Merge and upgrade to development version of Isabelle/HOL.

Isabelle_DOF-Example-II/paper.thy

@@ -751,7 +751,7 @@ This normal form is closed under deterministic and  communication operators.
 The advantage of this format is that we can mimick the well-known product automata construction
 for an arbitrary number of synchronized processes under normal form.
 We only show the case of the synchronous product of two processes: \<close>
-text*[T3::"theorem", short_name="\<open>Product Construction\<close>", level="Some 2"]\<open>
+Theorem*[T3, short_name="\<open>Product Construction\<close>", level="Some 2"]\<open>
 Parallel composition translates to normal form:
 @{cartouche [display,indent=5]\<open>(P\<^sub>n\<^sub>o\<^sub>r\<^sub>m\<lbrakk>\<tau>\<^sub>1,\<upsilon>\<^sub>1\<rbrakk> \<sigma>\<^sub>1) || (P\<^sub>n\<^sub>o\<^sub>r\<^sub>m\<lbrakk>\<tau>\<^sub>2,\<upsilon>\<^sub>2\<rbrakk> \<sigma>\<^sub>2) = 
     P\<^sub>n\<^sub>o\<^sub>r\<^sub>m\<lbrakk>\<lambda>(\<sigma>\<^sub>1,\<sigma>\<^sub>2). \<tau>\<^sub>1 \<sigma>\<^sub>1 \<inter> \<tau>\<^sub>2 \<sigma>\<^sub>2 , \<lambda>(\<sigma>\<^sub>1,\<sigma>\<^sub>2).\<lambda>e.(\<upsilon>\<^sub>1 \<sigma>\<^sub>1 e, \<upsilon>\<^sub>2 \<sigma>\<^sub>2 e)\<rbrakk> (\<sigma>\<^sub>1,\<sigma>\<^sub>2)\<close>}

Isabelle_DOF-Examples-Extra/technical_report/TR_my_commented_isabelle/TR_MyCommentedIsabelle.thy

@@ -347,7 +347,7 @@ text\<open>
 \<^item> \<^ML>\<open>Context.proper_subthy : theory * theory -> bool\<close> subcontext test
 \<^item> \<^ML>\<open>Context.Proof: Proof.context -> Context.generic \<close> A constructor embedding local contexts
 \<^item> \<^ML>\<open>Context.proof_of : Context.generic -> Proof.context\<close> the inverse
-\<^item> \<^ML>\<open>Context.theory_name : theory -> string\<close>
+\<^item> \<^ML>\<open>Context.theory_name : {long:bool} -> theory -> string\<close>
 \<^item> \<^ML>\<open>Context.map_theory: (theory -> theory) -> Context.generic -> Context.generic\<close>
 \<close>
 
@@ -358,7 +358,7 @@ text\<open>The structure \<^ML_structure>\<open>Proof_Context\<close> provides a
 \<^item> \<^ML>\<open>  Context.Proof: Proof.context -> Context.generic \<close>
   the path to a generic Context, i.e. a sum-type of global and local contexts
   in order to simplify system interfaces
-\<^item> \<^ML>\<open> Proof_Context.get_global: theory -> string -> Proof.context\<close>
+\<^item> \<^ML>\<open> Proof_Context.get_global: {long:bool} -> theory -> string -> Proof.context\<close>
 \<close>
 
 
@@ -891,7 +891,6 @@ datatype thy = Thy of
 \<^item>  \<^ML>\<open>Theory.axiom_space: theory -> Name_Space.T\<close>
 \<^item>  \<^ML>\<open>Theory.all_axioms_of: theory -> (string * term) list\<close>
 \<^item>  \<^ML>\<open>Theory.defs_of: theory -> Defs.T\<close>
-\<^item>  \<^ML>\<open>Theory.join_theory: theory list -> theory\<close>
 \<^item>  \<^ML>\<open>Theory.at_begin: (theory -> theory option) -> theory -> theory\<close>
 \<^item>  \<^ML>\<open>Theory.at_end: (theory -> theory option) -> theory -> theory\<close>
 \<^item>  \<^ML>\<open>Theory.begin_theory: string * Position.T -> theory list -> theory\<close>

Isabelle_DOF-Ontologies/CC_v3_1_R5/DOF-CC_terminology.sty

@@ -23,35 +23,35 @@
 
 
 \newkeycommand*{\mathcc}[label=,type=%
- , scholarly_paper.math_content.short_name ={}%
+ , scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontentDOTshortUNDERSCOREname ={}%
- , scholarly_paper.math_content.mcc     = % 
+ , scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontentDOTmcc     = % 
- , Isa_COL.text_element.level         =%
+ , IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTlevel         =%
- , Isa_COL.text_element.referentiable =%
+ , IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTreferentiable =%
- , Isa_COL.text_element.variants      =%
+ , IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTvariants      =%
- , scholarly_paper.text_section.main_author  =%
+ , scholarlyUNDERSCOREpaperDOTtextUNDERSCOREsectionDOTmainUNDERSCOREauthor  =%
- , scholarly_paper.text_section.fixme_list   =%
+ , scholarlyUNDERSCOREpaperDOTtextUNDERSCOREsectionDOTfixmeUNDERSCORElist   =%
- , Isa_COL.text_element.level                =%
+ , IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTlevel                =%
- , scholarly_paper.technical.definition_list =%
+ , scholarlyUNDERSCOREpaperDOTtechnicalDOTdefinitionUNDERSCORElist =%
- , scholarly_paper.technical.status          =%
+ , scholarlyUNDERSCOREpaperDOTtechnicalDOTstatus          =%
- , CC_terminology.concept_definition.tag=%
+ , CCUNDERSCOREterminologyDOTconceptUNDERSCOREdefinitionDOTtag=%
- , CC_terminology.concept_definition.short_tag=%
+ , CCUNDERSCOREterminologyDOTconceptUNDERSCOREdefinitionDOTshortUNDERSCOREtag=%
  ]
  [1]
  {%
     \begin{isamarkuptext}%
-      \ifthenelse{\equal{\commandkey{scholarly_paper.math_content.short_name}} {} }  
+      \ifthenelse{\equal{\commandkey{scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontentDOTshortUNDERSCOREname}} {} }  
         {%
-         \begin{\commandkey{scholarly_paper.math_content.mcc}}\label{\commandkey{label}}
+         \begin{\commandkey{scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontentDOTmcc}}\label{\commandkey{label}}
            #1
-         \end{\commandkey{scholarly_paper.math_content.mcc}}
+         \end{\commandkey{scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontentDOTmcc}}
         }{%
-         \begin{\commandkey{scholarly_paper.math_content.mcc}}[\commandkey{scholarly_paper.math_content.short_name}]\label{\commandkey{label}} 
+         \begin{\commandkey{scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontentDOTmcc}}[\commandkey{scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontentDOTshortUNDERSCOREname}]\label{\commandkey{label}} 
            #1 
-         \end{\commandkey{scholarly_paper.math_content.mcc}}
+         \end{\commandkey{scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontentDOTmcc}}
         }
     \end{isamarkuptext}%
  } 
 
-\expandafter\def\csname isaDof.text.scholarly_paper.math_content\endcsname{\mathcc}
+\expandafter\def\csname isaDofDOTtextDOTscholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent\endcsname{\mathcc}
 
 

Isabelle_DOF-Ontologies/CENELEC_50128/DOF-CENELEC_50128.sty

@@ -60,26 +60,26 @@
 }
 
 \newcommand{\SRACautorefname}{SRAC}
-\newisadof{text.CENELEC_50128.SRAC}%
+\newisadof{textDOTCENELECUNDERSCORE50128DOTSRAC}%
 [label=,type=%
-,Isa_COL.text_element.level=%
+,IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTlevel=%
-,Isa_COL.text_element.referentiable=%
+,IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTreferentiable=%
-,Isa_COL.text_element.variants=%
+,IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTvariants=%
-,CENELEC_50128.requirement.is_concerned=%
+,CENELECUNDERSCORE50128DOTrequirementDOTisUNDERSCOREconcerned=%
-,CENELEC_50128.requirement.long_name=%
+,CENELECUNDERSCORE50128DOTrequirementDOTlongUNDERSCOREname=%
-,CENELEC_50128.SRAC.formal_repr=%
+,CENELECUNDERSCORE50128DOTSRACDOTformalUNDERSCORErepr=%
-,CENELEC_50128.SRAC.assumption_kind=%
+,CENELECUNDERSCORE50128DOTSRACDOTassumptionUNDERSCOREkind=%
-,CENELEC_50128.EC.assumption_kind=%
+,CENELECUNDERSCORE50128DOTECDOTassumptionUNDERSCOREkind=%
-,CENELEC_50128.assumption.assumption_kind=%
+,CENELECUNDERSCORE50128DOTassumptionDOTassumptionUNDERSCOREkind=%
 ][1]{%
   \begin{isamarkuptext}%
-      \ifthenelse{\equal{\commandkey{CENELEC_50128.requirement.long_name}}{}}{%
+      \ifthenelse{\equal{\commandkey{CENELECUNDERSCORE50128DOTrequirementDOTlongUNDERSCOREname}}{}}{%
         \begin{SRAC}%
             \addxcontentsline{tos}{chapter}[]{\autoref{\commandkey{label}}}%
       }{%
-        \begin{SRAC}[\commandkey{CENELEC_50128.requirement.long_name}]%
+        \begin{SRAC}[\commandkey{CENELECUNDERSCORE50128DOTrequirementDOTlongUNDERSCOREname}]%
-          \addxcontentsline{tos}{chapter}[]{\autoref{\commandkey{label}}: \commandkey{CENELEC_50128.requirement.long_name}}%
+          \addxcontentsline{tos}{chapter}[]{\autoref{\commandkey{label}}: \commandkey{CENELECUNDERSCORE50128DOTrequirementDOTlongUNDERSCOREname}}%
-          \DOFindex{SRAC}{\commandkey{CENELEC_50128.requirement.long_name}}%
+          \DOFindex{SRAC}{\commandkey{CENELECUNDERSCORE50128DOTrequirementDOTlongUNDERSCOREname}}%
       }\label{\commandkey{label}}%
       #1%
     \end{SRAC}
@@ -113,26 +113,26 @@
 }
 
 \newcommand{\ECautorefname}{EC}
-\newisadof{text.CENELEC_50128.EC}%
+\newisadof{textDOTCENELECUNDERSCORE50128DOTEC}%
 [label=,type=%
-,Isa_COL.text_element.level=%
+,IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTlevel=%
-,Isa_COL.text_element.referentiable=%
+,IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTreferentiable=%
-,Isa_COL.text_element.variants=%
+,IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTvariants=%
-,CENELEC_50128.requirement.is_concerned=%
+,CENELECUNDERSCORE50128DOTrequirementDOTisUNDERSCOREconcerned=%
-,CENELEC_50128.requirement.long_name=%
+,CENELECUNDERSCORE50128DOTrequirementDOTlongUNDERSCOREname=%
-,CENELEC_50128.SRAC.formal_repr=%
+,CENELECUNDERSCORE50128DOTSRACDOTformalUNDERSCORErepr=%
-,CENELEC_50128.SRAC.assumption_kind=%
+,CENELECUNDERSCORE50128DOTSRACDOTassumptionUNDERSCOREkind=%
-,CENELEC_50128.EC.assumption_kind=%
+,CENELECUNDERSCORE50128DOTECDOTassumptionUNDERSCOREkind=%
-,CENELEC_50128.assumption.assumption_kind=%
+,CENELECUNDERSCORE50128DOTassumptionDOTassumptionUNDERSCOREkind=%
 ][1]{%
   \begin{isamarkuptext}%
-      \ifthenelse{\equal{\commandkey{CENELEC_50128.requirement.long_name}}{}}{%
+      \ifthenelse{\equal{\commandkey{CENELECUNDERSCORE50128DOTrequirementDOTlongUNDERSCOREname}}{}}{%
         \begin{EC}%
             \addxcontentsline{tos}{chapter}[]{\autoref{\commandkey{label}}}%
       }{%
-        \begin{EC}[\commandkey{CENELEC_50128.requirement.long_name}]%
+        \begin{EC}[\commandkey{CENELECUNDERSCORE50128DOTrequirementDOTlongUNDERSCOREname}]%
-          \addxcontentsline{toe}{chapter}[]{\autoref{\commandkey{label}}: \commandkey{CENELEC_50128.requirement.long_name}}%
+          \addxcontentsline{toe}{chapter}[]{\autoref{\commandkey{label}}: \commandkey{CENELECUNDERSCORE50128DOTrequirementDOTlongUNDERSCOREname}}%
-          \DOFindex{EC}{\commandkey{CENELEC_50128.requirement.long_name}}%
+          \DOFindex{EC}{\commandkey{CENELECUNDERSCORE50128DOTrequirementDOTlongUNDERSCOREname}}%
       }\label{\commandkey{label}}%
       #1%
     \end{EC}
@@ -155,23 +155,23 @@
 }
 
