefix,Content), Term ) :-
- * It is intended that the code should be very portable too. Clearly,
+	xml_subterm( Content, Term ).
- * some small changes will be needed between platforms, but these should
+
- * be limited to xml_utilities. xml_utilities contains most of the shared
+/* xml is intended to be a rather modular module: it should be easy to
- * code and most of the potentially non-portable code.
+ * build a program that can output XML, but not read it, or vice versa.
- */
+ * Similarly, you may be happy to dispense with diagnosis once you are
-:- ensure_loaded( xml_acquisition ).
+ * sure that your code will only try to make valid calls to xml_parse/2.
-:- ensure_loaded( xml_diagnosis ).
+ *
-:- ensure_loaded( xml_generation ).
+ * It is intended that the code should be very portable too. Clearly,
-:- ensure_loaded( xml_pp ).
+ * some small changes will be needed between platforms, but these should
-:- ensure_loaded( xml_utilities ).
+ * be limited to xml_utilities. xml_utilities contains most of the shared
+ * code and most of the potentially non-portable code.
+ */
+:- ensure_loaded( xml_acquisition ).
+:- ensure_loaded( xml_diagnosis ).
+:- ensure_loaded( xml_generation ).
+:- ensure_loaded( xml_pp ).
+:- ensure_loaded( xml_utilities ).

packages/yap-lbfgs/lbfgs.pl

@@ -40,7 +40,7 @@
 /**
 
 @defgroup YAP-LBFGS
-@ingroup YAPPackages
+@ingroup packages
 
 @short What is YAP-LBFGS? YAP-LBFGS is an interface to call libLBFGS, http://www.chokkan.org/software/liblbfgs/, from within
 YAP. libLBFGS is a C library for Limited-memory

pl/absf.yap

@@ -8,9 +8,11 @@
 *									 *
 *************************************************************************/
 
+%% @{
+
 /** @defgroup YAPAbsoluteFileName File Name Resolution
 
-   @ingroup YAPBuiltins
+   @ingroup builtins
 
   Support for file name resolution through absolute_file_name/3 and
   friends. These utility built-ins describe a list of directories that
@@ -18,9 +20,7 @@
   plus user-defined directories, directories based on environment
   variables and registry information to search for files.
 
-  @{
+  **/
-
- **/
 
 :- system_module( absolute_file_name, [absolute_file_name/2,
         absolute_file_name/3,

pl/arith.yap

@@ -57,6 +57,8 @@
 
 */
 
+%% @{
+
 /** @pred expand_exprs(- _O_,+ _N_) 
 	Control term expansion during compilation.
 

pl/arithpreds.yap

@@ -15,13 +15,14 @@
 *									 *
 *************************************************************************/
 
+%% @{
+
 /**
   @file arithpreds.yap
 
   @addtogroup arithmetic_preds
 
   
-  @{
 */
 
 :- system_module(arithmetic_predicates, [

pl/arrays.yap

@@ -15,6 +15,8 @@
 *									 *
 *************************************************************************/
 
+%% @{
+
 /**
 @addtogroup YAPArrays
 */
@@ -102,7 +104,4 @@ static_array_properties(Name, Size, Type) :-
 static_array_properties(Name, Size, Type) :-
 	'$do_error'(type_error(atom,Name),static_array_properties(Name,Size,Type)).
 
-
+%% @}
-
-	
-

pl/atoms.yap

@@ -8,6 +8,8 @@
  *									 *
  *************************************************************************/
 
+%% @{
+
 :- system_module( '$_atoms', [
 			      atom_concat/2,
 			      string_concat/2,
@@ -17,8 +19,11 @@
 
 :- use_system_module( '$_errors', ['$do_error'/2]).
 
