Add TODOs to delete references to where clause

The where clause for ontology classes is deprecated
in favor of the accepts and rejects clauses.

examples/technical_report/Isabelle_DOF-Manual/03_GuidedTour.thy

@@ -559,6 +559,9 @@ text\<open>
      where "(title       ~~ \<lbrakk>subtitle\<rbrakk>   ~~ \<lbrace>author\<rbrace>$^+$+  ~~  abstract    ~~
                introduction ~~  \<lbrace>technical || example\<rbrace>$^+$  ~~  conclusion ~~  
                bibliography)"
+    % TODO:
+    % Update to the new implementation.
+    % where is deprecated and the new implementation uses accepts and rejects.
   \<close>}
 
   In a integrated document source, the body of the content can be paranthesized into:
@@ -664,6 +667,10 @@ doc_class requirement = long_name :: "string option"
 doc_class requirement_analysis = no :: "nat"
    where "requirement_item +"
 
+% TODO:
+% Update to the new implementation.
+% where is deprecated and the new implementation uses accepts and rejects.
+
 doc_class hypothesis = requirement +
       hyp_type :: hyp_type <= physical  (* default *)
   

examples/technical_report/Isabelle_DOF-Manual/04_RefMan.thy

@@ -114,6 +114,9 @@ text\<open>
   \<^emph>\<open>is-a\<close> relation between classes;
   \<^item> classes may refer to other classes via a regular expression in a
     \<^emph>\<open>where\<close> clause;
+  % TODO:
+  % Update to the new implementation.
+  % where is deprecated and the new implementation uses accepts and rejects.
   \<^item> attributes may have default values in order to facilitate notation.
 \<close>
 
@@ -146,6 +149,9 @@ text\<open>
   classes and their inheritance relation structure meta-data of text-elements in an object-oriented 
   manner, monitor classes enforce structural organization of documents via the language specified 
   by the regular expression enforcing a sequence of text-elements.
+  % TODO:
+  % Update to the new implementation.
+  % where is deprecated and the new implementation uses accepts and rejects.
 
   A major design decision of ODL is to denote attribute values by HOL-terms and HOL-types. 
   Consequently, ODL can refer to any predefined type defined in the HOL library, \<^eg>,