 \newcommand{\assumptionautorefname}{assumption}
-\newisadof{text.CENELEC_50128.assumption}%
+\newisadof{textDOTCENELECUNDERSCORE50128DOTassumption}%
 [label=,type=%
-,Isa_COL.text_element.level=%
+,IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTlevel=%
-,Isa_COL.text_element.referentiable=%
+,IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTreferentiable=%
-,Isa_COL.text_element.variants=%
+,IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTvariants=%
-,CENELEC_50128.requirement.is_concerned=%
+,CENELECUNDERSCORE50128DOTrequirementDOTisUNDERSCOREconcerned=%
-,CENELEC_50128.requirement.long_name=%
+,CENELECUNDERSCORE50128DOTrequirementDOTlongUNDERSCOREname=%
-,CENELEC_50128.SRAC.formal_repr=%
+,CENELECUNDERSCORE50128DOTSRACDOTformalUNDERSCORErepr=%
-,CENELEC_50128.SRAC.assumption_kind=%
+,CENELECUNDERSCORE50128DOTSRACDOTassumptionUNDERSCOREkind=%
-,CENELEC_50128.assumption.assumption_kind=%
+,CENELECUNDERSCORE50128DOTassumptionDOTassumptionUNDERSCOREkind=%
 ][1]{%
   \begin{isamarkuptext}%
-      \ifthenelse{\equal{\commandkey{CENELEC_50128.requirement.long_name}}{}}{%
+      \ifthenelse{\equal{\commandkey{CENELECUNDERSCORE50128DOTrequirementDOTlongUNDERSCOREname}}{}}{%
         \begin{assumption}%
       }{%
-        \begin{assumption}[\commandkey{CENELEC_50128.requirement.long_name}]%
+        \begin{assumption}[\commandkey{CENELECUNDERSCORE50128DOTrequirementDOTlongUNDERSCOREname}]%
-          \DOFindex{assumption}{\commandkey{CENELEC_50128.requirement.long_name}}%
+          \DOFindex{assumption}{\commandkey{CENELECUNDERSCORE50128DOTrequirementDOTlongUNDERSCOREname}}%
       }\label{\commandkey{label}}%
       #1%
     \end{assumption}
@@ -196,23 +196,23 @@
 
 
 \newcommand{\hypothesisautorefname}{hypothesis}
-\newisadof{text.CENELEC_50128.hypothesis}%
+\newisadof{textDOTCENELECUNDERSCORE50128DOThypothesis}%
 [label=,type=%
-,Isa_COL.text_element.level=%
+,IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTlevel=%
-,Isa_COL.text_element.referentiable=%
+,IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTreferentiable=%
-,Isa_COL.text_element.variants=%
+,IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTvariants=%
-,CENELEC_50128.requirement.is_concerned=%
+,CENELECUNDERSCORE50128DOTrequirementDOTisUNDERSCOREconcerned=%
-,CENELEC_50128.requirement.long_name=%
+,CENELECUNDERSCORE50128DOTrequirementDOTlongUNDERSCOREname=%
-,CENELEC_50128.SRAC.formal_repr=%
+,CENELECUNDERSCORE50128DOTSRACDOTformalUNDERSCORErepr=%
-,CENELEC_50128.SRAC.hypothesis_kind=%
+,CENELECUNDERSCORE50128DOTSRACDOThypothesisUNDERSCOREkind=%
-,CENELEC_50128.hypothesis.hyp_type=%
+,CENELECUNDERSCORE50128DOThypothesisDOThypUNDERSCOREtype=%
 ][1]{%
   \begin{isamarkuptext}%
-      \ifthenelse{\equal{\commandkey{CENELEC_50128.requirement.long_name}}{}}{%
+      \ifthenelse{\equal{\commandkey{CENELECUNDERSCORE50128DOTrequirementDOTlongUNDERSCOREname}}{}}{%
         \begin{hypothesis}%
       }{%
-        \begin{hypothesis}[\commandkey{CENELEC_50128.requirement.long_name}]%
+        \begin{hypothesis}[\commandkey{CENELECUNDERSCORE50128DOTrequirementDOTlongUNDERSCOREname}]%
-          \DOFindex{hypothesis}{\commandkey{CENELEC_50128.requirement.long_name}}%
+          \DOFindex{hypothesis}{\commandkey{CENELECUNDERSCORE50128DOTrequirementDOTlongUNDERSCOREname}}%
       }\label{\commandkey{label}}%
       #1%
     \end{hypothesis}

Isabelle_DOF-Unit-Tests/AssnsLemmaThmEtc.thy

@@ -180,7 +180,6 @@ text*[tu15::scholarly_paper.experiment ]\<open>Lectus accumsan velit ultrices, .
 text*[tu16::scholarly_paper.hypothesis ]\<open>Lectus accumsan velit ultrices, ...\<close>
 text*[tu17::scholarly_paper.math_proof ]\<open>Lectus accumsan velit ultrices, ...\<close>
 text*[tu18::scholarly_paper.consequence]\<open>Lectus accumsan velit ultrices, ...\<close>
-text*[tu26::scholarly_paper.math_explanation]\<open>Lectus accumsan velit ultrices, ...\<close>
 text*[tu19::scholarly_paper.math_formal]\<open>Lectus accumsan velit ultrices, ...\<close>
 text*[tu20::scholarly_paper.proposition]\<open>Lectus accumsan velit ultrices, ...\<close>
 text*[tu21::scholarly_paper.math_content    ]\<open>Lectus accumsan velit ultrices, ...\<close>
@@ -194,4 +193,44 @@ text*[tu8::scholarly_paper.tech_code]        \<open>Lectus accumsan velit ultric
 text*[tu27::scholarly_paper.engineering_content]\<open>Lectus accumsan velit ultrices, ...\<close>
 text*[tu14::scholarly_paper.evaluation ]\<open>Lectus accumsan velit ultrices, ...\<close>
 
+text\<open> @{axiom tu1} @{lemma tu2} @{example tu3} @{premise tu4} @{theorem tu5} @{assertion tu6} 
+      @{technical tu9} @{assumption             tu10 }  @{definition             tu13 }
+      @{experiment      tu15 } @{hypothesis      tu16 } @{math_proof      tu17 }
+      @{consequence     tu18 } @{math_formal     tu19 } @{proposition     tu20 }
+      @{math_content    tu21 } @{math_example    tu22 } @{conclusion_stmt tu23 }
+      @{math_motivation tu24 } @{tech_definition tu25 } @{eng_example     tu28 }
+      @{tech_example    tt10 } @{tech_code       tu8 }  @{engineering_content tu27 }
+      @{evaluation      tu14 }
+    \<close>
+
+subsection\<open>The Use in Macros\<close>
+
+Lemma*[ttu2::scholarly_paper.lemma    ]\<open>Lectus accumsan velit ultrices, ...\<close>
+Example*[ttu3::scholarly_paper.math_example  ]\<open>Lectus accumsan velit ultrices, ...\<close>
+Premise*[ttu4::scholarly_paper.premise  ]\<open>Lectus accumsan velit ultrices, ...\<close>
+Theorem*[ttu5::scholarly_paper.theorem  ]\<open>Lectus accumsan velit ultrices, ...\<close>
+Assertion*[ttu6::scholarly_paper.assertion]\<open>Lectus accumsan velit ultrices, ...\<close>
+Corollary*[ttu7::scholarly_paper.corollary]\<open>Lectus accumsan velit ultrices, ...\<close>
+Assumption*[ttu10::scholarly_paper.assumption ]\<open>Lectus accumsan velit ultrices, ...\<close>
+Definition*[ttu13::scholarly_paper.definition ]\<open>Lectus accumsan velit ultrices, ...\<close>
+Hypothesis*[ttu16::scholarly_paper.hypothesis ]\<open>Lectus accumsan velit ultrices, ...\<close>
+Proof*[ttu17::scholarly_paper.math_proof ]\<open>Lectus accumsan velit ultrices, ...\<close>
+Consequence*[ttu18::scholarly_paper.consequence]\<open>Lectus accumsan velit ultrices, ...\<close>
+Proposition*[ttu20::scholarly_paper.proposition]\<open>Lectus accumsan velit ultrices, ...\<close>
+Conclusion*[ttu23::scholarly_paper.conclusion_stmt ]\<open>Lectus accumsan velit ultrices, ...\<close>
+(* Definition*[ttu25::scholarly_paper.tech_definition ]\<open>Lectus accumsan velit ultrices, ...\<close> 
+   interesting modeling bug.
+*)
+(*Example*[ttu28::scholarly_paper.eng_example     ]\<open>Lectus accumsan velit ultrices, ...\<close>
+   interesting modeling bug.
+*)  
+text\<open> @{lemma ttu2} @{math_example ttu3} @{premise ttu4} @{theorem ttu5} @{assertion ttu6} 
+      @{assumption ttu10 }  @{definition ttu13 }
+      @{hypothesis      ttu16 } @{math_proof      ttu17 }
+      @{consequence     ttu18 } @{proposition     ttu20 }
+      @{math_content    tu21 }  @{conclusion_stmt ttu23 }
+      @ \<open>{eng_example     ttu28 }\<close>
+      @ \<open>{tech_example    tt10 }\<close>  
+    \<close>
+
 end

Isabelle_DOF/ROOT

@@ -46,11 +46,11 @@ session "Isabelle_DOF" (AFP) = "Functional-Automata" +
     "figures/definition-use-CSP-pdf.png"
     "figures/definition-use-CSP.png"
     "figures/MyCommentedIsabelle.png"
-    "figures/doc-mod-generic.png"
+    "figures/doc-mod-generic.pdf"
-    "figures/doc-mod-isar.png"
+    "figures/doc-mod-isar.pdf"
-    "figures/doc-mod-onto-docinst.png"
+    "figures/doc-mod-onto-docinst.pdf"
-    "figures/doc-mod-DOF.png"
+    "figures/doc-mod-DOF.pdf"
-    "figures/doc-mod-term-aq.png"
+    "figures/doc-mod-term-aq.pdf"
   export_classpath
 
 

Isabelle_DOF/document/root.bib

@@ -20,7 +20,7 @@
 @Manual{	  wenzel:isabelle-isar:2020,
   title		= {The Isabelle/Isar Reference Manual},
   author	= {Makarius Wenzel},
-  year		= 2020,
+  year		= 2022,
   note		= {Part of the Isabelle distribution.}
 }
 