+%% @{
+
 /**
- * @addtogroup Predicates_on_Atoms
+  * @addtogroup Predicates_on_Atoms
+  * @ingroup YAPChars
  *
 */									 
 

pl/attributes.yap

@@ -1,6 +1,6 @@
 /*************************************************************************
 *									 *
-*	 YAP Prolog 							 *
+  *	 YAP Prolog 							 *
 *									 *
 *	Yap Prolog was developed at NCCUP - Universidade do Porto	 *
 *									 *
@@ -15,17 +15,22 @@
 *									 *
 *************************************************************************/
 
+%% @{
 
-/** @defgroup Attributed_Variables Attributed Variables
+/**
-@ingroup YAPExtensions
+  @file attributes.yap
+  
+  @defgroup Attributed_Variables Attributed Variables
+  @ingroup extensions
 
 YAP supports attributed variables, originally developed at OFAI by
 Christian Holzbaur. Attributes are a means of declaring that an
-arbitrary term is a property for a variable. These properties can be
+  arbitrary term is a property for a variable. These properties can be
 updated during forward execution. Moreover, the unification algorithm is
 aware of attributed variables and will call user defined handlers when
-trying to unify these variables.
+  trying to unify these variables.
 
+  
 Attributed variables provide an elegant abstraction over which one can
 extend Prolog systems. Their main application so far has been in
 implementing constraint handlers, such as Holzbaur's CLPQR, Fruewirth
@@ -42,85 +47,13 @@ work with. Most packages included in YAP that use attributed
 variables, such as CHR, CLP(FD), and CLP(QR), rely on the SWI-Prolog
 interface.
 
-@{
+  + Old_Style_Attribute_Declarations
+  
+  + New_Style_Attribute_Declarations
+  
  */
 
 
-
-/** @defgroup New_Style_Attribute_Declarations hProlog and SWI-Prolog style Attribute Declarations
-@ingroup Attributed_Variables
-@{
-
-The following documentation is taken from the SWI-Prolog manual.
-
-Binding an attributed variable schedules a goal to be executed at the
-first possible opportunity. In the current implementation the hooks are
-executed immediately after a successful unification of the clause-head
-or successful completion of a foreign language (built-in) predicate. Each
-attribute is associated to a module and the hook attr_unify_hook/2 is
-executed in this module.  The example below realises a very simple and
-incomplete finite domain reasoner.
-
-~~~~~
-:- module(domain,
-      [ domain/2            % Var, ?Domain
-      ]).
-:- use_module(library(ordsets)).
-
-domain(X, Dom) :-
-    var(Dom), !,
-    get_attr(X, domain, Dom).
-domain(X, List) :-
-    list_to_ord_set(List, Domain),
-    put_attr(Y, domain, Domain),
-    X = Y.
-
-%    An attributed variable with attribute value Domain has been
-%    assigned the value Y
-
-attr_unify_hook(Domain, Y) :-
-    (   get_attr(Y, domain, Dom2)
-    ->  ord_intersection(Domain, Dom2, NewDomain),
-        (   NewDomain == []
-        ->    fail
-        ;    NewDomain = [Value]
-        ->    Y = Value
-        ;    put_attr(Y, domain, NewDomain)
-        )
-    ;   var(Y)
-    ->  put_attr( Y, domain, Domain )
-    ;   ord_memberchk(Y, Domain)
-    ).
-
-%    Translate attributes from this module to residual goals
-
-attribute_goals(X) -->
-    { get_attr(X, domain, List) },
-    [domain(X, List)].
-~~~~~
-
-Before explaining the code we give some example queries:
-
-The predicate `domain/2` fetches (first clause) or assigns
-(second clause) the variable a <em>domain</em>, a set of values it can
-be unified with.  In the second clause first associates the domain
-with a fresh variable and then unifies X to this variable to deal
-with the possibility that X already has a domain. The
-predicate attr_unify_hook/2 is a hook called after a variable with
-a domain is assigned a value.  In the simple case where the variable
-is bound to a concrete value we simply check whether this value is in
-the domain. Otherwise we take the intersection of the domains and either
-fail if the intersection is empty (first example), simply assign the
-value if there is only one value in the intersection (second example) or
-assign the intersection as the new domain of the variable (third
-example). The nonterminal `attribute_goals/3` is used to translate
-remaining attributes to user-readable goals that, when executed, reinstate
-these attributes.
-
-*/
-
-
-
 :- module('$attributes', [
 			  delayed_goals/4
 			  ]).
@@ -145,6 +78,83 @@ these attributes.
         woken_att_do/4]).
 
