Large directory restructuring.

This commit restructures the file hierarchy:
1) implementation is moved into src/ directory to clean up
   the main directory and to make it easier for users to
   find the README.md.
2) ontologies (both, the Isabelle-part and the LaTeX-part) are
   now structured into directories.

.ci/Jenkinsfile

@@ -4,15 +4,15 @@ pipeline {
     stages {
         stage('Build Docker') {
             steps {
-                sh 'cp patches/thy_output.ML .ci/isabelle4isadof/'
+                sh 'cp src/patches/thy_output.ML .ci/isabelle4isadof/'
                 sh 'docker build -t logicalhacking:isabelle4dof .ci/isabelle4isadof'
                 sh 'rm -f .ci/isabelle4isadof/thy_output.ML'
             }
         }
         stage('Check Docker') {
-            when { changeset "patches/*" } 
+            when { changeset "src/patches/*" } 
             steps {
-                sh 'cp patches/thy_output.ML .ci/isabelle4isadof/'
+                sh 'cp src/patches/thy_output.ML .ci/isabelle4isadof/'
                 sh 'docker build --no-cache -t logicalhacking:isabelle4dof .ci/isabelle4isadof'
                 sh 'rm -f .ci/isabelle4isadof/thy_output.ML'
             }

README.md

@@ -37,7 +37,7 @@ The installer will
 * apply a patch to Isabelle that is necessary to use Isabelle/DOF. 
   If this patch installations fails, you need to manually replace 
   the file ``Isabelle2019/src/Pure/Thy/thy_output.ML`` in the Isabelle
-  distribution with the file ``patches/thy_output.ML`` from the  
+  distribution with the file ``src/patches/thy_output.ML`` from the  
   Isabelle/DOF distribution:        
         ```console
         cp patches/thy_output.ML `isabelle getenv -b ISABELLE_HOME`/src/Pure/Thy/

ROOTS

@@ -1 +1,2 @@
+src
 examples

document-generator/README.md

@@ -1,26 +0,0 @@
-# Isabelle_DOF: Document Preparation Setup
-
-This directory contains the LaTeX setup for Isabelle's 
-document generation system. 
-
-
-## Tips and Tricks
-
-During debugging of LaTeX errors, it can be very helpful to use 
-more than 79 characters for error messages (otherwise, long errors
-are truncated)"
-``` bash
-max_print_line=200 error_line=200 half_error_line=100  pdflatex root.tex
-```
-
-## Team
-
-Main contacts:
-* [Achim D. Brucker](http://www.brucker.ch/)
-* [Burkhart Wolff](https://www.lri.fr/~wolff/)
-
-## License
-
-This project is licensed under a 2-clause BSD license.
-
-SPDX-License-Identifier: BSD-2-Clause

examples/math_exam/MathExam/MathExam.thy

@@ -1,11 +1,10 @@
 (*<*)
 theory MathExam
-  imports "Isabelle_DOF.mathex_onto"
+  imports "Isabelle_DOF.mathex"
     HOL.Real
 begin
 (*>*)   
-open_monitor*[exam::MathExam] 
-
+(* open_monitor*[exam::MathExam]  *)
 
 section*[header::Header,examSubject= "[algebra]", 
             date="''02-05-2018''", timeAllowed="90::int"] \<open>Exam number 1\<close>
@@ -94,6 +93,6 @@ text*[q2::Task, local_grade="threeStars", mark="3::int", type="formal"]
    with a difference of 5.
 \<close> 
 (* this does not work on the level of the LaTeX output for known restrictions of the Toplevel. *)
-close_monitor*[exam :: MathExam] 
+(* close_monitor*[exam :: MathExam] *)
 
 end

examples/scholarly_paper/2018_cicm/IsaDofApplications.thy

@@ -389,7 +389,7 @@ text\<open> The document class \inlineisar+figure+ --- supported by the \isadof
 such as @{docitem_ref \<open>fig_figures\<close>}.
 \<close>
          