Isabelle_DOF/latex/styles/DOF-COL.sty

@@ -21,23 +21,23 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % begin: figure*
 \NewEnviron{isamarkupfigure*}[1][]{\isaDof[env={figure},#1]{\BODY}}
-\newisadof{figure.Isa_COL.figure}%
+\newisadof{figureDOTIsaUNDERSCORECOLDOTfigure}%
 [label=,type=%
-,Isa_COL.figure.relative_width=%
+,IsaUNDERSCORECOLDOTfigureDOTrelativeUNDERSCOREwidth=%
-,Isa_COL.figure.placement=%
+,IsaUNDERSCORECOLDOTfigureDOTplacement=%
-,Isa_COL.figure.src=%
+,IsaUNDERSCORECOLDOTfigureDOTsrc=%
-,Isa_COL.figure.spawn_columns=enum False True%
+,IsaUNDERSCORECOLDOTfigureDOTspawnUNDERSCOREcolumns=enum False True%
 ][1]{%
   \begin{figure}[]
     \centering
-    \ifcommandkey{Isa_COL.figure.relative_width}
+    \ifcommandkey{IsaUNDERSCORECOLDOTfigureDOTrelativeUNDERSCOREwidth}
     {%
-      \gdef\dof@width{\commandkey{Isa_COL.figure.relative_width}}
+      \gdef\dof@width{\commandkey{IsaUNDERSCORECOLDOTfigureDOTrelativeUNDERSCOREwidth}}
-      \gdef\dof@src{\commandkey{Isa_COL.figure.src}}
+      \gdef\dof@src{\commandkey{IsaUNDERSCORECOLDOTfigureDOTsrc}}
       \FPdiv\scale{\dof@width}{100}%
       \includegraphics[width=\scale\textwidth]{\dof@src}%
     }{%
-      \gdef\dof@src{\commandkey{Isa_COL.figure.src}}
+      \gdef\dof@src{\commandkey{IsaUNDERSCORECOLDOTfigureDOTsrc}}
       \includegraphics[]{\dof@src}%
     } 
     \caption{#1}\label{\commandkey{label}}%
@@ -50,44 +50,44 @@
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % begin: side_by_side_figure*
-\NewEnviron{isamarkupsideUNDERSCOREbyUNDERSCOREsideUNDERSCOREfigure*}[1][]{\isaDof[env={side_by_side_figure},#1]{\BODY}}
+\NewEnviron{isamarkupsideUNDERSCOREbyUNDERSCOREsideUNDERSCOREfigure*}[1][]{\isaDof[env={sideUNDERSCOREbyUNDERSCOREsideUNDERSCOREfigure},#1]{\BODY}}
-\newisadof{side_by_side_figure.Isa_COL.side_by_side_figure}%
+\newisadof{sideUNDERSCOREbyUNDERSCOREsideUNDERSCOREfigureDOTIsaUNDERSCORECOLDOTsideUNDERSCOREbyUNDERSCOREsideUNDERSCOREfigure}%
 [label=,type=%
-,Isa_COL.figure.relative_width=%
+,IsaUNDERSCORECOLDOTfigureDOTrelativeUNDERSCOREwidth=%
-,Isa_COL.figure.placement=%
+,IsaUNDERSCORECOLDOTfigureDOTplacement=%
-,Isa_COL.figure.src=%
+,IsaUNDERSCORECOLDOTfigureDOTsrc=%
-,Isa_COL.side_by_side_figure.anchor=%
+,IsaUNDERSCORECOLDOTsideUNDERSCOREbyUNDERSCOREsideUNDERSCOREfigureDOTanchor=%
-,Isa_COL.side_by_side_figure.caption=%
+,IsaUNDERSCORECOLDOTsideUNDERSCOREbyUNDERSCOREsideUNDERSCOREfigureDOTcaption=%
-,Isa_COL.side_by_side_figure.relative_width2=%
+,IsaUNDERSCORECOLDOTsideUNDERSCOREbyUNDERSCOREsideUNDERSCOREfigureDOTrelativeUNDERSCOREwidthTWO=%
-,Isa_COL.side_by_side_figure.src2=%
+,IsaUNDERSCORECOLDOTsideUNDERSCOREbyUNDERSCOREsideUNDERSCOREfigureDOTsrcTWO=%
-,Isa_COL.side_by_side_figure.anchor2=%
+,IsaUNDERSCORECOLDOTsideUNDERSCOREbyUNDERSCOREsideUNDERSCOREfigureDOTanchorTWO=%
-,Isa_COL.side_by_side_figure.caption2=%
+,IsaUNDERSCORECOLDOTsideUNDERSCOREbyUNDERSCOREsideUNDERSCOREfigureDOTcaptionTWO=%
-,Isa_COL.side_by_side_figure.placement=%
+,IsaUNDERSCORECOLDOTsideUNDERSCOREbyUNDERSCOREsideUNDERSCOREfigureDOTplacement=%
-,Isa_COL.figure.spawn_columns=enum False True%
+,IsaUNDERSCORECOLDOTfigureDOTspawnUNDERSCOREcolumns=enum False True%
 ][1]{%
   \begin{figure}[]
-    \subfloat[\label{\commandkey{Isa_COL.side_by_side_figure.anchor}}\commandkey{Isa_COL.side_by_side_figure.caption}]%
+    \subfloat[\label{\commandkey{IsaUNDERSCORECOLDOTsideUNDERSCOREbyUNDERSCOREsideUNDERSCOREfigureDOTanchor}}\commandkey{IsaUNDERSCORECOLDOTsideUNDERSCOREbyUNDERSCOREsideUNDERSCOREfigureDOTcaption}]%
-      {\ifcommandkey{Isa_COL.figure.relative_width}%
+      {\ifcommandkey{IsaUNDERSCORECOLDOTfigureDOTrelativeUNDERSCOREwidth}%
        {%
-          \gdef\dof@width{\commandkey{Isa_COL.figure.relative_width}}
+          \gdef\dof@width{\commandkey{IsaUNDERSCORECOLDOTfigureDOTrelativeUNDERSCOREwidth}}
-          \gdef\dof@src{\commandkey{Isa_COL.figure.src}}
+          \gdef\dof@src{\commandkey{IsaUNDERSCORECOLDOTfigureDOTsrc}}
           \FPdiv\scale{\dof@width}{100}%
           \includegraphics[width=\scale\textwidth]{\dof@src}%
         }{%
-          \gdef\dof@src{\commandkey{Isa_COL.figure.src}}
+          \gdef\dof@src{\commandkey{IsaUNDERSCORECOLDOTfigureDOTsrc}}
           \includegraphics[]{\dof@src}%
         }% 
       }%
       \hfill%
-      \subfloat[\label{\commandkey{Isa_COL.side_by_side_figure.anchor2}}\commandkey{Isa_COL.side_by_side_figure.caption2}]%
+      \subfloat[\label{\commandkey{IsaUNDERSCORECOLDOTsideUNDERSCOREbyUNDERSCOREsideUNDERSCOREfigureDOTanchorTWO}}\commandkey{IsaUNDERSCORECOLDOTsideUNDERSCOREbyUNDERSCOREsideUNDERSCOREfigureDOTcaptionTWO}]%
-      {\ifcommandkey{Isa_COL.side_by_side_figure.relative_width2}%
+      {\ifcommandkey{IsaUNDERSCORECOLDOTsideUNDERSCOREbyUNDERSCOREsideUNDERSCOREfigureDOTrelativeUNDERSCOREwidthTWO}%
         {%
-          \gdef\dof@width{\commandkey{Isa_COL.side_by_side_figure.relative_width2}}
+          \gdef\dof@width{\commandkey{IsaUNDERSCORECOLDOTsideUNDERSCOREbyUNDERSCOREsideUNDERSCOREfigureDOTrelativeUNDERSCOREwidthTWO}}
-          \gdef\dof@src{\commandkey{Isa_COL.side_by_side_figure.src2}}
+          \gdef\dof@src{\commandkey{IsaUNDERSCORECOLDOTsideUNDERSCOREbyUNDERSCOREsideUNDERSCOREfigureDOTsrcTWO}}
           \FPdiv\scale{\dof@width}{100}%
           \includegraphics[width=\scale\textwidth]{\dof@src}%
         }{%
-          \gdef\dof@src{\commandkey{Isa_COL.side_by_side_figure.src2}}
+          \gdef\dof@src{\commandkey{IsaUNDERSCORECOLDOTsideUNDERSCOREbyUNDERSCOREsideUNDERSCOREfigureDOTsrcTWO}}
           \includegraphics[]{\dof@src}%
         }% 
       }%

Isabelle_DOF/latex/styles/DOF-core.sty

@@ -53,27 +53,27 @@
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % begin: newcommand wrapper
-\newcommand\newisadof[1]{\expandafter\newkeycommand\csname isaDof.#1\endcsname}%
+\newcommand\newisadof[1]{\expandafter\newkeycommand\csname isaDofDOT#1\endcsname}%
-\newcommand\renewisadof[1]{\expandafter\renewkeycommand\csname isaDof.#1\endcsname}%
+\newcommand\renewisadof[1]{\expandafter\renewkeycommand\csname isaDofDOT#1\endcsname}%
-\newcommand\provideisadof[1]{\expandafter\providekeycommand\csname isaDof.#1\endcsname}%
+\newcommand\provideisadof[1]{\expandafter\providekeycommand\csname isaDofDOT#1\endcsname}%
 % end: newcommand wrapper
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % begin: generic dispatcher
 \newkeycommand+[\|]\isaDof[env={UNKNOWN},label=,type={dummyT},args={}][1]{%
-  \ifcsname isaDof.\commandkey{type}\endcsname%
+  \ifcsname isaDofDOT\commandkey{type}\endcsname%
-      \csname isaDof.\commandkey{type}\endcsname%
+      \csname isaDofDOT\commandkey{type}\endcsname%
               [label=\commandkey{label},\commandkey{args}]{#1}%
   \else%
-  \ifcsname isaDof.\commandkey{env}.\commandkey{type}\endcsname%
+  \ifcsname isaDofDOT\commandkey{env}DOT\commandkey{type}\endcsname%
-      \csname isaDof.\commandkey{env}.\commandkey{type}\endcsname%
+      \csname isaDofDOT\commandkey{env}DOT\commandkey{type}\endcsname%
               [label=\commandkey{label},\commandkey{args}]{#1}%
   \else%
       \message{Isabelle/DOF: Using default LaTeX representation for concept %
         "\commandkey{env}.\commandkey{type}".}%
-      \ifcsname isaDof.\commandkey{env}\endcsname%
+      \ifcsname isaDofDOT\commandkey{env}\endcsname%
-         \csname isaDof.\commandkey{env}\endcsname%
+         \csname isaDofDOT\commandkey{env}\endcsname%
                 [label=\commandkey{label}]{#1}%
       \else%
       \errmessage{Isabelle/DOF: No LaTeX representation for concept %

Isabelle_DOF/ontologies/scholarly_paper/DOF-scholarly_paper.sty

@@ -73,9 +73,9 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % begin: title*
 \NewEnviron{isamarkuptitle*}[1][]{\isaDof[env={title},#1]{\BODY}}
-\newisadof{title.scholarly_paper.title}%
+\newisadof{titleDOTscholarlyUNDERSCOREpaperDOTtitle}%
 [label=,type=%
-,scholarly_paper.title.short_title=%
+,scholarlyUNDERSCOREpaperDOTtitleDOTshortUNDERSCOREtitle=%
 ][1]{%
   \immediate\write\@auxout{\noexpand\title{#1}}%
 }
@@ -85,9 +85,9 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % begin: subtitle*
 \NewEnviron{isamarkupsubtitle*}[1][]{\isaDof[env={subtitle},#1]{\BODY}}
-\newisadof{subtitle.scholarly_paper.subtitle}%
+\newisadof{subtitleDOTscholarlyUNDERSCOREpaperDOTsubtitle}%
 [label=,type=%
-,scholarly_paper.subtitle.abbrev=%
+,scholarlyUNDERSCOREpaperDOTsubtitleDOTabbrev=%
 ][1]{%
   \immediate\write\@auxout{\noexpand\subtitle{#1}}%
 }
@@ -128,21 +128,21 @@
 }
 
 \NewEnviron{isamarkupauthor*}[1][]{\isaDof[env={text},#1]{\BODY}}
-\provideisadof{text.scholarly_paper.author}%
+\provideisadof{textDOTscholarlyUNDERSCOREpaperDOTauthor}%
 [label=,type=%
-,scholarly_paper.author.email=%
+,scholarlyUNDERSCOREpaperDOTauthorDOTemail=%
-,scholarly_paper.author.affiliation=%
+,scholarlyUNDERSCOREpaperDOTauthorDOTaffiliation=%
-,scholarly_paper.author.orcid=%
+,scholarlyUNDERSCOREpaperDOTauthorDOTorcid=%
-,scholarly_paper.author.http_site=%
+,scholarlyUNDERSCOREpaperDOTauthorDOThttpUNDERSCOREsite=%
 ][1]{%
   \stepcounter{dof@cnt@author}
-  \def\dof@a{\commandkey{scholarly_paper.author.affiliation}}
+  \def\dof@a{\commandkey{scholarlyUNDERSCOREpaperDOTauthorDOTaffiliation}}
-  \ifthenelse{\equal{\commandkey{scholarly_paper.author.orcid}}{}}{%
+  \ifthenelse{\equal{\commandkey{scholarlyUNDERSCOREpaperDOTauthorDOTorcid}}{}}{%
     \protected@write\@auxout{}{\string\addauthor{#1\string\inst{\thedof@cnt@author}}}%
   }{%
-    \protected@write\@auxout{}{\string\addauthor{#1\string\inst{\thedof@cnt@author}\string\orcidID{\commandkey{scholarly_paper.author.orcid}}}}%
+    \protected@write\@auxout{}{\string\addauthor{#1\string\inst{\thedof@cnt@author}\string\orcidID{\commandkey{scholarlyUNDERSCOREpaperDOTauthorDOTorcid}}}}%
   }
-  \protected@write\@auxout{}{\string\addaffiliation{\dof@a\\\string\email{\commandkey{scholarly_paper.author.email}}}}%
+  \protected@write\@auxout{}{\string\addaffiliation{\dof@a\\\string\email{\commandkey{scholarlyUNDERSCOREpaperDOTauthorDOTemail}}}}%
 }
 % end: scholarly_paper.author
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -151,15 +151,15 @@
 % begin: scholarly_paper.abstract
 \providecommand{\keywords}[1]{\mbox{}\\[2ex]\mbox{}\noindent{\textbf{Keywords:}} #1}
 \NewEnviron{isamarkupabstract*}[1][]{\isaDof[env={text},#1]{\BODY}}
-\newisadof{text.scholarly_paper.abstract}%
+\newisadof{textDOTscholarlyUNDERSCOREpaperDOTabstract}%
 [label=,type=%
-,scholarly_paper.abstract.keywordlist=%
+,scholarlyUNDERSCOREpaperDOTabstractDOTkeywordlist=%
 ][1]{%
   \begin{isamarkuptext}%
     \begin{abstract}%
       #1%
-      \ifthenelse{\equal{\commandkey{scholarly_paper.abstract.keywordlist}}{}}{}{%     
+      \ifthenelse{\equal{\commandkey{scholarlyUNDERSCOREpaperDOTabstractDOTkeywordlist}}{}}{}{%     
-        \keywords{\commandkey{scholarly_paper.abstract.keywordlist}}%
+        \keywords{\commandkey{scholarlyUNDERSCOREpaperDOTabstractDOTkeywordlist}}%
       }%
     \end{abstract}%
   \end{isamarkuptext}%
@@ -172,84 +172,84 @@
 %\newtheorem{theorem}{Theorem} 
 \newtheorem{defn}{Definition} 
 \newcommand{\defnautorefname}{Definition} 
-\NewEnviron{isamarkupDefinition*}[1][]{\isaDof[env={text},#1,type={scholarly_paper.math_content}]{\BODY}}
+\NewEnviron{isamarkupDefinition*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
 \newtheorem{axm}{Axiom}
 \newcommand{\axmautorefname}{Axiom}
-\NewEnviron{isamarkupAxiom*}[1][]{\isaDof[env={text},#1,type={scholarly_paper.math_content}]{\BODY}}
+\NewEnviron{isamarkupAxiom*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
 \newtheorem{theom}{Theorem}
 \newcommand{\theomautorefname}{Theorem}
-\NewEnviron{isamarkupTheorem*}[1][]{\isaDof[env={text},#1,type={scholarly_paper.math_content}]{\BODY}}
+\NewEnviron{isamarkupTheorem*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
 \newtheorem{lemm}{Lemma}
 \newcommand{\lemmautorefname}{Lemma}
-\NewEnviron{isamarkupLemma*}[1][]{\isaDof[env={text},#1,type={scholarly_paper.math_content}]{\BODY}}
+\NewEnviron{isamarkupLemma*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
 \newtheorem{corr}{Corollary}
 \newcommand{\corrautorefname}{Corollary}
-\NewEnviron{isamarkupCorollary*}[1][]{\isaDof[env={text},#1,type={scholarly_paper.math_content}]{\BODY}}
+\NewEnviron{isamarkupCorollary*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
 \newtheorem{prpo}{Proposition}
 \newcommand{\prpoautorefname}{Proposition}
-\NewEnviron{isamarkupProposition*}[1][]{\isaDof[env={text},#1,type={scholarly_paper.math_content}]{\BODY}}
+\NewEnviron{isamarkupProposition*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
 \newtheorem{rulE}{Rule}
 \newcommand{\rulEautorefname}{Rule}
-\NewEnviron{isamarkupRule*}[1][]{\isaDof[env={text},#1,type={scholarly_paper.math_content}]{\BODY}}
+\NewEnviron{isamarkupRule*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
 \newtheorem{assn}{Assertion}    
 \newcommand{\assnautorefname}{Assertion}    
-\NewEnviron{isamarkupAssertion*}[1][]{\isaDof[env={text},#1,type={scholarly_paper.math_content}]{\BODY}}
+\NewEnviron{isamarkupAssertion*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
 \newtheorem{hypt}{Hypothesis}
 \newcommand{\hyptautorefname}{Hypothesis}
-\NewEnviron{isamarkupHypothesis*}[1][]{\isaDof[env={text},#1,type={scholarly_paper.math_content}]{\BODY}}
+\NewEnviron{isamarkupHypothesis*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
 \newtheorem{assm}{Assumption}
 \newcommand{\assmautorefname}{Assumption}
-\NewEnviron{isamarkupAssumption*}[1][]{\isaDof[env={text},#1,type={scholarly_paper.math_content}]{\BODY}}
+\NewEnviron{isamarkupAssumption*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
 \newtheorem{prms}{Premise}
 \newcommand{\prmsautorefname}{Premise}
-\NewEnviron{isamarkupPremise*}[1][]{\isaDof[env={text},#1,type={scholarly_paper.math_content}]{\BODY}}
+\NewEnviron{isamarkupPremise*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
 \newtheorem{cons}{Consequence}
 \newcommand{\consautorefname}{Consequence}
-\NewEnviron{isamarkupConsequence*}[1][]{\isaDof[env={text},#1,type={scholarly_paper.math_content}]{\BODY}}
+\NewEnviron{isamarkupConsequence*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
-\newtheorem{conc_stmt}{Conclusion}
+\newtheorem{concUNDERSCOREstmt}{Conclusion}
-\newcommand{\concstmtautorefname}{Conclusion}
+\newcommand{\concUNDERSCOREstmtautorefname}{Conclusion}
-\NewEnviron{isamarkupConclusion*}[1][]{\isaDof[env={text},#1,type={scholarly_paper.math_content}]{\BODY}}
+\NewEnviron{isamarkupConclusion*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
-\newtheorem{prf_stmt}{Proof}
+\newtheorem{prfUNDERSCOREstmt}{Proof}
-\newcommand{\prfstmtautorefname}{Proof}
+\newcommand{\prfUNDERSCOREstmtautorefname}{Proof}
-\NewEnviron{isamarkupProof*}[1][]{\isaDof[env={text},#1,type={scholarly_paper.math_content}]{\BODY}}
+\NewEnviron{isamarkupProof*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
-\newtheorem{expl_stmt}{Example}
+\newtheorem{explUNDERSCOREstmt}{Example}
-\newcommand{\explstmtautorefname}{Example}
+\newcommand{\explUNDERSCOREstmtautorefname}{Example}
-\NewEnviron{isamarkupExample*}[1][]{\isaDof[env={text},#1,type={scholarly_paper.math_content}]{\BODY}}
+\NewEnviron{isamarkupExample*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
 \newtheorem{rmrk}{Remark}
 \newcommand{\rmrkautorefname}{Remark}
-\NewEnviron{isamarkupRemark*}[1][]{\isaDof[env={text},#1,type={scholarly_paper.math_content}]{\BODY}}
+\NewEnviron{isamarkupRemark*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
 \newtheorem{notn}{Notation}
 \newcommand{\notnautorefname}{Notation}
-\NewEnviron{isamarkupNotation*}[1][]{\isaDof[env={text},#1,type={scholarly_paper.math_content}]{\BODY}}
+\NewEnviron{isamarkupNotation*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
 \newtheorem{tmgy}{Terminology}
 \newcommand{\tmgyautorefname}{Terminology}
-\NewEnviron{isamarkupTerminology*}[1][]{\isaDof[env={text},#1,type={scholarly_paper.math_content}]{\BODY}}
+\NewEnviron{isamarkupTerminology*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
 