 
+
+
+
+
+/**
+  @{  
+  @defgroup New_Style_Attribute_Declarations hProlog and SWI-Prolog style Attribute Declarations
+  @ingroup Attributed_Variables
+  
+  The following documentation is taken from the SWI-Prolog manual.
+
+  Binding an attributed variable schedules a goal to be executed at the
+  first possible opportunity. In the current implementation the hooks are
+  executed immediately after a successful unification of the clause-head
+  or successful completion of a foreign language (built-in) predicate. Each
+  attribute is associated to a module and the hook attr_unify_hook/2 is
+  executed in this module.  The example below realises a very simple and
+  incomplete finite domain reasoner.
+
+  ~~~~~
+  :- module(domain,
+  [ domain/2            % Var, ?Domain %
+  ]).
+  :- use_module(library(ordsets)).
+
+  domain(X, Dom) :-
+  var(Dom), !,
+  get_attr(X, domain, Dom).
+  domain(X, List) :-
+  list_to_ord_set(List, Domain),
+  put_attr(Y, domain, Domain),
+  X = Y.
+
+                                %    An attributed variable with attribute value Domain has been %
+                                %    assigned the value Y %
+
+  attr_unify_hook(Domain, Y) :-
+  (   get_attr(Y, domain, Dom2)
+  ->  ord_intersection(Domain, Dom2, NewDomain),
+  (   NewDomain == []
+  ->    fail
+  ;    NewDomain = [Value]
+  ->    Y = Value
+  ;    put_attr(Y, domain, NewDomain)
+  )
+  ;   var(Y)
+  ->  put_attr( Y, domain, Domain )
+  ;   ord_memberchk(Y, Domain)
+  ).
+
+                                %    Translate attributes from this module to residual goals %
+
+  attribute_goals(X) -->
+  { get_attr(X, domain, List) },
+  [domain(X, List)].
+  ~~~~~
+
+  Before explaining the code we give some example queries:
+
+  The predicate `domain/2` fetches (first clause) or assigns
+  (second clause) the variable a <em>domain</em>, a set of values it can
+  be unified with.  In the second clause first associates the domain
+  with a fresh variable and then unifies X to this variable to deal
+  with the possibility that X already has a domain. The
+  predicate attr_unify_hook/2 is a hook called after a variable with
+  a domain is assigned a value.  In the simple case where the variable
+  is bound to a concrete value we simply check whether this value is in
+  the domain. Otherwise we take the intersection of the domains and either
+  fail if the intersection is empty (first example), simply assign the
+  value if there is only one value in the intersection (second example) or
+  assign the intersection as the new domain of the variable (third
+  example). The nonterminal `attribute_goals/3` is used to translate
+  remaining attributes to user-readable goals that, when executed, reinstate
+  these attributes.
+
+*/
+
 :- dynamic attributes:attributed_module/3, attributes:modules_with_attributes/1.
 
 /** @pred get_attr(+ _Var_,+ _Module_,- _Value_) 

pl/boot.yap

@@ -15,12 +15,13 @@
 *									 *
 *************************************************************************/
 
+%% @{  
+
 /**
 
 @defgroup YAPControl Control Predicates
-@ingroup YAPBuiltins
+@ingroup builtins
-@{
+  
-
 */
 
 
@@ -1529,8 +1530,6 @@ The goal `throw( _Ball_)` throws an exception. Execution is
 stopped, and the exception is sent to the ancestor goals until reaching
 a matching catch/3, or until reaching top-level.
 
-@}
-
 */
 throw(_Ball) :-
 	% use existing ball
@@ -1590,6 +1589,6 @@ log_event( String, Args ) :-
 	log_event( M ).
 
 /**
-@}
+  @}
 */
 

pl/callcount.yap

@@ -15,11 +15,11 @@
 *									 *
 *************************************************************************/
 
+%% @{
 
 /** @defgroup Profiling Profiling Prolog Programs
-@ingroup YAPExtensions
+@ingroup extensions
-@{
+  
-
 YAP includes two profilers. The count profiler keeps information on the
 number of times a predicate was called. This information can be used to
 detect what are the most commonly called predicates in the program.  The
@@ -35,15 +35,11 @@ implementation.
 