-subsection*[mathex_onto::example]\<open> The Math-Exam Scenario \<close> 
+subsection*[mathex::example]\<open> The Math-Exam Scenario \<close> 
 text\<open> The Math-Exam Scenario is an application with mixed formal and 
 semi-formal content. It addresses applications where the author of the exam is not present 
 during the exam and the preparation requires a very rigorous process, as the french 

examples/technical_report/IsaDof_Manual/03_GuidedTour.thy

@@ -251,7 +251,7 @@ doc_class srac = ec  +
 \end{isar}
 \<close>
 
-section*[mathex_onto::example]\<open> The Math-Exam Scenario \<close> 
+section*[mathex::example]\<open> The Math-Exam Scenario \<close> 
 text\<open> The Math-Exam Scenario is an application with mixed formal and 
 semi-formal content. It addresses applications where the author of the exam is not present 
 during the exam and the preparation requires a very rigorous process, as the french 

install

@@ -125,7 +125,7 @@ check_afp_entries() {
 
 check_isa_dof_patch() {
     echo "* Check availability of Isabelle/DOF patch:"
-    src="patches/thy_output.ML"
+    src="src/patches/thy_output.ML"
     dst="$ISABELLE_HOME/src/Pure/Thy/thy_output.ML"
      
     if command -v cmp > /dev/null 2>&1 && cmp -s "$src" "$dst" ; then
@@ -185,7 +185,7 @@ install_and_register(){
     DIR="$ISABELLE_HOME_USER/DOF/latex"
     echo "  - Installing LaTeX styles in $DIR"
     mkdir -p "$DIR"
-    cp $GEN_DIR/latex/*.sty "$DIR"
+    cp $GEN_DIR/*/*/*.sty "$DIR"
 
     DIR="$ISABELLE_HOME_USER/etc"
     echo "  - Registering Isabelle/DOF"
@@ -221,7 +221,7 @@ done
 
 
 ACTUAL_ISABELLE_VERSION=`$ISABELLE version`
-GEN_DIR=document-generator
+GEN_DIR=src
 PROG=`echo $0 | sed 's|.*/||'`;
 VARS=`$ISABELLE getenv ISABELLE_HOME_USER ISABELLE_HOME ISABELLE_TOOLS`
 for i in $VARS; do 

Isa_DOF.thy → src/DOF/Isa_DOF.thy

@@ -1525,7 +1525,7 @@ end
 (* the following 2 lines set parser and converter for LaTeX generation of meta-attributes. 
    Currently of *all* commands, no distinction between text* and text command. 
    This code depends on a MODIFIED Isabelle2017 version resulting from applying the files
-   under Isabell_DOF/patches. 
+   under src/patches. 
  *)
 (* REMARK PORT 2018 : transmission of meta-args to LaTeX crude and untested. Can be found in
    present_token. *)

ROOT → src/ROOT

@@ -3,12 +3,8 @@ session "Isabelle_DOF" = "Functional-Automata" +
   sessions
     "Regular-Sets"
   theories
-    Isa_DOF
-    "ontologies/Conceptual"
-    "ontologies/CENELEC_50128"
-    "ontologies/scholarly_paper"
-    "ontologies/technical_report"
-    "ontologies/mathex_onto"
+    "DOF/Isa_DOF"
+    "ontologies/ontologies"
 
 session "Isabelle_DOF-tests" = "Isabelle_DOF" + 
   options [document = false]

ontologies/CENELEC_50128.thy → src/ontologies/CENELEC_50128/CENELEC_50128.thy

@@ -12,7 +12,7 @@ identifies:
 
 (*<<*)  
 theory CENELEC_50128
-  imports  "../Isa_COL"
+  imports  "../../DOF/Isa_COL"
 begin
 (*>>*) 
 
@@ -726,4 +726,4 @@ Proof_Context.init_global;
 \<close>
 
 end      
-  
+  

ontologies/Conceptual.thy → src/ontologies/Conceptual/Conceptual.thy

@@ -1,5 +1,5 @@
 theory Conceptual
-  imports "../Isa_DOF" "../Isa_COL"
+  imports "../../DOF/Isa_DOF" "../../DOF/Isa_COL"
 begin
 
 doc_class A =

ontologies/math_paper.thy → src/ontologies/math_paper/math_paper.thy

@@ -12,7 +12,7 @@ proving environment after all ! So this ontology provides:
   
   
 theory math_paper
-  imports  "../Isa_DOF"  
+  imports  "../../DOF/Isa_DOF"  
 begin
   
    

ontologies/mathex_onto.thy → src/ontologies/mathex/mathex.thy

@@ -1,5 +1,5 @@
-theory mathex_onto
- imports "../Isa_COL"
+theory mathex
+ imports "../../DOF/Isa_COL"
 begin
   