-\newisadof{text.scholarly_paper.math_content}%
+\newisadof{textDOTscholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}%
 [label=,type=%
- , scholarly_paper.math_content.short_name ={}%
+ , scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontentDOTshortUNDERSCOREname ={}%
- , scholarly_paper.math_content.mcc     = % 
+ , scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontentDOTmcc     = % 
- , Isa_COL.text_element.level         =%
+ , IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTlevel         =%
- , Isa_COL.text_element.referentiable =%
+ , IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTreferentiable =%
- , Isa_COL.text_element.variants      =%
+ , IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTvariants      =%
- , scholarly_paper.text_section.main_author  =%
+ , scholarlyUNDERSCOREpaperDOTtextUNDERSCOREsectionDOTmainUNDERSCOREauthor  =%
- , scholarly_paper.text_section.fixme_list   =%
+ , scholarlyUNDERSCOREpaperDOTtextUNDERSCOREsectionDOTfixmeUNDERSCORElist   =%
- , Isa_COL.text_element.level                =%
+ , IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTlevel                =%
- , scholarly_paper.technical.definition_list =%
+ , scholarlyUNDERSCOREpaperDOTtechnicalDOTdefinitionUNDERSCORElist =%
- , scholarly_paper.technical.status          =%
+ , scholarlyUNDERSCOREpaperDOTtechnicalDOTstatus          =%
  ]
  [1]
  {%
     \begin{isamarkuptext}%
-      \ifthenelse{\equal{\commandkey{scholarly_paper.math_content.short_name}} {} }  
+      \ifthenelse{\equal{\commandkey{scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontentDOTshortUNDERSCOREname}} {} }  
         {%
-         \begin{\commandkey{scholarly_paper.math_content.mcc}}\label{\commandkey{label}}
+         \begin{\commandkey{scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontentDOTmcc}}\label{\commandkey{label}}
            #1
-         \end{\commandkey{scholarly_paper.math_content.mcc}}
+         \end{\commandkey{scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontentDOTmcc}}
         }{%
-         \begin{\commandkey{scholarly_paper.math_content.mcc}}[\commandkey{scholarly_paper.math_content.short_name}]\label{\commandkey{label}} 
+         \begin{\commandkey{scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontentDOTmcc}}[\commandkey{scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontentDOTshortUNDERSCOREname}]\label{\commandkey{label}} 
            #1 
-         \end{\commandkey{scholarly_paper.math_content.mcc}}
+         \end{\commandkey{scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontentDOTmcc}}
         }
     \end{isamarkuptext}%
  } 

Isabelle_DOF/ontologies/scholarly_paper/scholarly_paper.thy

@@ -53,12 +53,12 @@ ML\<open>
 val _ =
   Monitor_Command_Parser.document_command \<^command_keyword>\<open>abstract*\<close> "Textual Definition"
     {markdown = true, body = true}
-    (Onto_Macros.enriched_document_cmd_exp (SOME "abstract") []) (K(K I));
+    (Onto_Macros.enriched_document_cmd_exp (SOME "abstract") []) [] I;
 
 val _ =
   Monitor_Command_Parser.document_command \<^command_keyword>\<open>author*\<close> "Textual Definition"
     {markdown = true, body = true}
-    (Onto_Macros.enriched_document_cmd_exp (SOME "author") []) (K(K I));
+    (Onto_Macros.enriched_document_cmd_exp (SOME "author") []) [] I;
 \<close>
 
 text\<open>Scholarly Paper is oriented towards the classical domains in science:
@@ -203,7 +203,6 @@ datatype math_content_class =
   | "notn"       \<comment>\<open>notation\<close>  
   | "tmgy"       \<comment>\<open>terminology\<close>
 
-
 text\<open>Instances of the \<open>doc_class\<close> \<^verbatim>\<open>math_content\<close> are by definition @{term "semiformal"}; they may
 be non-referential, but in this case they will not have a @{term "short_name"}.\<close>
 
@@ -444,49 +443,50 @@ fun doc_cmd kwd txt flag key =
       in
         Onto_Macros.enriched_formal_statement_command  default [("mcc",key)] meta_args thy
       end)
-      (Onto_Macros.transform_attr [("mcc",key)])
+      [\<^const_name>\<open>mcc\<close>]
+      (Onto_Macros.transform_attr [(\<^const_name>\<open>mcc\<close>,key)])
 
 in
 
 val _ = doc_cmd \<^command_keyword>\<open>Definition*\<close> "Freeform Definition" 
-                Definition_default_class "defn";
+                Definition_default_class \<^const_name>\<open>defn\<close>;
 
 val _ = doc_cmd \<^command_keyword>\<open>Lemma*\<close>      "Freeform Lemma Description" 
-                 Lemma_default_class "lemm";
+                 Lemma_default_class \<^const_name>\<open>lemm\<close>;
 
 val _ = doc_cmd \<^command_keyword>\<open>Theorem*\<close>    "Freeform Theorem" 
-                 Theorem_default_class "theom";
+                 Theorem_default_class \<^const_name>\<open>theom\<close>;
 
 (* cut and paste to make it runnable, but nonsensical so far: *)
 val _ = doc_cmd \<^command_keyword>\<open>Proposition*\<close> "Freeform Proposition"
-                  Proposition_default_class "prpo";
+                  Proposition_default_class \<^const_name>\<open>prpo\<close>;
 
 val _ = doc_cmd \<^command_keyword>\<open>Premise*\<close> "Freeform Premise"
-                  Premise_default_class "prms";
+                  Premise_default_class \<^const_name>\<open>prms\<close>;
 
 val _ = doc_cmd \<^command_keyword>\<open>Corollary*\<close> "Freeform Corollary"
-                  Corollary_default_class "corr";
+                  Corollary_default_class \<^const_name>\<open>corr\<close>;
 
 val _ = doc_cmd \<^command_keyword>\<open>Consequence*\<close> "Freeform Consequence"
-                  Consequence_default_class "cons";
+                  Consequence_default_class \<^const_name>\<open>cons\<close>;
                       
 val _ = doc_cmd \<^command_keyword>\<open>Conclusion*\<close> "Freeform Conclusion"
-                  Conclusion_default_class "conc_stmt";
+                  Conclusion_default_class \<^const_name>\<open>conc_stmt\<close>;
                            
 val _ = doc_cmd \<^command_keyword>\<open>Assumption*\<close> "Freeform Assumption"
-                  Assumption_default_class "assm";
+                  Assumption_default_class \<^const_name>\<open>assm\<close>;
 
 val _ = doc_cmd \<^command_keyword>\<open>Hypothesis*\<close> "Freeform Hypothesis"
-                  Hypothesis_default_class "prpo";
+                  Hypothesis_default_class \<^const_name>\<open>prpo\<close>;
 
 val _ = doc_cmd \<^command_keyword>\<open>Assertion*\<close> "Freeform Assertion"
-                  Assertion_default_class "assn";
+                  Assertion_default_class \<^const_name>\<open>assn\<close>;
 
 val _ = doc_cmd \<^command_keyword>\<open>Proof*\<close> "Freeform Proof"
-                  Proof_default_class "prf_stmt";
+                  Proof_default_class \<^const_name>\<open>prf_stmt\<close>;
 
 val _ = doc_cmd \<^command_keyword>\<open>Example*\<close> "Freeform Example"
-                  Example_default_class "expl_stmt";
+                  Example_default_class \<^const_name>\<open>expl_stmt\<close>;
 end
 end 
 \<close>

Isabelle_DOF/ontologies/technical_report/DOF-technical_report.sty

@@ -34,16 +34,16 @@
 
 \newisadof{text.technical_report.SML}%
 [  label=,type=%
- , Isa_COL.text_element.level=%
+ , IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTlevel=%
- , Isa_COL.text_element.referentiable=%
+ , IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTreferentiable=%
- , Isa_COL.text_element.variants=%
+ , IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTvariants=%
- , scholarly_paper.text_section.main_author=%
+ , scholarlyUNDERSCOREpaperDOTtextUNDERSCOREsectionDOTmainUNDERSCOREauthor=%
- , scholarly_paper.text_section.fixme_list=%
+ , scholarlyUNDERSCOREpaperDOTtextUNDERSCOREsectionDOTfixmeUNDERSCORElist=%
- , scholarly_paper.technical.definition_list=%
+ , scholarlyUNDERSCOREpaperDOTtechnicalDOTdefinitionUNDERSCORElist=%
- , scholarly_paper.technical.status=%
+ , scholarlyUNDERSCOREpaperDOTtechnicalDOTstatus=%
- , scholarly_paper.technical.formal_results=%
+ , scholarlyUNDERSCOREpaperDOTtechnicalDOTformalUNDERSCOREresults=%
- , technical_report.code.checked=%
+ , technicalUNDERSCOREreportDOTcodeDOTchecked=%
- , technical_report.code.caption=%
+ , technicalUNDERSCOREreportDOTcodeDOTcaption=%
 ]
 [1]
 {%

Isabelle_DOF/thys/Isa_COL.thy

@@ -103,17 +103,11 @@ fun transform_cid thy NONE X = X
                              end  
 in
 