  */
 
-/**
+%% @{  
-@}
-*/
-
 
 /** @defgroup Call_Counting Counting Calls
 @ingroup Profiling
-@{
+  
-
 Predicates compiled with YAP's flag call_counting set to
 `on` update counters on the numbers of calls and of
 retries. Counters are actually decreasing counters, so that they can be
@@ -63,10 +59,7 @@ The code for the call counters piggybacks on the profiling
 code. Therefore, activating the call counters also activates the profiling
 counters.
 
-These are  the predicates that access and manipulate the call counters:
+These are  the predicates that access and manipulate the call counters. 
-
-
- 
 */
 
 :- system_module( '$_callcount', [call_count/3,
@@ -151,6 +144,7 @@ call_count(Calls, Retries, Both) :-
 '$check_if_call_count_on'(Calls, A) :-
 	'$do_error'(type_error(integer,Calls),call_count(A)).
 
+%% @}
 
 /**
 @}

pl/checker.yap

@@ -69,6 +69,8 @@
         '$syntax_check_multiple'/2,
         '$syntax_check_single_var'/2]).
 
+%% @{
+
 /**
 
 @defgroup   YAPStyle Checker
@@ -113,9 +115,7 @@ By default, style checking is disabled in YAP unless we are in
 The style_check/1 built-in is now deprecated. Please use
 `set_prolog_flag/1` instead.
 
-@{
+  **/
-
-**/
 %
 % A Small style checker for YAP
 

pl/chtypes.yap

@@ -17,6 +17,12 @@
 
 :- system_module( '$_chtypes', [], []).
 
+/**
+  * @defgroup YAPChars Sequences of Characters: atoms, strings, lists of codes.  
+  * @ingroup builtins     
+  *
+*/                                                                       
+
 /*
   
 In addition, there is the library library(ctype) providing compatibility to some other Prolog systems. The predicates of this library are defined in terms of code_type/2.

pl/consult.yap

@@ -65,9 +65,11 @@
 
 :- use_system_module( '$_preds', ['$current_predicate'/4]).
 
+%% @{  
+
 /**
-  \defgroup YAPConsulting Loading files into YAP
+  @defgroup YAPConsulting Loading files into YAP
-  @ingroup YAPLoading
+  @ingroup consult
 
   We present the main predicates and directives available to load
 files and to set-up the Prolog environment. We discuss
@@ -79,10 +81,9 @@ files and to set-up the Prolog environment. We discuss
   @{
 
 @defgroup YAPReadFiles The Predicates that Read Source Files
-@ingroup  YAPConsulting
+@ingroup  consult
-
-@{
 
+  
  */
 
 
@@ -947,19 +948,20 @@ source_file(Mod:Pred, FileName) :-
 
   SWI-compatible predicate. True if the predicate specified by  _ModuleAndPred_ was loaded from file  _File_, where  _File_ is an absolute path name (see `absolute_file_name/2`).
 
-  @}
-  
 */
 
+%% @}
+
+%% @{
+{
+
 /** @addtogroup YAPLibraries Library Predicates
 
 Library files reside in the library_directory path (set by the
 `LIBDIR` variable in the Makefile for YAP). Currently,
 most files in the library are from the Edinburgh Prolog library. 
 
-  @{
+*/
-  
- */
 prolog_load_context(directory, DirName) :- 
         ( source_location(F, _)
         -> file_directory_name(F, DirName) ;
@@ -1223,15 +1225,15 @@ unload_file( F0 ) :-
     erase(R),
     fail.
 
+%% @}
+
 
 /**
 
-@}
+  @{
 
 @addtogroup YAPModules
 
-@{
-
 **/
 
 %
@@ -1339,8 +1341,10 @@ account the following observations:
 @}
 **/
 
+%%   @{  
+
 /** @defgroup  YAPCompilerSettings Directing and Configuring the Compiler
-    @ingroup  YAPConsulting
+    @ingroup  YAPProgramming
 
   The YAP system also includes a number of primitives designed to set
   compiler parameters and to track the state of the compiler. One
@@ -1352,7 +1356,6 @@ account the following observations:
 This section presents a set of built-ins predicates designed to set the 
 environment for the compiler.
 