 (*<<*)  
@@ -98,4 +98,4 @@ doc_class MathExam =
   accepts "\<lbrace>Author\<rbrace>\<^sup>+  ~~  Header ~~  \<lbrace>Exercise ~~ Solution\<rbrace>\<^sup>+ "
   
 (*>>*)
-end
+end

src/ontologies/ontologies.thy

@@ -0,0 +1,12 @@
+theory 
+  ontologies
+imports
+  "CENELEC_50128/CENELEC_50128"
+  "Conceptual/Conceptual"
+  "mathex/mathex"
+  "math_paper/math_paper"
+  "scholarly_paper/scholarly_paper"
+  "small_math/small_math"
+  "technical_report/technical_report"
+begin
+end

ontologies/scholarly_paper.thy → src/ontologies/scholarly_paper/scholarly_paper.thy

@@ -1,7 +1,7 @@
 section\<open>An example ontology for a scholarly paper\<close>
 
 theory scholarly_paper
-   imports "../Isa_COL"
+   imports "../../DOF/Isa_COL"
 begin
 
 doc_class title =

ontologies/small_math.thy → src/ontologies/small_math/small_math.thy

@@ -1,7 +1,7 @@
 section\<open>An example ontology for a math paper\<close>
 
 theory small_math
-   imports "../Isa_COL"
+   imports "../../DOF/Isa_COL"
 begin
 
 doc_class title =

ontologies/technical_report.thy → src/ontologies/technical_report/technical_report.thy

@@ -1,7 +1,7 @@
 section\<open>An example ontology for a scholarly paper\<close>
 
 theory technical_report
-   imports "scholarly_paper"
+   imports "../scholarly_paper/scholarly_paper"
 begin
 
 (* for reports paper: invariant: level \<ge> -1 *)

tests/AssnsLemmaThmEtc.thy → src/tests/AssnsLemmaThmEtc.thy

@@ -1,8 +1,8 @@
 theory 
   AssnsLemmaThmEtc
 imports 
-  "../ontologies/Conceptual"  
-  "../ontologies/math_paper"
+  "../ontologies/Conceptual/Conceptual"  
+  "../ontologies/math_paper/math_paper"
 begin
 
 section\<open>Elementary Creation of Doc-items and Access of their Attibutes\<close>

tests/Attributes.thy → src/tests/Attributes.thy

@@ -1,7 +1,7 @@
 theory 
   Attributes
 imports 
-  "../ontologies/Conceptual"
+  "../ontologies/Conceptual/Conceptual"
 begin
 
 section\<open>Elementary Creation of Doc-items and Access of their Attibutes\<close>

tests/Concept_Example.thy → src/tests/Concept_Example.thy

@@ -3,7 +3,7 @@ chapter\<open>Setting and modifying attributes of doc-items\<close>
 theory 
   Concept_Example
 imports 
-  "../ontologies/Conceptual" (* we use the generic "Conceptual" ontology *)
+  "../ontologies/Conceptual/Conceptual" (* we use the generic "Conceptual" ontology *)
 begin
 
 text\<open>@{theory "Isabelle_DOF-tests.Conceptual"} provides a monitor @{typ M} enforcing a particular document structure.

tests/Concept_ExampleInvariant.thy → src/tests/Concept_ExampleInvariant.thy

@@ -3,7 +3,7 @@ chapter\<open>Setting and modifying attributes of doc-items\<close>
 theory 
   Concept_ExampleInvariant
 imports 
-  "../ontologies/Conceptual" (* we use the generic "Conceptual" ontology *)
+  "../ontologies/Conceptual/Conceptual" (* we use the generic "Conceptual" ontology *)
 begin
 
 section\<open>Example: Standard Class Invariant\<close>

tests/InnerSyntaxAntiquotations.thy → src/tests/InnerSyntaxAntiquotations.thy

@@ -3,7 +3,7 @@ chapter\<open>Inner Syntax Antiquotations (ISA)'s\<close>
 theory 
   InnerSyntaxAntiquotations
 imports 
-  "../ontologies/Conceptual"
+  "../ontologies/Conceptual/Conceptual"
 begin
 
 text\<open>Since the syntax chosen for values of doc-class attributes is HOL-syntax --- requiring