-fun transform_attr S cid_long thy doc_attrs =
+fun transform_attr S doc_attrs =
   let
     fun transform_attr' [] doc_attrs = doc_attrs
       | transform_attr' (s::S) (doc_attrs) =
-          let fun markup2string s = s |> YXML.content_of
+          let val (name', value) = s
-                                      |> Symbol.explode 
-                                      |> List.filter (fn c => c <> Symbol.DEL)
-                                      |> String.concat
-              fun toLong n = DOF_core.get_attribute_info cid_long (markup2string n) thy
-                             |> the |> #long_name
-              val (name', value) = s |> (fn (n, v) => (toLong n, v))
               val doc_attrs' = doc_attrs
                                |> map (fn (name, term) => if name = name'
                                                           then (name, value)
@@ -154,7 +148,7 @@ end (* local *)
 
 fun heading_command (name, pos) descr level =
   Monitor_Command_Parser.document_command (name, pos) descr
-    {markdown = false, body = true} (enriched_text_element_cmd level) (K(K I));
+    {markdown = false, body = true} (enriched_text_element_cmd level) [] I;
 
 val _ = heading_command \<^command_keyword>\<open>title*\<close> "section heading" NONE;
 val _ = heading_command \<^command_keyword>\<open>subtitle*\<close> "section heading" NONE;

Isabelle_DOF/thys/Isa_DOF.thy

@@ -841,6 +841,10 @@ val check_opening_ml_invs = check_invs get_opening_ml_invariants
 
 val check_closing_ml_invs = check_invs get_closing_ml_invariants
 
+(* Output name for LaTeX macros.
+   Also rewrite "." to allow macros with objects long names *)
+val output_name = Latex.output_name o translate_string (fn "." => "DOT" | s => s)
+
 val ISA_prefix = "Isabelle_DOF_"
 
 val doc_class_prefix = ISA_prefix ^ "doc_class_"
@@ -2134,19 +2138,21 @@ fun close_monitor_command (args as (((oid, pos), cid_pos),
     end 
 
 
-fun meta_args_2_latex thy transform_attr
+fun meta_args_2_latex thy sem_attrs transform_attr
       ((((lab, pos), cid_opt), attr_list) : ODL_Meta_Args_Parser.meta_args_t) =
     (* for the moment naive, i.e. without textual normalization of 
        attribute names and adapted term printing *)
-    let val l   = DOF_core.get_instance_name_global lab thy |> enclose "{" "}"
+    let val l   = DOF_core.get_instance_name_global lab thy |> DOF_core.output_name
+                                                            |> enclose "{" "}"
                                                             |> prefix "label = "
       (*  val _   = writeln("meta_args_2_string lab:"^ lab ^":"^ (@{make_string } cid_opt) ) *)
         val cid_long = case cid_opt of
                                 NONE => DOF_core.cid_of lab thy
                               | SOME(cid,_) => DOF_core.get_onto_class_name_global' cid thy        
         (* val _   = writeln("meta_args_2_string cid_long:"^ cid_long ) *)
-        val cid_txt  = "type = " ^ (enclose "{" "}" cid_long);
+        val cid_txt  = cid_long |> DOF_core.output_name
-
+                                |> enclose "{" "}"
+                                |> prefix "type = "
         fun ltx_of_term _ _ (c as \<^Const_>\<open>Cons \<^Type>\<open>char\<close> for _ _\<close>) = HOLogic.dest_string c
           | ltx_of_term _ _ \<^Const_>\<open>Nil _\<close> = ""
           | ltx_of_term _ _ \<^Const_>\<open>numeral _ for t\<close> = Int.toString(HOLogic.dest_numeral t)
@@ -2191,8 +2197,24 @@ fun meta_args_2_latex thy transform_attr
         val default_args_filtered = filter (fn (a,_) => not (exists (fn b => b = a) 
                                     (map (fn (c,_) => c) actual_args))) default_args
         val transformed_args = (actual_args@default_args_filtered)
-                               |> transform_attr cid_long thy
+                               |> transform_attr
-        val str_args = transformed_args
+        fun update_sem_std_attrs [] attrs = attrs
+          | update_sem_std_attrs (attr::attrs) attrs' =
+              let val attrs'' = attrs' |> map (fn (name, value) =>
+                                let val value' = value |> Long_Name.base_name
+                                in 
+                                  if name = attr
+                                  then if value' (*|> Symbol_Pos.is_identifier*)
+                                                  |>  Symbol.is_ascii_identifier
+                                        then (name, DOF_core.output_name value')
+                                        else ISA_core.err ("Bad name of semantic attribute"
+                                                           ^ name ^ ": " ^ value
+                                                           ^ ". Name must be ASCII") pos
+                                else (name, value') end)
+              in update_sem_std_attrs attrs attrs'' end
+        val updated_sem_std_attrs = update_sem_std_attrs sem_attrs transformed_args
+        val updated_sem_std_attrs' = updated_sem_std_attrs |> map (apfst DOF_core.output_name)
+        val str_args = updated_sem_std_attrs'
                        |> map (fn (lhs,rhs) => lhs^" = "^(enclose "{" "}" rhs)) 
                       
         val label_and_type = String.concat [ l, ",", cid_txt]
@@ -2218,15 +2240,15 @@ fun gen_enriched_document_cmd' {inline} cid_transform attr_transform
 (* {markdown = true} sets the parsing process such that in the text-core
    markdown elements are accepted. *)
 
-fun document_output {markdown: bool, markup: Latex.text -> Latex.text} transform_attr meta_args text ctxt =
+fun document_output {markdown: bool, markup: Latex.text -> Latex.text} sem_attrs transform_attr meta_args text ctxt =
   let
     val thy = Proof_Context.theory_of ctxt;
     val _ = Context_Position.reports ctxt (Document_Output.document_reports text);
-    val output_meta = meta_args_2_latex thy transform_attr meta_args;
+    val output_meta = meta_args_2_latex thy sem_attrs transform_attr meta_args;
     val output_text = Document_Output.output_document ctxt {markdown = markdown} text;
   in markup (output_meta @ output_text) end;
 
-fun document_output_reports name {markdown, body} transform_attr meta_args text ctxt =
+fun document_output_reports name {markdown, body} sem_attrs transform_attr meta_args text ctxt =
   let
     (*val pos = Input.pos_of text;
     val _ =
@@ -2236,16 +2258,16 @@ fun document_output_reports name {markdown, body} transform_attr meta_args text
     fun markup xml =
       let val m = if body then Markup.latex_body else Markup.latex_heading
       in [XML.Elem (m (Latex.output_name name), xml)] end;
-  in document_output {markdown = markdown, markup = markup} transform_attr meta_args text ctxt end;
+  in document_output {markdown = markdown, markup = markup} sem_attrs transform_attr meta_args text ctxt end;
 
 
 (* document output commands *)
 
-fun document_command (name, pos) descr mark cmd transform_attr =
+fun document_command (name, pos) descr mark cmd sem_attrs transform_attr =
   Outer_Syntax.command (name, pos) descr
     (ODL_Meta_Args_Parser.attributes -- Parse.document_source >> (fn (meta_args, text) =>
       Toplevel.theory' (fn _ => cmd meta_args)
-          (SOME (Toplevel.presentation_context #> document_output_reports name mark transform_attr meta_args text)))); 
+          (SOME (Toplevel.presentation_context #> document_output_reports name mark sem_attrs transform_attr meta_args text)))); 
 
 
 (* Core Command Definitions *)
@@ -2271,14 +2293,14 @@ val _ =
 
 val _ =
   document_command \<^command_keyword>\<open>text*\<close> "formal comment (primary style)"
-    {markdown = true, body = true} (gen_enriched_document_cmd {inline=true} I I) (K(K I));
+    {markdown = true, body = true} (gen_enriched_document_cmd {inline=true} I I) [] I;
 
 
 (* This is just a stub at present *)
 val _ =
   document_command \<^command_keyword>\<open>text-macro*\<close> "formal comment macro"
     {markdown = true, body = true}
-    (gen_enriched_document_cmd {inline=false} (* declare as macro *) I I) (K(K I));
+    (gen_enriched_document_cmd {inline=false} (* declare as macro *) I I) [] I;
 
  
 val (declare_reference_default_class, declare_reference_default_class_setup) 
@@ -2553,6 +2575,9 @@ ML\<open>
 
 local
 
+fun elaborate stmt ctxt = stmt |> map (apsnd (map (apfst (DOF_core.elaborate_term ctxt)
+                                              #> apsnd (map (DOF_core.elaborate_term ctxt)))))
+
 fun prep_statement prep_att prep_stmt raw_elems raw_stmt ctxt =
   let
     val (stmt, elems_ctxt) = prep_stmt raw_elems raw_stmt ctxt;
@@ -2562,11 +2587,7 @@ fun prep_statement prep_att prep_stmt raw_elems raw_stmt ctxt =
     (case raw_stmt of
       Element.Shows _ =>
         let val stmt' = Attrib.map_specs (map prep_att) stmt
-            val stmt'' = stmt' |> map (fn (b, ts) =>
+            val stmt'' = elaborate stmt' ctxt
-                                (b, ts |> map (fn (t', t's) =>
-                                          (DOF_core.elaborate_term ctxt t',
-                                          t's |> map (fn t'' => 
-                                                 DOF_core.elaborate_term ctxt t'')))))
         in (([], prems, stmt'', NONE), stmt_ctxt) end
     | Element.Obtains raw_obtains =>
         let
@@ -2581,11 +2602,7 @@ fun prep_statement prep_att prep_stmt raw_elems raw_stmt ctxt =
             ||> Proof_Context.restore_stmt asms_ctxt;
 
           val stmt' = [(Binding.empty_atts, [(#2 (#1 (Obtain.obtain_thesis ctxt)), [])])];
-          val stmt'' = stmt' |> map (fn (b, ts) =>
+          val stmt'' = elaborate stmt' ctxt
-                                (b, ts |> map (fn (t', t's) =>
-                                          (DOF_core.elaborate_term ctxt t',
-                                          t's |> map (fn t'' => 
-                                                 DOF_core.elaborate_term ctxt t'')))))
         in ((Obtain.obtains_attribs raw_obtains, prems, stmt'', SOME that'), that_ctxt) end)
   end;
 
@@ -2826,7 +2843,7 @@ fun pretty_docitem_antiquotation_generic cid_decl ctxt ({unchecked, define}, src
            |(true,true)  => XML.enclose("{\\isaDofmacroDef[type={"^cid_decl^"}]{")"}}" 
            |(false,true) => XML.enclose("{\\isaDofmacroExp[type={"^cid_decl^"}]{")"}}"
         )
-        (Latex.text (str, pos))
+        (Latex.text (DOF_core.output_name str, pos))
     end      
 
 

Isabelle_DOF/thys/manual/M_00_Frontmatter.thy

@@ -36,8 +36,11 @@ define_shortcut* TeXLive \<rightleftharpoons> \<open>\TeXLive\<close>
 text\<open>Note that these setups assume that the associated \<^LaTeX> macros 
      are defined, \<^eg>, in the document prelude. \<close>
 
-define_macro* index  \<rightleftharpoons> \<open>\index{\<close> _ \<open>}\<close>
+define_macro* index     \<rightleftharpoons> \<open>\index{\<close> _ \<open>}\<close>
-define_macro* bindex \<rightleftharpoons> \<open>\bindex{\<close> _ \<open>}\<close>
+define_macro* bindex    \<rightleftharpoons> \<open>\bindex{\<close> _ \<open>}\<close>
+define_macro* nolinkurl \<rightleftharpoons> \<open>\nolinkurl{\<close> _ \<open>}\<close>
+define_macro* center    \<rightleftharpoons> \<open>\center{\<close> _ \<open>}\<close>
+define_macro* ltxinline \<rightleftharpoons> \<open>\inlineltx|\<close> _ \<open>|\<close>
 
 
 ML\<open>

Isabelle_DOF/thys/manual/M_02_Background.thy

@@ -106,9 +106,9 @@ text\<open>
 
 side_by_side_figure*[docModGenConcr::side_by_side_figure,anchor="''docModGen''",
                       caption="''Schematic Representation.''",relative_width="45",
-                      src="''figures/doc-mod-generic.png''",anchor2="''docModIsar''",
+                      src="''figures/doc-mod-generic.pdf''",anchor2="''docModIsar''",
                       caption2="''The Isar Instance.''",relative_width2="45",
-                      src2="''figures/doc-mod-isar.png''"]\<open>A Representation of a Document Model.\<close>
+                      src2="''figures/doc-mod-isar.pdf''"]\<open>A Representation of a Document Model.\<close>
 
 text\<open>The body of a theory file consists of a sequence of \<^emph>\<open>commands\<close> that must be introduced
 by a command keyword such as \<^boxed_theory_text>\<open>requirement\<close> above. Command keywords may mark 
@@ -184,13 +184,13 @@ text\<open>Antiquotations seen as semantic macros are partial functions of type
 
 side_by_side_figure*[docModOnto::side_by_side_figure,anchor="''docModGen''",
                       caption="''A Document with Ontological Annotations.''",relative_width="47",
-                      src="''figures/doc-mod-DOF.png''",anchor2="''docModDOF''",
+                      src="''figures/doc-mod-DOF.pdf''",anchor2="''docModDOF''",
                       caption2="''Ontological References.''",relative_width2="47",
-                      src2="''figures/doc-mod-onto-docinst.png''"]\<open>Documents conform to Ontologies.\<close>
+                      src2="''figures/doc-mod-onto-docinst.pdf''"]\<open>Documents conform to Ontologies.\<close>
 
 text\<open>Since Isabelle's commands are freely programmable, it is possible to implement  \<^dof> as an 
 extension of the system. In particular, the ontology language of \<^dof> provides an  ontology 
-definition language ODL that \<^emph>\<open>generates\<close> anti-quotations and the infrastructure to check and evaluate 
+definition language ODL\<^bindex>\<open>ODL\<close> that \<^emph>\<open>generates\<close> anti-quotations and the infrastructure to check and evaluate 
 them. This allows for checking an annotated document with respect to a given ontology, which may be 
 specific for  a given domain-specific universe of discourse (see @{figure "docModOnto"}). ODL will 
 be described in  @{text_section (unchecked) "isadof_tour"} in more detail.\<close>