-  @{
 */
 
   
@@ -1365,8 +1368,6 @@ internal conventions are Unix and this predicates is equivalent to =/2
 directory-separator, limit the filename length map dots, except for the
 last one, onto underscores.
 
-@{
-
 */
 
 % add_multifile_predicate when we start consult
@@ -1495,15 +1496,17 @@ initialization(G,OPT) :-
 @}
 */
 
+%%   @{  
+
+
+
 /**
 
 @defgroup Conditional_Compilation Conditional Compilation
 
 @ingroup  YAPCompilerSettings
 
-  @{
+  Conditional compilation builds on the same principle as
-  
-Conditional compilation builds on the same principle as
 term_expansion/2, goal_expansion/2 and the expansion of
 grammar rules to compile sections of the source-code
 conditionally. One of the reasons for introducing conditional
@@ -1533,12 +1536,9 @@ section_2.
 section_3.
 :- else.
 section_else.
-:- endif.
+  :- endif.
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
+  
-
-@{
-
 */
 
 /** @pred    if( : _Goal_) 
@@ -1687,8 +1687,5 @@ consult_depth(LV) :- '$show_consult_level'(LV).
   @}
 
   @}
-
-  @}
-
 */
 

pl/corout.yap

@@ -16,9 +16,10 @@
 *************************************************************************/
 
 
-/** @defgroup CohYroutining Co-routining
+/**
-@ingroup YAPExtensions
+  @defgroup CohYroutining Co-routining
-@{
+  @ingroup extensions
+  @{
 
 Prolog uses a simple left-to-right flow of control. It is sometimes
 convenient to change this control so that goals will only be executed
@@ -119,16 +120,14 @@ The routines in this section fetch or set the entire attribute list of a
 variables. Use of these predicates is anticipated to be restricted to
 printing and other special purpose operations.
 
+*/
 
-
+/**
- @pred get_attrs(+ _Var_,- _Attributes_) 
+ @pred get_attrs(+ _Var_,- _Attributes_)
-
-
 
 Get all attributes of  _Var_.  _Attributes_ is a term of the form
 `att( _Module_,  _Value_,  _MoreAttributes_)`, where  _MoreAttributes_ is
 `[]` for the last attribute.
-
  
 */
 attribute_goals(Var) -->
@@ -162,9 +161,9 @@ remove_when_declarations(Goal, Goal).
 				%
 % operators defined in this module:
 %
-/** @pred freeze(? _X_,: _G_) 
+/**
-
+  @pred freeze(? _X_,: _G_)
-
+  
 Delay execution of goal  _G_ until the variable  _X_ is bound.
 
  
@@ -618,5 +617,6 @@ check_first_attvar([_|Vs], V0) :-
 	check_first_attvar(Vs, V0).
 
 /**
-@}
+  @}
+  @}
 */

pl/debug.yap

@@ -46,7 +46,7 @@
 -----------------------------------------------------------------------------*/
 
 /** @defgroup Deb_Preds Debugging Predicates
-@ingroup YAPBuiltins
+@ingroup builtins
 
 @{
 The

pl/depth_bound.yap

@@ -18,7 +18,7 @@
 /**
 
 @defgroup DepthLimited Depth Limited Search
-@ingroup YAPExtensions
+@ingroup extensions
 
 YAP implements various extensions to the default Prolog search. One of
 the most iseful s restricting the maximum search depth.

pl/flags.yap

@@ -27,7 +27,7 @@
         yap_flag/3], []).
 
 /** @defgroup Flags  YAP Execution Flags
-    @ingroup YAPBuiltins
+    @ingroup builtins
     @{
 */
 

pl/grammar.yap

@@ -18,7 +18,7 @@
 
 /** 
 @defgroup Grammars Grammar Rules
-@ingroup YAPBuiltins
+@ingroup builtins
 @{
 
 Grammar rules in Prolog are both a convenient way to express definite

pl/init.yap

@@ -14,7 +14,7 @@
 * comments:	initializing the full prolog system			 *
 *									 *
 *************************************************************************/
-%%   @defgroup YAPBuiltins  YAP  Built-Ins
+%%   @defgroup builtins  YAP  Built-Ins
 
 /*
   

pl/load_foreign.yap

@@ -25,7 +25,7 @@
 :- use_system_module( '$_modules', ['$do_import'/3]).
 
