Further updates to the new project structure (contributes to #23).

Isabelle_DOF/thys/manual/03_GuidedTour.thy

@@ -85,8 +85,9 @@ subsection*[document::example]\<open>Document Generation\<close>
 text\<open>\<^isadof> provides an enhanced setup for generating PDF document. In particular, it does 
 not make use of a file called \<^verbatim>\<open>document/root.tex\<close>. Instead, the use of document templates and 
 ontology represenations is done within theory files. To make use of this feature, one needs
-to add the option \<^verbatim>\<open>document_build = dof\<close> to the \<^verbatim>\<open>ROOT\<close> file. An example \<^verbatim>\<open>ROOT\<close> file looks
-as follows:
+to add the option \<^verbatim>\<open>document_build = dof\<close> to the \<^verbatim>\<open>ROOT\<close> file. 
+An example \<^verbatim>\<open>ROOT\<close> file looks as follows:
+
 \begin{config}{ROOT}
 session example = HOL +
   options [document = pdf, document_output = "output", document_build = dof]

Isabelle_DOF/thys/manual/04_RefMan.thy

@@ -502,10 +502,9 @@ text\<open>
 section\<open>The Standard Ontology Libraries\<close>
 text\<open> We will describe the backbone of the Standard Library with the
 already mentioned hierarchy \<^verbatim>\<open>COL\<close> (the common ontology library),
- \<^verbatim>\<open>scholarly_paper\<close> (for MINT-oriented scientific papers), 
- \<^verbatim>\<open>technical_report\<close> (for MINT-oriented technical reports), and
-the example for a domain-specific ontology 
-\<^verbatim>\<open>CENELEC_50128\<close>.\<close>
+ \<^verbatim>\<open>scholarly_paper\<close> (for MINT-oriented scientific papers) or 
+ \<^verbatim>\<open>technical_report\<close> (for MINT-oriented technical reports).
+\<close>
 
 subsection\<open>Common Ontology Library (COL)\<close>
 (*<*)
@@ -1184,19 +1183,14 @@ text\<open>
 \begin{minipage}{.9\textwidth}\footnotesize
 \dirtree{%
 .1 .
-.2 src.
-.3 ontologies\DTcomment{Ontologies}.
-.4 ontologies.thy\DTcomment{Ontology Registration}.
-.4 scholarly\_paper\DTcomment{scholarly\_paper}.
-.5 scholarly\_paper.thy.
-.5 DOF-scholarly\_paper.sty.
-.4 technical\_report\DTcomment{technical\_paper}.
-.5 technical\_report.thy.
-.5 DOF-technical\_report.sty.
-.4 CENELEC\_50128\DTcomment{CENELEC\_50128}.
-.5 CENELEC\_50128.thy.
-.5 DOF-CENELEC\_50128.sty.
-.4 \ldots.
+.2 ontologies\DTcomment{Ontologies}.
+.3 ontologies.thy\DTcomment{Ontology Registration}.
+.3 scholarly\_paper\DTcomment{scholarly\_paper}.
+.4 scholarly\_paper.thy.
+.4 DOF-scholarly\_paper.sty.
+.3 technical\_report\DTcomment{technical\_paper}.
+.4 technical\_report.thy.
+.4 DOF-technical\_report.sty.
 }
 \end{minipage}
 \end{center}
@@ -1204,16 +1198,13 @@ text\<open>
 text\<open>
   Developing a new ontology ``\<^boxed_bash>\<open>foo\<close>'' requires the 
   following steps:
-  \<^item> create a new sub-directory \<^boxed_bash>\<open>foo\<close> in the directory \<^boxed_bash>\<open>ontologies\<close>
   \<^item> definition of the ontological concepts, using \<^isadof>'s Ontology Definition Language (ODL), in 
     a new theory file \<^path>\<open>ontologies/foo/foo.thy\<close>.  
   \<^item> definition of the document representation for the ontological concepts in a \LaTeX-style 
-    file \<^path>\<open>ontologies/foo/DOF-foo.sty\<close>
-  \<^item> registration (as import) of the new ontology in the file \<^path>\<open>ontologies/ontologies.thy\<close>. 
-  \<^item> activation of the new document setup by executing the install script. You can skip the lengthy 
-    checks for the AFP entries and the installation of the Isabelle patch by using the 
-    \<^boxed_bash>\<open>--skip-afp\<close> option:
-    @{boxed_bash [display] \<open>ë\prompt{\isadofdirn}ë ./install --skip-afp\<close>}
+    stored in the same directory as the theory file containing the ODL definitions. The file name should 
+    start with the prefix ``DOF-``. For instance: \<^path>\<open>DOF-foo.sty\<close>
+  \<^item> registration of the \LaTeX-style by adding a suitable \<^theory_text>\<open>define_ontology\<close> 
+    command to the theory containing the ODL definitions.
 \<close>
 
 subsection\<open>Document Templates\<close>
@@ -1226,12 +1217,11 @@ text\<open>
 \begin{minipage}{.9\textwidth}\footnotesize
 \dirtree{%
 .1 .
-.2 src.
-.3 document-templates\DTcomment{Document templates}.
-.4 root-lncs.tex.
-.4 root-scrartcl.tex.
-.4 root-scrreprt-modern.tex.
-.4 root-scrreprt.tex.
+.2 document-templates\DTcomment{Document templates}.
+.3 root-lncs.tex.
+.3 root-scrartcl.tex.
+.3 root-scrreprt-modern.tex.
+.3 root-scrreprt.tex.
 }
 \end{minipage}
 \end{center}
@@ -1240,7 +1230,8 @@ text\<open>
 text\<open>
   Developing a new document template ``\<^boxed_bash>\<open>bar\<close>'' requires the following steps:
   \<^item> develop a new \<^LaTeX>-template \<^boxed_bash>\<open>src/document-templates/root-bar.tex\<close>
-  \<^item> add a suitable \<^theory_text>\<open>define_template\<close> command to theory \<^theory>\<open>Isabelle_DOF.Isa_DOF\<close>.
+  \<^item> add a suitable \<^theory_text>\<open>define_template\<close> command to a theory that is 
+   imported by the project that shall use the new document template. 
 \<close>
 
 
@@ -1332,10 +1323,8 @@ text\<open>
   requires that information is written into an auxiliary file during the first run of \<^LaTeX>
   so that the information is available at further runs of \<^LaTeX>. While, on the one hand, 
   this is a standard process (\<^eg>, used for updating references), implementing it correctly
-  requires a solid understanding of \<^LaTeX>'s expansion mechanism. In this context, the recently 
-  introduced \inlineltx|\expanded{}|-primitive 
-  (see \<^url>\<open>https://www.texdev.net/2018/12/06/a-new-primitive-expanded\<close>) is particularly useful. 
-  Examples of its use can be found, \<^eg>, in the ontology-style 
+  requires a solid understanding of \<^LaTeX>'s expansion mechanism. 
+  Examples of this can be found, \<^eg>, in the ontology-style 
   \<^file>\<open>../../ontologies/scholarly_paper/DOF-scholarly_paper.sty\<close>.
   For details about the expansion mechanism
   in general, we refer the reader to the \<^LaTeX> literature (\<^eg>,~@{cite "knuth:texbook:1986"