Isabelle_DOF/thys/manual/M_03_GuidedTour.thy

@@ -23,7 +23,7 @@ chapter*[isadof_tour::text_section]\<open>\<^isadof>: A Guided Tour\<close>
 
 text\<open>
   In this chapter, we will give an introduction into using \<^isadof> for users that want to create and 
-  maintain documents following an existing document ontology.
+  maintain documents following an existing document ontology\<^bindex>\<open>ontology\<close> in ODL\<^bindex>\<open>ODL\<close>.
 \<close>
 
 section*[getting_started::technical]\<open>Getting Started\<close>
@@ -34,7 +34,7 @@ text\<open>
   \<^LaTeX>. We assume a basic familiarity with a Linux/Unix-like command line (i.e., a shell). 
   Furthermore, we focus on the installation of the latest official release of  \<^isadof> as 
   available in the Archive of Formal Proofs (AFP).\<^footnote>\<open>If you want to work with the development version 
-  of Isabelle/DOF, please obtain its source code from the Isabelle/DOF Git repostitory 
+  of \<^isadof>, please obtain its source code from the \<^isadof> Git repostitory 
   (\<^url>\<open>https://git.logicalhacking.com/Isabelle_DOF/Isabelle_DOF\<close> and follow the instructions
   in provided \<^verbatim>\<open>README.MD\<close> file.\<close>
 
@@ -72,11 +72,12 @@ text\<open>
 By installing the AFP in the previous steps, you already installed \<^isadof>. In fact, \<^isadof> 
 is currently consisting out of two AFP entries:
 
-\<^item> Isabelle\_DOF: This entry
+\<^item> \<^verbatim>\<open>Isabelle_DOF\<close>: This entry
-  contains the Isabelle/DOF system itself, including the Isabelle/DOF manual.
+  contains the \<^isadof> system itself, including the \<^isadof> manual.
-\<^item> Isabelle\_DOF-Example-I: This entry contains an example of 
+\<^item> \<^verbatim>\<open>Isabelle_DOF-Example-I\<close>: This entry contains an example of 
-  an academic paper written using the Isabelle/DOF system oriented towards 
+  an academic paper written using the \<^isadof> system oriented towards an 
-\<^item> Isabelle\_DOF-Example-II: This entry contains another example of 
+  introductory paper.
+\<^item> \<^verbatim>\<open>Isabelle_DOF-Example-II\<close>: This entry contains another example of 
   a mathematics-oriented academic paper.
 
 It is recommended to follow structure one of these papers.\<close>
@@ -143,10 +144,10 @@ want to use. Otherwise, they will not be available.
 
 paragraph\<open>Warning.\<close>
 text\<open>
-Note that the session @{session "Isabelle_DOF"} needs to be part of the ``main'' session 
+Note that the session \<^session>\<open>Isabelle_DOF\<close> needs to be part of the ``main'' session 
-hierarchy. Loading the Isabelle/DOF theories as part of a session section, e.g., 
+hierarchy. Loading the \<^isadof> theories as part of a session section, e.g., 
 \<close>
-text\<open>
+text\<open>\<^latex>\<open>
 \begin{config}{ROOT}
 session example = HOL +
   options [document = pdf, document_output = "output", document_build = dof]
@@ -156,7 +157,7 @@ session example = HOL +
   theories
     C
 \end{config}
-\<close>
+\<close>\<close>
 text\<open>
 will not work. Trying to build a document using such a setup will result in the 
 following error message:
@@ -214,35 +215,31 @@ text\<open>At times, this causes idiosyncrasies like the ones cited in the follo
 \<close>
 
 section*[scholar_onto::example]\<open>Writing Academic Publications in \<^boxed_theory_text>\<open>scholarly_paper\<close>\<close>  
-subsection\<open>Writing Academic Papers\<close>
+subsection\<open>A Selection of major Examples\<close>
 text\<open> 
-  The ontology \<^verbatim>\<open>scholarly_paper\<close>
+  The ontology \<^verbatim>\<open>scholarly_paper\<close>  \<^index>\<open>ontology!scholarly\_paper\<close> is an ontology modeling 
-  \<^index>\<open>ontology!scholarly\_paper\<close> is an ontology modeling 
+  academic/scientific papers, with a slight bias towards texts in the domain of mathematics and
-  academic/scientific papers, with a slight bias towards texts in the domain of mathematics and engineering. 
+  engineering. We explain first the principles of its underlying ontology, and then we present two 
-  We explain first the principles of its underlying ontology, and then we present two ``real'' 
+  ``real'' examples from our own publication practice.
-  examples from our own publication practice.
+     \<^enum> The iFM 2020 paper~@{cite "taha.ea:philosophers:2020"} is a typical mathematical text,
-\<close>
+       heavy in definitions with complex  mathematical notation and a lot of non-trivial cross-referencing
-text\<open>
+       between statements, definitions and proofs which are ontologically tracked. However, wrt.
-  \<^enum> The iFM 2020 paper~@{cite "taha.ea:philosophers:2020"} is a typical mathematical text,
+       the possible linking between the underlying formal theory and this mathematical presentation,        it follows a pragmatic path without any ``deep'' linking to types, terms and theorems, 
-    heavy in definitions with complex  mathematical notation and a lot of non-trivial cross-referencing
+       deliberately not exploiting \<^isadof> 's full potential with this regard.
-    between statements, definitions and proofs which are ontologically tracked. However, wrt.
+     \<^enum> In the CICM 2018 paper~@{cite "brucker.ea:isabelle-ontologies:2018"}, we deliberately
-    the possible linking between the underlying formal theory and this mathematical presentation,
+       refrain from integrating references to formal content in order to demonstrate that \<^isadof> is not 
-    it follows a pragmatic path without any ``deep'' linking to types, terms and theorems, 
+       a framework from Isabelle users to Isabelle users only, but people just avoiding as much as
-    deliberately not exploiting \<^isadof> 's full potential with this regard.
+       possible \<^LaTeX> notation.
-  \<^enum> In the CICM 2018 paper~@{cite "brucker.ea:isabelle-ontologies:2018"}, we deliberately
-    refrain from integrating references to formal content in order to demonstrate that \<^isadof> is not 
-    a  framework from Isabelle users to Isabelle users only, but people just avoiding as much as
-    possible \<^LaTeX> notation.
 
   The \<^isadof> distribution contains both examples using the ontology \<^verbatim>\<open>scholarly_paper\<close> in 
-  the directory \nolinkurl{examples/scholarly_paper/2018-cicm-isabelle_dof-applications/} or
+  the directory \<^nolinkurl>\<open>examples/scholarly_paper/2018-cicm-isabelle_dof-applications/\<close> or
-  \nolinkurl{examples/scholarly_paper/2020-iFM-CSP}.
+   \<^nolinkurl>\<open>examples/scholarly_paper/2020-iFM-CSP\<close>.
 
   You can inspect/edit the example in Isabelle's IDE, by either 
-  \<^item> starting Isabelle/jEdit using your graphical user interface (\<^eg>, by clicking on the 
+     \<^item> starting Isabelle/jEdit using your graphical user interface (\<^eg>, by clicking on the 
-    Isabelle-Icon provided by the Isabelle installation) and loading the file 
+       Isabelle-Icon provided by the Isabelle installation) and loading the file 
-    \nolinkurl{examples/scholarly_paper/2018-cicm-isabelle_dof-applications/IsaDofApplications.thy},
+       \<^nolinkurl>\<open>examples/scholarly_paper/2018-cicm-isabelle_dof-applications/IsaDofApplications.thy"\<close>
-  \<^item> starting Isabelle/jEdit from the command line by, \<^eg>, calling:
+     \<^item> starting Isabelle/jEdit from the command line by, \<^eg>, calling:
 
 @{boxed_bash [display]\<open>ë\prompt{\isadofdirn}ë 
   isabelle jedit -d . examples/scholarly_paper/2020-iFM-CSP/paper.thy \<close>}
@@ -312,7 +309,7 @@ as follows:
 Additional means assure that the following invariant is maintained in a document 
 conforming to \<^verbatim>\<open>scholarly_paper\<close>:
 
-\center {\<open>level > 0\<close>}
+\<^center>\<open>\<open>level > 0\<close>\<close>
 \<close>
 
 text\<open>\<^vs>\<open>1.0cm\<close>\<close>
@@ -464,10 +461,6 @@ in which the text-elements instances are expected to appear in the textual order
 defined by \<^typ>\<open>article\<close>.
 \<close>
 
-
-figure*[doc_termAq::figure,relative_width="80",src="''figures/doc-mod-term-aq.png''"]
-                      \<open>Term-Antiquotations Referencing to Annotated Elements\<close>
-
 side_by_side_figure*[exploring::side_by_side_figure,anchor="''fig-Dogfood-II-bgnd1''",
                       caption="''Exploring a reference of a text-element.''",relative_width="48",
                       src="''figures/Dogfood-II-bgnd1''",anchor2="''fig-bgnd-text_section''",
@@ -485,12 +478,21 @@ side_by_side_figure*["hyperlinks"::side_by_side_figure,anchor="''fig:Dogfood-IV-
 
 text\<open> 
   From these class definitions, \<^isadof> also automatically generated editing 
-  support for Isabelle/jEdit. In \autoref{fig-Dogfood-II-bgnd1} and 
+  support for Isabelle/jEdit. In 
-  \autoref{fig-bgnd-text_section} we show how hovering over links permits to explore its 
+  @{figure "exploring"}(left)
+  % \autoref{fig-Dogfood-II-bgnd1} 
+  and
+  @{figure "exploring"}(right)
+  % \autoref{fig-bgnd-text_section} 
+  we show how hovering over links permits to explore its 
   meta-information. Clicking on a document class identifier permits to hyperlink into the 
-  corresponding class definition (\autoref{fig:Dogfood-IV-jumpInDocCLass}); hovering over an 
+  corresponding class definition (
-  attribute-definition (which is qualified in order to disambiguate; 
+  @{figure "hyperlinks"}(left)
-  \autoref{fig:Dogfood-V-attribute}) shows its type.
+  %\autoref{fig:Dogfood-IV-jumpInDocCLass})
+  ; hovering over an attribute-definition (which is qualified in order to disambiguate; cf.
+  @{figure "hyperlinks"}(right)
+  %\autoref{fig:Dogfood-V-attribute}
+  ) shows its type.
 \<close>
 
 figure*[figDogfoodVIlinkappl::figure,relative_width="80",src="''figures/Dogfood-VI-linkappl.png''"]
@@ -499,17 +501,68 @@ figure*[figDogfoodVIlinkappl::figure,relative_width="80",src="''figures/Dogfood-
 text\<open> 
 An ontological reference application in @{figure "figDogfoodVIlinkappl"}: the 
 ontology-dependant antiquotation \<^boxed_theory_text>\<open>@{example \<open>ex1\<close>}\<close> refers to the corresponding 
-text-element \<^boxed_theory_text>\<open>ex1\<close>.
+text-element \<^boxed_theory_text>\<open>ex1\<close>. Hovering allows for inspection, clicking for jumping to the 
-Hovering allows for inspection, clicking for jumping to the definition.
+definition. If the  link does not exist or  has a non-compatible type, the text is not validated,
-If the  link does not exist or  has a non-compatible type, the text is not validated, \<^ie>,
+ \<^ie>, Isabelle/jEdit will respond with an error.\<close>
-Isabelle/jEdit will respond with an error.\<close>
 
 text\<open>We advise users to experiment with different notation variants.
 Note, further, that the Isabelle \<^latex>\<open>@\{cite ...\}\<close>-text-anti-quotation makes its checking
 on the level of generated \<^verbatim>\<open>.aux\<close>-files, which are not necessarily up-to-date. Ignoring the PIDE
-error-message and compiling a with a consistent bibtex usually makes disappear this behavior. 
+error-message and compiling it with a consistent bibtex usually makes disappear this behavior. 
 \<close>
 