 /** @defgroup LoadForeign Access to Foreign Language Programs
-@ingroup YAPBuiltins
+@ingroup builtins
 
 */
 

pl/messages.yap

@@ -16,9 +16,10 @@
 *									 *
 *************************************************************************/
 
-/** @defgroup Messages Message Handling
+/**
-@ingroup YAPControl
+  @defgroup Messages Message Handling
-@{
+  @ingroup YAPControl
+  @{
 
 The interaction between YAP and the user relies on YAP's ability to
 portray messages. These messages range from prompts to error
@@ -679,5 +680,6 @@ pred_arity(H,Name,Arity) :-
 
 
 /**
-@}
+  @}
+  @}
 */

pl/modules.yap

@@ -15,83 +15,11 @@
 *									 *
 *************************************************************************/
 
-/**
-
-  @defgroup YAPPackages The YAP packages
-
-
-  @defgroup YAPLibrary The YAP Library
-
-  Library files reside in the library_directory path (set by the
-  `LIBDIR` variable in the Makefile for YAP). Several files in the
-  library are originally from the public-domain Edinburgh Prolog library. 
-
-  +  @ref maplist
-
-  +  @ref Apply Apply Macros
-  
-  +  @ref Association_Lists 
-  
-  +  @ref AVL_Trees 
-  
-  +  @ref  Exo_Intervals
-  
-  +  @ref Heaps 
-  
-  +  @ref Lists
-  
-  +  @ref LineUtilities
-  
-  +  @ref matrix 
-  
-  +  @ref NonhYBacktrackable_Data_Structures 
-  
-  +  @ref Ordered_Sets 
-  
-  +  @ref Pseudo_Random 
-  
-  +  @ref Queues Queues
-  
-  +  @ref PseudoRandom
-  
-  +  @ref RedhYBlack_Trees
-  
-  +  @ref RegExp
-
-  +  @ref Splay_Trees 
-  
-  +  @ref System 
-  
-  +  @ref Terms 
-  
-  +  @ref Tries 
-  
-  +  @ref Cleanup 
-  
-  +  @ref Timeout
-  
-  +  @ref Trees
-  
-  +  @ref UGraphs
-  
-  +  @ref DGraphs 
-  
-  +  @ref UnDGraphs
-  
-  +  @ref DBUsage
-  
-  +  @ref lambda
-
-  +  @ref clpfd
-  
-  +  @ref Block_Diagram 
-*/  
-
 /**
 
    \defgroup YAPModules The YAP Module system 
 
-   @ingroup YAPLoading
+   @ingroup consult
 
   The YAP module system is based on the Quintus/SISCtus module
 system ˜\cite quintus . In this design, modules are named collections of predicates,
@@ -127,7 +55,7 @@ YAP  includes a number of libraries and packages, most of them
 
 The main mechanism to change the current type-in module is by using
 the module/2 declaration.This declaration sets the source module when
-it starts consulting a file, and resets it at the end.  One can set
+  it starts consulting a file, and resets it at the end.  One can set
 the type-in module permanently by using the built-in `module/1`.
 
 \subsection Explicit Naming

pl/os.yap

@@ -22,10 +22,12 @@
 	 ], [] ).
 :- use_system_module( '$_errors', ['$do_error'/2]).
 
-/** @defgroup YAPOS Access to Operating System Functionality
+%% @{
-@ingroup YAPBuiltins
-@{
 
+
+/** @defgroup YAPOS Access to Operating System Functionality
+@ingroup builtins
+  
 The following built-in predicates allow access to underlying
 Operating System functionality.
 

pl/preds.yap

@@ -1,6 +1,6 @@
 /*************************************************************************
 *									 *
-*	 YAP Prolog 							 *
+  *	 YAP Prolog 							 *
 *									 *
 *	Yap Prolog was developed at NCCUP - Universidade do Porto	 *
 *									 *
@@ -16,7 +16,7 @@
 *************************************************************************/
 
 /** @defgroup Database Using the Clausal Data Base
-@ingroup YAPBuiltins
+@ingroup builtins
 @{
 