+subsection*["using-term-aq"::technical, main_author = "Some @{author ''bu''}"]
+   \<open>Using Term-Antiquotations\<close>
+
+text\<open>The present version of \<^isadof> is the first version that supports the novel feature of
+\<^dof>-generated term-antiquotations\<^bindex>\<open>term-antiquotations\<close>, \<^ie>, antiquotations embedded
+in HOL-\<open>\<lambda>\<close>-terms possessing arguments that were validated in the ontological context.
+These \<open>\<lambda>\<close>-terms may occur in definitions, lemmas, or in values to define attributes 
+in class instances. They have the format:\<close>
+
+text\<open>\<^center>\<open>\<open>@{name arg\<^sub>1 ... arg\<^sub>n\<^sub>-\<^sub>1} arg\<^sub>n\<close>\<close>\<close>
+
+text\<open>Logically, they are defined as an identity in the last argument \<open>arg\<^sub>n\<close>; thus,
+ontologically checked prior arguments \<open>arg\<^sub>1 ... arg\<^sub>n\<^sub>-\<^sub>1\<close> can be ignored during a proof
+process; ontologically, they can be used to assure the traceability of, \<^eg>, semi-formal 
+assumptions throughout their way to formalisation and use in lemmas and proofs. \<close> 
+
+figure*[doc_termAq::figure,relative_width="50",src="''figures/doc-mod-term-aq.pdf''"]
+                      \<open>Term-Antiquotations Referencing to Annotated Elements\<close>
+text\<open>As shown in @{figure \<open>doc_termAq\<close>}, this feature of  \<^isadof> substantially increases
+the expressibility of links between the formal and the informal in \<^dof> documents.\<close>
+
+text\<open> In the following, we describe a common scenario linking semi-formal assumptions and
+formal ones:
+
+@{boxed_theory_text [display]
+\<open>
+declare_reference*[e2::"definition"]
+
+Assumption*[a1::"assumption", short_name="\<open>safe environment.\<close>"]
+\<open>The system shall only be used in the temperature range from 0 to 60 degrees Celsius.
+ Formally, this is stated as follows in @{definition (unchecked) \<open>e2\<close>}.\<close>
+
+definition*[e2, status=formal] safe_env :: "state \<Rightarrow> bool" 
+   where "safe_env \<sigma> \<equiv> (temp \<sigma> \<in> {0 .. 60})"
+
+theorem*[e3::"theorem"] safety_preservation::" @{assumption \<open>a1\<close>} (safe_env \<sigma>) \<Longrightarrow> ...  "
+\<close>}
+\<close>
+text\<open>Note that Isabelle procedes in a strict ``declaration-before-use''-manner, \<^ie> assumes
+linear visibility on all references. This also holds for the declaration of ontological 
+references. In order to represent cyclic dependencies, it is therefore necessary to 
+start with the forward declaration \<^theory_text>\<open>declare_reference*\<close>. From there on, this reference
+can be used in text, term, and code-contexts, albeit its definition appears textually later.
+The corresponding freeform-formulation of this assumption can be explicitly referred in the
+assumption of a theorem establishing the link. The \<^theory_text>\<open>theorem*\<close>-variant of the common 
+Isabelle/Isar  \<^theory_text>\<open>theorem\<close>-command will in contrast to the latter not ignore \<open>\<open>a1\<close>\<close>,
+ \<^ie> parse just as string, but also validate it in the previous context.
+
+Note that the \<^theory_text>\<open>declare_reference*\<close> command will appear in the \<^LaTeX> generated from this 
+document fragment. In order to avoid this, one has to enclose this command into the 
+document comments :\<close>
+text\<open>\<^center>\<open>\<open>(*<*) ... (*>*)\<close>\<close>\<close>
 
 
 section*[tech_onto::example]\<open>Writing Technical Reports in \<^boxed_theory_text>\<open>technical_report\<close>\<close>  
@@ -595,7 +648,7 @@ In the \<^pdf> output, these text-fragments were displayed verbatim.
 
 
 
-section\<open>Style Guide\<close>
+section\<open>Some Recommendations: A little Style Guide\<close>
 text\<open>
   The document generation of \<^isadof> is based on Isabelle's document generation framework, 
   using \<^LaTeX>{} as the underlying back-end. As Isabelle's document generation framework, it is 
@@ -613,11 +666,18 @@ text\<open> This is \emph{emphasized} and this is a
 text\<open> This is *\<open>emphasized\<close> and this is a 
         citation @{cite "brucker.ea:isabelle-ontologies:2018"}.\<close>
 \<close>}
+The list of standard Isabelle document antiquotations, as well as their options and styles,
+can be found in the Isabelle reference manual @{cite "wenzel:isabelle-isar:2020"}, also be found
+under \<^url>\<open>https://www.cl.cam.ac.uk/research/hvg/Isabelle/dist/Isabelle2022/doc/isar-ref.pdf\<close>, 
+section 4.2.
 
-Clearly, this is not always possible and, in fact, often \<^isadof> documents will contain 
+In practice,  \<^isadof> documents with ambitious layout will contain a certain number of
 \<^LaTeX>-commands, but this should be restricted to layout improvements that otherwise are (currently)
-not possible. As far as possible, the use of \<^LaTeX>-commands should be restricted to the definition 
+not possible. As far as possible, raw \<^LaTeX> should be restricted to the definition 
-of ontologies and document templates (see @{docitem (unchecked) \<open>isadof_ontologies\<close>}).
+of ontologies and  macros (see @{docitem (unchecked) \<open>isadof_ontologies\<close>}). If raw 
+ \<^LaTeX> commands can not be avoided, it is recommended to use the Isabelle document comment
+\<^latex>\<open>\verb+\+\verb+<^latex>+\<close>\<open>\<open>argument\<close>\<close> to isolate these parts
+(cf. \<^url>\<open>https://www.cl.cam.ac.uk/research/hvg/Isabelle/dist/Isabelle2022/doc/isar-ref.pdf\<close>). 
 
 Restricting the use of \<^LaTeX> has two advantages: first, \<^LaTeX> commands can circumvent the 
 consistency checks of \<^isadof> and, hence, only if no \<^LaTeX> commands are used, \<^isadof> can 

Isabelle_DOF/thys/manual/M_04_RefMan.thy

@@ -43,7 +43,7 @@ text\<open>
     \<^boxed_theory_text>\<open>text*\<close>, \<^boxed_theory_text>\<open>declare_reference*\<close>, \<^etc>.;
     They allow for the annotation of text-elements with meta-information defined in ODL,
   \<^item> the \<^isadof> library \<^theory>\<open>Isabelle_DOF.Isa_COL\<close> providing
-    ontological basic (documents) concepts as well as supporting infrastructure, 
+    ontological basic (documents) concepts \<^bindex>\<open>ontology\<close> as well as supporting infrastructure, 
   \<^item> an infrastructure for ontology-specific \<^emph>\<open>layout definitions\<close>, exploiting this meta-information, 
     and 
   \<^item> an infrastructure for generic \<^emph>\<open>layout definitions\<close> for documents following, \<^eg>, the format 
@@ -51,27 +51,29 @@ text\<open>
 \<close>
 text\<open>
   Similarly to Isabelle, which is based on a core logic \<^theory>\<open>Pure\<close> and then extended by libraries
-  to major systems like \<^verbatim>\<open>HOL\<close>, \<^isadof> has a generic core infrastructure \<^dof> and then
+  to major systems like \<^verbatim>\<open>HOL\<close>, \<^isadof> has a generic core infrastructure \<^dof> and then presents 
-  presents itself to users via major library extensions,  which add domain-specific 
+  itself to users via major library extensions,  which add domain-specific  system-extensions. 
-  system-extensions. Ontologies in \<^isadof> are not just a sequence of descriptions in 
+  Ontologies\<^bindex>\<open>ontology\<close> in \<^isadof> are not just a sequence of descriptions in \<^isadof>'s Ontology 
-  \<^isadof>'s Ontology Definition Language (ODL). Rather, they are themselves presented as integrated 
+  Definition Language (ODL)\<^bindex>\<open>ODL\<close>. Rather, they are themselves presented as integrated 
   sources that provide textual descriptions, abbreviations, macro-support and even ML-code. 
   Conceptually, the library of \<^isadof> is currently organized as follows\<^footnote>\<open>The \<^emph>\<open>technical\<close> 
   organization is slightly different and shown in 
-  @{technical (unchecked) \<open>infrastructure\<close>}.\<close>: 
+  @{technical (unchecked) \<open>infrastructure\<close>}.\<close>
+  \<^bindex>\<open>COL\<close>\<^bindex>\<open>scholarly\_paper\<close>\<^bindex>\<open>technical\_report\<close> \<^bindex>\<open>CENELEC\<close>: 
 %
+\<^latex>\<open>
 \begin{center}
 \begin{minipage}{.9\textwidth}\footnotesize
 \dirtree{%
 .1 COL\DTcomment{The Common Ontology Library}.
 .2 scholarly\_paper\DTcomment{Scientific Papers}.
-.3 technical\_report\DTcomment{Extended Papers}.
+.3 technical\_report\DTcomment{Extended Papers, Technical Reports}.
 .4 CENELEC\_50128\DTcomment{Papers according to CENELEC\_50128}.
 .4 CC\_v3\_1\_R5\DTcomment{Papers according to Common Criteria}. 
 .4 \ldots.
 }
 \end{minipage}
-\end{center}
+\end{center}\<close>
 
  These libraries not only provide ontological concepts, but also syntactic sugar in Isabelle's
  command language Isar that is of major importance for users (and may be felt as \<^isadof> key 
@@ -95,27 +97,25 @@ text\<open>
 
 section\<open>The Ontology Definition Language (ODL)\<close>
 text\<open>
-  ODL shares some similarities with meta-modeling languages such as UML class 
+ ODL shares some similarities with meta-modeling languages such as UML class 
-  models: It builds upon concepts like class, inheritance, class-instances, attributes, references 
+ models: It builds upon concepts like class, inheritance, class-instances, attributes, references 
-  to instances, and class-invariants. Some concepts like  advanced type-checking, referencing to 
+ to instances, and class-invariants. Some concepts like  advanced type-checking, referencing to 
-  formal entities of Isabelle, and monitors are due to its specific application in the 
+ formal entities of Isabelle, and monitors are due to its specific application in the 
-  Isabelle context. Conceptually, ontologies specified in ODL consist of:
+ Isabelle context. Conceptually, ontologies specified in ODL consist of:
-  \<^item> \<^emph>\<open>document classes\<close> (\<^boxed_theory_text>\<open>doc_class\<close>) \<^index>\<open>doc\_class\<close> that describe concepts,
+    \<^item> \<^emph>\<open>document classes\<close> (\<^boxed_theory_text>\<open>doc_class\<close>) \<^index>\<open>doc\_class\<close> that describe concepts,
-    the keyword (\<^boxed_theory_text>\<open>onto_class\<close>) \<^index>\<open>onto\_class\<close> is accepted equally,
+      the keyword (\<^boxed_theory_text>\<open>onto_class\<close>) \<^index>\<open>onto\_class\<close> is accepted equally,
-  \<^item> an optional document base class expressing single inheritance
+    \<^item> an optional document base class expressing single inheritance  class extensions,
-  class extensions,
+    \<^item> \<^emph>\<open>attributes\<close> specific to document classes, where
-  \<^item> \<^emph>\<open>attributes\<close> specific to document classes, where
+      \<^item> attributes are HOL-typed,
-    \<^item> attributes are HOL-typed,
+      \<^item> attributes of instances of document elements are mutable,
-    \<^item> attributes of instances of document elements are mutable,
+      \<^item> attributes can refer to other document classes, thus, document
-    \<^item> attributes can refer to other document classes, thus, document
+        classes must also be HOL-types (such attributes are called  \<^emph>\<open>links\<close>),
-      classes must also be HOL-types (such attributes are called
+      \<^item> attribute values were denoted by HOL-terms,
-      \<^emph>\<open>links\<close>),
+    \<^item> a special link, the reference to a super-class, establishes an
-    \<^item> attribute values were denoted by HOL-terms,
+      \<^emph>\<open>is-a\<close> relation between classes,
-  \<^item> a special link, the reference to a super-class, establishes an
+    \<^item> classes may refer to other classes via a regular expression in an
-  \<^emph>\<open>is-a\<close> relation between classes,
+      \<^emph>\<open>accepts\<close> clause, or via a list in a \<^emph>\<open>rejects\<close> clause,
-  \<^item> classes may refer to other classes via a regular expression in an
+    \<^item> attributes may have default values in order to facilitate notation.
-    \<^emph>\<open>accepts\<close> clause, or via a list in a \<^emph>\<open>rejects\<close> clause,
-  \<^item> attributes may have default values in order to facilitate notation.
 \<close>
 
 text\<open>
@@ -262,13 +262,14 @@ A document class\<^bindex>\<open>document class\<close> can be defined using the
 text\<open>
   \<^isadof> provides a default document representation (\<^ie>, content and layout of the generated 
   \<^pdf>) that only prints the main text, omitting all attributes. \<^isadof> provides the 
-  \inlineltx|\newisadof[]{}|\<^index>\<open>newisadof@\<^boxed_latex>\<open>\newisadof\<close>\<close>\<^index>\<open>document class!PDF\<close>
+  \<^ltxinline>\<open>\newisadof[]{}\<close>\<^index>\<open>newisadof@\<^boxed_latex>\<open>\newisadof\<close>\<close>\<^index>\<open>document class!PDF\<close>
   command for defining a dedicated layout for a document class in \<^LaTeX>. Such a document 
   class-specific \<^LaTeX>-definition can not only provide a specific layout (\<^eg>, a specific 
   highlighting, printing of certain attributes), it can also generate entries in the table of 
-  contents or an index. Overall, the \inlineltx|\newisadof[]{}| command follows the structure
+  contents or an index. Overall, the  \<^ltxinline>\<open>\newisadof[]{}\<close> command follows the structure
   of the \<^boxed_theory_text>\<open>doc_class\<close>-command:
 