 Predicates in YAP may be dynamic or static. By default, when
@@ -1167,6 +1167,7 @@ predicate_erased_statistics(P,NCls,Sz,ISz) :-
 Defines the relation:  _P_ is a currently defined predicate whose name is the atom  _A_. 
 */
 current_predicate(A,T) :-
+	'$system_module'(M),
 	'$ground_module'(T, M, T0),
 	(
 	 '$current_predicate'(A, M, T0, _)
@@ -1187,7 +1188,6 @@ system_predicate(A,T) :-
 	;
 	 '$current_predicate'(A, prolog, T0, Flags)
 	),
-	Flags /\ 0x00004000 =\= 0,
 	\+ '$hidden'(A).
 
 /** @pred  system_predicate( ?_P_ )

pl/protect.yap

@@ -19,6 +19,13 @@
 
 % This protects all code from further changes
 % and also makes it impossible from some predicates to be seen
+'$protect' :-
+	fail,
+        '$system_mod'( M ),
+        '$current_predicate'(A, M, T0, Flags),
+        NFlags is Flags \/ 0x00004000,
+	'$flags'(M:T0, Flags, NFlags),
+	fail.
 '$protect' :-
 	current_atom(Name),
 	atom_codes(Name,[0'$|_]),
@@ -30,8 +37,8 @@
 '$protect'.
 
 '$hide_predicates'(Name) :-
-	'$current_predicate'(Name, prolog, P, _),
+	'$current_predicate'(Name, Mod, P, _),
-	'$hide_predicate'(P,prolog),
+	'$hide_predicate'(P,Mod),
 	fail.
 '$hide_predicates'(_).
 

pl/qly.yap

@@ -45,7 +45,7 @@
 /**
 
 @defgroup YAPSaving Saving and Loading Prolog States
-@ingroup YAPLoading
+@ingroup consult
 
 YAP can save and read images of its current state to files, known as
 saved states. It is possible to save the entire state or just a module

pl/setof.yap

@@ -17,7 +17,7 @@
 
 
 /** @defgroup Sets Collecting Solutions to a Goal
-@ingroup YAPBuiltins
+@ingroup builtins
 @{
 
 When there are several solutions to a goal, if the user wants to collect all

pl/tabling.yap

@@ -17,7 +17,7 @@
 :- use_system_module( '$_errors', ['$do_error'/2]).
 
 /** @defgroup Tabling Tabling
-@ingroup YAPExtensions
+@ingroup extensions
 @{
 
  *YAPTab* is the tabling engine that extends YAP's execution

pl/threads.yap

@@ -17,7 +17,7 @@
 
 /**
   @defgroup Threads Threads
-  @ingroup YAPExtensions
+  @ingroup extensions
   @{
 
   YAP implements a SWI-Prolog compatible multithreading

pl/yio.yap

@@ -55,7 +55,7 @@
 :- use_system_module( '$_errors', ['$do_error'/2]).
 
 /** @defgroup InputOutput Input/Output Predicates
-@ingroup YAPBuiltins
+@ingroup builtins
 
 Some of the Input/Output predicates described below will in certain conditions
 provide error messages and abort only if the file_errors flag is set.

swi/library/aggregate.pl

@@ -51,7 +51,7 @@
 	aggregate_all(?,?,0,-).
 
 /** <module> Aggregation operators on backtrackable predicates
-@ingroup SWILibrary
+@ingroup swi
 
 This library provides aggregating operators  over   the  solutions  of a
 predicate. The operations are a generalisation   of the bagof/3, setof/3

swi/library/base64.pl

@@ -35,7 +35,7 @@
 	  ]).
 
 /** <module> Base64 encoding and decoding
-@ingroup SWILibrary
+@ingroup swi
 
 Prolog-based base64 encoding using  DCG   rules.  Encoding  according to
 rfc2045. For example:

swi/library/broadcast.pl

@@ -48,7 +48,7 @@
 	listener/4.
 
 /** <module> Event service
-@ingroup SWILibrary
+@ingroup swi
 
 Generic broadcasting service. Broadcasts are   made  using the predicate
 broadcast(+Templ). All registered  `listeners'  will   have  their  goal