+% bu: not embeddable macro: too many guillemots ...
 \begin{ltx}[escapechar=ë]
 \newisadof{ë\<open>class_id\<close>ë}[label=,type=, ë\<open>attribute_decl\<close>ë][1]{%
   % ë\LaTeXë-definition of the document class representation
@@ -282,17 +283,17 @@ text\<open>
   needs to declare all attributes of the document class. Within the \<^LaTeX>-definition of the document
   class representation, the identifier \<^boxed_latex>\<open>#1\<close> refers to the content of the main text of the 
   document class (written in \<^boxed_theory_text>\<open>\<open> ... \<close>\<close>) and the attributes can be referenced
-  by their name using the \inlineltx|\commandkey{...}|-command (see the documentation of the 
+  by their name using the  \<^ltxinline>\<open>\commandkey{...}\<close>-command (see the documentation of the 
   \<^LaTeX>-package ``keycommand''~@{cite "chervet:keycommand:2010"} for details). Usually, the 
   representations definition needs to be wrapped in a 
-  \inlineltx|\begin{isarmarkup}...\end{isamarkup}|-environment, to ensure the correct context 
+  \<^ltxinline>\<open>\begin{isarmarkup}...\end{isamarkup}\<close>-environment, to ensure the correct context 
   within Isabelle's \<^LaTeX>-setup. 
   % TODO:
   % Clarify \newisadof signature: \newisadof[]{} vs \newisadof{}[]{}.
   Moreover, \<^isadof> also provides the following two variants of \inlineltx|\newisadof{}[]{}|:
-  \<^item>  \inlineltx|\renewisadof{}[]{}|\<^index>\<open>renewisadof@\<^boxed_latex>\<open>\renewisadof\<close>\<close> for re-defining 
+  \<^item>  \<^ltxinline>\<open>\renewisadof{}[]{}\<close>\<^index>\<open>renewisadof@\<^boxed_latex>\<open>\renewisadof\<close>\<close> for re-defining 
      (over-writing) an already defined command, and  
-  \<^item>  \inlineltx|\provideisadof{}[]{}|\<^index>\<open>provideisadof@\<^boxed_latex>\<open>\provideisadof\<close>\<close> for providing 
+  \<^item>  \<^ltxinline>\<open>\provideisadof{}[]{}\<close>\<^index>\<open>provideisadof@\<^boxed_latex>\<open>\provideisadof\<close>\<close> for providing 
      a definition if it is not yet defined. 
 \<close>
 text\<open>
@@ -451,9 +452,7 @@ term*\<open>@{B--test- \<open>b\<close>}\<close>
 
 declare_reference*["text-elements-expls"::technical]
 (*>*)
-ML\<open>
 
-\<close>
 subsection*["subsec:onto-term-ctxt"::technical]\<open>Ontological Term-Contexts and their Management\<close>
 text\<open> 
 \<^item> \<open>annotated_term_element\<close>
@@ -634,6 +633,7 @@ text\<open>
  \<^bindex>\<open>COL\<close> \<^footnote>\<open>contained in \<^theory>\<open>Isabelle_DOF.Isa_COL\<close>\<close>
  that introduces several ontology concepts; its  overall class-tree it provides looks as follows:
 %
+\<^latex>\<open>
 \begin{center}
 \begin{minipage}{.9\textwidth}\footnotesize
 \dirtree{%
@@ -649,7 +649,7 @@ text\<open>
 .1 \ldots.
 }
 \end{minipage}
-\end{center}\<close>
+\end{center}\<close>\<close>
 
 text\<open>
 In particular it defines the super-class \<^typ>\<open>text_element\<close>: the root of all 
@@ -709,6 +709,7 @@ text\<open> The \<^verbatim>\<open>scholarly_paper\<close> ontology is oriented
 mathematics, informatics, natural sciences, technology, or engineering.
 
 It extends \<^verbatim>\<open>COL\<close> by the following concepts:
+\<^latex>\<open>
 \begin{center}
 \begin{minipage}{.9\textwidth}\footnotesize
 \dirtree{%
@@ -733,7 +734,7 @@ It extends \<^verbatim>\<open>COL\<close> by the following concepts:
 .5 scholarly\_paper.corollary\DTcomment{Freeform}.
 .5 scholarly\_paper.math\_example\DTcomment{Freeform}.
 .5 scholarly\_paper.math\_semiformal\DTcomment{Freeform}.
-.5 scholarly\_paper.math\_formal\DTcomment{Formal(=Checked) Content}.
+.5 scholarly\_paper.math\_formal\DTcomment{Formal Content}.
 .6 scholarly\_paper.assertion\DTcomment{Assertions}.
 .4 scholarly\_paper.tech\_example\DTcomment{...}.
 .4 scholarly\_paper.math\_motivation\DTcomment{...}.
@@ -749,10 +750,10 @@ It extends \<^verbatim>\<open>COL\<close> by the following concepts:
 }
 \end{minipage}
 \end{center}
-\<close>
+\<close>\<close>
-(*
+
-TODO: There are some slight problems in  the hierarchy ...
+
-*)
+text\<open>Recall that \<^emph>\<open>Formal Content\<close> means \<^emph>\<open>machine-checked, validated content\<close>.\<close>
 
 text\<open>A pivotal abstract class in the hierarchy is:
 @{boxed_theory_text [display]
@@ -789,9 +790,12 @@ of the \<^isadof> language:
 
 \<^item> \<open>derived_text_elements \<close> :
 \<^rail>\<open>
-    (  ( @@{command "author*"} 
+    (  ( @@{command "author*"}     | @@{command "abstract*"} 
-       | @@{command "abstract*"} 
+       | @@{command "Definition*"} | @@{command "Lemma*"}      | @@{command "Theorem*"} 
-       | @@{command "Definition*"}  | @@{command "Lemma*"} | @@{command "Theorem*"} 
+       | @@{command "Proposition*"}| @@{command "Proof*"}      | @@{command "Example*"}  
+       | @@{command "Premise*"}    | @@{command "Assumption*"} | @@{command "Hypothesis*"}
+       | @@{command "Corollary*"}  | @@{command "Consequence*"}| @@{command "Assertion*"}
+       | @@{command "Conclusion*"} 
        ) 
        \<newline>
        '[' meta_args ']' '\<open>' text '\<close>'
@@ -800,6 +804,9 @@ of the \<^isadof> language:
   \<close>
 \<close>
 
+
+
+
 text\<open>Usually, command macros for text elements will assign the generated instance
 to the default class corresponding for this class.
 For pragmatic reasons, \<^theory_text>\<open>Definition*\<close>,  \<^theory_text>\<open>Lemma*\<close> and  \<^theory_text>\<open>Theorem*\<close> represent an exception
@@ -876,12 +883,14 @@ ML\<open>writeln (DOF_core.print_doc_class_tree
                                          orelse String.isPrefix "Isa_COL" l *)) 
                  toLaTeX)\<close>
 (*>*)
-text\<open> The \<^verbatim>\<open>technical_report\<close> ontology in \<^theory>\<open>Isabelle_DOF.technical_report\<close> extends
+text\<open> The \<^verbatim>\<open>technical_report\<close> \<^bindex>\<open>technical\_report\<close> ontology in
-\<^verbatim>\<open>scholarly_paper\<close> by concepts needed
+ \<^theory>\<open>Isabelle_DOF.technical_report\<close> extends
+\<^verbatim>\<open>scholarly_paper\<close>  \<^bindex>\<open>scholarly\_paper\<close> \<^bindex>\<open>ontology\<close> by concepts needed 
 for larger reports in the domain of mathematics and engineering. The concepts are fairly 
 high-level arranged at root-class level,
 
 %
+\<^latex>\<open>
 \begin{center}
 \begin{minipage}{.9\textwidth}\footnotesize
 \dirtree{%
@@ -900,7 +909,7 @@ high-level arranged at root-class level,
 }
 \end{minipage}
 \end{center}
-\<close>
+\<close>\<close>
 
 
 
@@ -931,21 +940,21 @@ end
 
 Second, given an implementation of the functionality of the new keyword (implemented in SML), 
 the new keyword needs to be registered, together with its parser, as outer syntax:
-
+\<^latex>\<open>
 \begin{sml}
 val _ =
   Outer_Syntax.command ("section*", <@>{here}) "section heading"
     (attributes -- Parse.opt_target -- Parse.document_source --| semi
       >> (Toplevel.theory o (enriched_document_command (SOME(SOME 1)) 
            {markdown = false} )));
-\end{sml}
+\end{sml}\<close>
 \<close>
 
 text\<open>
 Finally, for the document generation, a new dispatcher has to be defined in \<^LaTeX>---this is 
 mandatory, otherwise the document generation will break. These dispatchers always follow the same 
 schemata:
-
+\<^latex>\<open>
 \begin{ltx}
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % begin: section*-dispatcher
@@ -953,17 +962,17 @@ schemata:
 % end: section*-dispatcher
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \end{ltx}
-
+\<close>
   After the definition of the dispatcher, one can, optionally, define a custom representation 
   using the \<^boxed_latex>\<open>\newisadof\<close>-command, as introduced in the previous section: 
-
+\<^latex>\<open>
 \begin{ltx}
 \newisadof{section}[label=,type=][1]{%
   \isamarkupfalse%
     \isamarkupsection{#1}\label{\commandkey{label}}%
   \isamarkuptrue%
 }
-\end{ltx}
+\end{ltx}\<close>
 \<close>
 
 
@@ -1300,6 +1309,7 @@ text\<open>
   Technically, ontologies\<^index>\<open>ontology!directory structure\<close> are stored in a directory 
   \<^boxed_bash>\<open>ontologies\<close> and consist of an Isabelle theory file and a \<^LaTeX>-style file:
 %
+\<^latex>\<open>
 \begin{center}
 \begin{minipage}{.9\textwidth}\footnotesize
 \dirtree{%
@@ -1314,7 +1324,7 @@ text\<open>
 .4 DOF-technical\_report.sty.
 }
 \end{minipage}
-\end{center}
+\end{center}\<close>
 \<close>
 text\<open>
   Developing a new ontology ``\<^boxed_bash>\<open>foo\<close>'' requires the 
@@ -1334,6 +1344,7 @@ text\<open>
   etc.) of the generated documents. Document-templates 
   are stored in a directory 
   \<^path>\<open>src/document-templates\<close>:\<^index>\<open>document template!directory structure\<close>
+\<^latex>\<open>
 \begin{center}
 \begin{minipage}{.9\textwidth}\footnotesize
 \dirtree{%
@@ -1345,7 +1356,7 @@ text\<open>
 .3 root-scrreprt.tex.
 }
 \end{minipage}
-\end{center}
+\end{center}\<close>
 \<close>
 
 text\<open>
@@ -1380,6 +1391,7 @@ text\<open>
   adding a new template, call the \<^boxed_bash>\<open>install\<close> script (see \<^technical>\<open>infrastructure\<close>).  
   The common structure of an \<^isadof> document template looks as follows: 
 
+\<^latex>\<open>
 \begin{ltx}[escapechar=ë, numbers=left,numberstyle=\tiny,xleftmargin=5mm]
 \documentclass{article}        % The LaTeX-class of your template ë\label{lst:dc}ë  
 %% The following part is (mostly) required by Isabelle/DOF, do not modify
@@ -1404,7 +1416,7 @@ text\<open>
 \maketitle\input{session}
 \IfFileExists{root.bib}{\bibliography{root}}{}
 \end{document}
-\end{ltx}
+\end{ltx}\<close>
 \<close>
 
 subsection\<open>Tips, Tricks, and Known Limitations\<close>
@@ -1470,7 +1482,7 @@ text\<open>
   information into an \<^boxed_latex>\<open>\author\<close> and a \<^boxed_latex>\<open>\institution\<close> statement, each of 
   which containing the information for all authors. The collection of the author information 
   is provided by the following \<^LaTeX>-code:
-
+\<^latex>\<open>
 \begin{ltx}
 \def\dof@author{}%
 \newcommand{\DOFauthor}{\author{\dof@author}}
@@ -1485,7 +1497,7 @@ text\<open>
     \leftadd\dof@author{\protect\and #1}%
   }
 }
-\end{ltx}
+\end{ltx}\<close>
 
 The new command \<^boxed_latex>\<open>\addauthor\<close> and a similarly defined command \<^boxed_latex>\<open>\addaffiliation\<close>
 can now be used in the definition of the representation of the concept 
@@ -1494,6 +1506,7 @@ job's aux-file. The intermediate step of writing this information into the job's
 as the author and affiliation information is required right at the beginning of the document 
 while  \<^isadof> allows defining  authors at  any place within a document:
 
+\<^latex>\<open>
 \begin{ltx}
 \provideisadof{text.scholarly_paper.author}%
 [label=,type=%
@@ -1517,19 +1530,18 @@ while  \<^isadof> allows defining  authors at  any place within a document:
                \string\addaffiliation{\dof@a\\\string\email{%
                     \commandkey{scholarly_paper.author.email}}}}%
 }
-\end{ltx}
+\end{ltx}\<close>
 
 Finally, the collected information is used in the  \<^boxed_latex>\<open>\author\<close> command using the 
 \<^boxed_latex>\<open>AtBeginDocument\<close>-hook:
-
+\<^latex>\<open>
 \begin{ltx}
 \newcommand{\DOFauthor}{\author{\dof@author}}
 \AtBeginDocument{%
   \DOFauthor
 }
 
-\end{ltx}
+\end{ltx}\<close>
-
 
 \<close>
 
@@ -1538,15 +1550,15 @@ subsubsection\<open>Restricting the Use of Ontologies to Specific Templates\<clo
 text\<open>
   As ontology representations might rely on features only provided by certain templates 
   (\<^LaTeX>-classes), authors of ontology representations might restrict their use to 
-  specific classes. This can, \<^eg>, be done using the \inlineltx|\@ifclassloaded{}| command:
+  specific classes. This can, \<^eg>, be done using the \<^ltxinline>\<open>\@ifclassloaded{}\<close> command:
-
+\<^latex>\<open>
 \begin{ltx}
 \@ifclassloaded{llncs}{}%
 {% LLNCS class not loaded
     \PackageError{DOF-scholarly_paper}
     {Scholarly Paper only supports LNCS as document class.}{}\stop%
 }
-\end{ltx}
+\end{ltx}\<close>
 
   For a real-world example testing for multiple classes, see 
   \<^file>\<open>../../ontologies/scholarly_paper/DOF-scholarly_paper.sty\<close>: