diff --git a/document-generator/Tools/DOF_mkroot b/document-generator/Tools/DOF_mkroot
index b48ab2e3..63a711f9 100755
--- a/document-generator/Tools/DOF_mkroot
+++ b/document-generator/Tools/DOF_mkroot
@@ -135,17 +135,15 @@ fi
 if [ "$DOC" = true ]; then
   $ISABELLE_TOOL mkroot -d -n "$NAME" "$DIR"
   echo "    \"preamble.tex\"" >> "$DIR"/ROOT
-  echo "    \"ontologies.tex\"" >> "$DIR"/ROOT
   echo "    \"build\"" >> "$DIR"/ROOT
-  sed -i -e "s/root.tex/root.inf/" "$DIR"/ROOT
+  sed -i -e "s/root.tex/isadof.cfg/" "$DIR"/ROOT
   rm -f "$DIR"/document/root.tex
   TITLE=$(echo "$NAME" | tr _ - | tr -d '\\')
   AUTHOR=$(echo "By $USER" | tr _ - | tr -d '\\')
-  echo $TEMPLATE > "$DIR"/document/root.inf
+  echo "Template: $TEMPLATE" > "$DIR"/document/isadof.cfg
   cp "$ISABELLE_HOME_USER/DOF/document-template/build" "$DIR"/document/
-  cp "$ISABELLE_HOME_USER/DOF/document-template/ontologies.tex" "$DIR"/document/
   for o in $ONTOLOGY; do
-    echo "\usepackage{DOF-$o}" >> "$DIR"/document/ontologies.tex;
+    echo "Ontology: $o" >> "$DIR"/document/isadof.cfg;
   done
   sed -e "s/<AUTHOR>/$AUTHOR/" -e "s/<TITLE>/$TITLE/" "$ISABELLE_HOME_USER/DOF/document-template/preamble.tex" > "$DIR"/document/preamble.tex
 else
diff --git a/document-generator/document-template/build_lib.sh b/document-generator/document-template/build_lib.sh
index 8aa2a9b9..6de6fcf6 100755
--- a/document-generator/document-template/build_lib.sh
+++ b/document-generator/document-template/build_lib.sh
@@ -49,17 +49,64 @@ if [ ! -f $ISABELLE_HOME_USER/DOF/latex/DOF-core.sty ]; then
     exit 1
 fi
 
-if [ ! -f root.inf ]; then 
+if [ -f "$DIR/$ROOT_NAME.tex" ]; then 
+    echo ""
+    echo "Error: Found root file ($DIR/$ROOT_NAME.tex)"
+    echo "====="
+    echo "Isabelle/DOF does not use the Isabelle root file setup. Please check"
+    echo "your project setup. Your $DIR/isadof.cfg should define a Isabelle/DOF"
+    echo "template and your project should not include a root file."
+    echo ""
+    exit 1
+fi
+
+if [ -f "$DIR/ontologies.tex" ]; then 
+    echo ""
+    echo "Error: Old project setup, found a ontologies file ($DIR/ontologies.tex)"
+    echo "====="
+    echo "Isabelle/DOF does no longer support the use of $DIR/ontologies.tex. The"
+    echo "required ontologies should be defined in $DIR/isadof.cfg."
+    echo ""
+    exit 1
+fi
+
+if [ -f "$DIR/$ROOT_NAME.tex" ]; then 
+    echo ""
+    echo "Error: Found root file ($DIR/$ROOT_NAME.tex)"
+    echo "====="
+    echo "Isabelle/DOF does not make use of the Isabelle root file mechanism."
+    echo "Please check your Isabelle/DOF setup."
+    exit 1
+fi
+
+if [ ! -f isadof.cfg ]; then 
     echo ""
     echo "Error: Isabelle/DOF document setup not correct"
     echo "====="
-    echo "Could not find root.inf. Please upgrade your Isabelle/DOF document"
+    echo "Could not find isadof.cfg. Please upgrade your Isabelle/DOF document"
     echo "setup manually."
     exit 1
 fi
 
-ROOT="$ISABELLE_HOME_USER/DOF/document-template/root-$(cat root.inf).tex"
-if [ ! -f $ROOT]; then 
+TEMPLATE=""
+ONTOLOGY="core"
+CONFIG="isadof.cfg"
+while IFS= read -r line;do
+    fields=($(printf "%s" "$line"|cut -d':' --output-delimiter=' ' -f1-))
+    if [[ "${fields[0]}" = "Template" ]]; then 
+	TEMPLATE="${fields[1]}"
+    fi                      
+    if [[ "${fields[0]}" = "Ontology" ]]; then 
+	ONTOLOGY="$ONTOLOGY ${fields[1]}"
+    fi
+done < $CONFIG
+
+for o in $ONTOLOGY; do
+  echo "\usepackage{DOF-$o}" >> ontologies.tex;
+done
+
+ROOT="$ISABELLE_HOME_USER/DOF/document-template/root-$TEMPLATE.tex"
+if [ ! -f $ROOT ]; then 
     echo ""
     echo "Error: Isabelle/DOF document setup not correct"
     echo "====="
@@ -72,10 +119,10 @@ cp $ROOT root.tex
 cp $ISABELLE_HOME_USER/DOF/latex/*.sty .
 cp $ISABELLE_HOME_USER/DOF/latex/*.sty .
 
-$ISABELLE_TOOL latex -o sty "$ROOT_NAME.tex" && \
-$ISABELLE_TOOL latex -o "$OUTFORMAT" "$ROOT_NAME.tex" && \
-{ [ ! -f "$ROOT_NAME.bib" ] || $ISABELLE_TOOL latex -o bbl "$ROOT_NAME.tex"; } && \
-{ [ ! -f "$ROOT_NAME.idx" ] || $ISABELLE_TOOL latex -o idx "$ROOT_NAME.tex"; } && \
-$ISABELLE_TOOL latex -o "$OUTFORMAT" "$ROOT_NAME.tex" && \
-$ISABELLE_TOOL latex -o "$OUTFORMAT" "$ROOT_NAME.tex"
+$ISABELLE_TOOL latex -o sty "root.tex" && \
+$ISABELLE_TOOL latex -o "$OUTFORMAT" "root.tex" && \
+{ [ ! -f "$ROOT_NAME.bib" ] || $ISABELLE_TOOL latex -o bbl "root.tex"; } && \
+{ [ ! -f "$ROOT_NAME.idx" ] || $ISABELLE_TOOL latex -o idx "root.tex"; } && \
+$ISABELLE_TOOL latex -o "$OUTFORMAT" "root.tex" && \
+$ISABELLE_TOOL latex -o "$OUTFORMAT" "root.tex"
 
diff --git a/document-generator/document-template/ontologies.tex b/document-generator/document-template/ontologies.tex
deleted file mode 100644
index 88f585f8..00000000
--- a/document-generator/document-template/ontologies.tex
+++ /dev/null
@@ -1,14 +0,0 @@
-%% Copyright (C) 2018 The University of Sheffield
-%%               2018 The University of Paris-Sud
-%%
-%% License:
-%%   This program can be redistributed and/or modified under the terms
-%%   of the LaTeX Project Public License Distributed from CTAN
-%%   archives in directory macros/latex/base/lppl.txt; either
-%%   version 1 of the License, or any later version.
-%%   OR
-%%   The 2-clause BSD-style license.
-%%  
-%%   SPDX-License-Identifier: LPPL-1.0+ OR BSD-2-Clause
-
-%% This file is used for including the LaTeX ontology mappings. 
diff --git a/examples/math_exam/BAC2017/ROOT b/examples/math_exam/BAC2017/ROOT
index 61540428..cf671977 100644
--- a/examples/math_exam/BAC2017/ROOT
+++ b/examples/math_exam/BAC2017/ROOT
@@ -6,7 +6,6 @@ session "BAC2017" = "Isabelle_DOF" +
   theories
      BAC2017
   document_files
-    "root.inf"
+    "isadof.cfg"
     "preamble.tex"
-    "ontologies.tex"
     "build"
diff --git a/examples/math_exam/BAC2017/document/isadof.cfg b/examples/math_exam/BAC2017/document/isadof.cfg
new file mode 100644
index 00000000..f13f22b5
--- /dev/null
+++ b/examples/math_exam/BAC2017/document/isadof.cfg
@@ -0,0 +1,2 @@
+Template: scrartcl
+Ontology: mathex
diff --git a/examples/math_exam/BAC2017/document/ontologies.tex b/examples/math_exam/BAC2017/document/ontologies.tex
deleted file mode 100644
index 8e80a84c..00000000
--- a/examples/math_exam/BAC2017/document/ontologies.tex
+++ /dev/null
@@ -1,17 +0,0 @@
-% This file was modified by the DOF LaTeX converter, version 0.0.3
-%% Copyright (C) 2018 The University of Sheffield
-%%               2018 The University of Paris-Sud
-%%
-%% License:
-%%   This program can be redistributed and/or modified under the terms
-%%   of the LaTeX Project Public License Distributed from CTAN
-%%   archives in directory macros/latex/base/lppl.txt; either
-%%   version 1 of the License, or any later version.
-%%   OR
-%%   The 2-clause BSD-style license.
-%%  
-%%   SPDX-License-Identifier: LPPL-1.0+ OR BSD-2-Clause
-
-%% This file is used for including the LaTeX ontology mappings. 
-\usepackage{DOF-core}
-\usepackage{DOF-mathex}
diff --git a/examples/math_exam/BAC2017/document/root.inf b/examples/math_exam/BAC2017/document/root.inf
deleted file mode 100644
index 52343f0f..00000000
--- a/examples/math_exam/BAC2017/document/root.inf
+++ /dev/null
@@ -1 +0,0 @@
-scrartcl
diff --git a/examples/math_exam/MathExam/ROOT b/examples/math_exam/MathExam/ROOT
index 3474ce43..9f5e87ee 100644
--- a/examples/math_exam/MathExam/ROOT
+++ b/examples/math_exam/MathExam/ROOT
@@ -4,8 +4,7 @@ session "MathExam" = "Isabelle_DOF" +
     MathExam
   document_files
     "preamble.tex"
-    "root.inf"
-    "ontologies.tex"
+    "isadof.cfg"
     "preamble.tex"
     "build"
     "figures/Polynomialdeg5.png"
diff --git a/examples/math_exam/MathExam/document/isadof.cfg b/examples/math_exam/MathExam/document/isadof.cfg
new file mode 100644
index 00000000..f13f22b5
--- /dev/null
+++ b/examples/math_exam/MathExam/document/isadof.cfg
@@ -0,0 +1,2 @@
+Template: scrartcl
+Ontology: mathex
diff --git a/examples/math_exam/MathExam/document/ontologies.tex b/examples/math_exam/MathExam/document/ontologies.tex
deleted file mode 100644
index 8e80a84c..00000000
--- a/examples/math_exam/MathExam/document/ontologies.tex
+++ /dev/null
@@ -1,17 +0,0 @@
-% This file was modified by the DOF LaTeX converter, version 0.0.3
-%% Copyright (C) 2018 The University of Sheffield
-%%               2018 The University of Paris-Sud
-%%
-%% License:
-%%   This program can be redistributed and/or modified under the terms
-%%   of the LaTeX Project Public License Distributed from CTAN
-%%   archives in directory macros/latex/base/lppl.txt; either
-%%   version 1 of the License, or any later version.
-%%   OR
-%%   The 2-clause BSD-style license.
-%%  
-%%   SPDX-License-Identifier: LPPL-1.0+ OR BSD-2-Clause
-
-%% This file is used for including the LaTeX ontology mappings. 
-\usepackage{DOF-core}
-\usepackage{DOF-mathex}
diff --git a/examples/math_exam/MathExam/document/root.inf b/examples/math_exam/MathExam/document/root.inf
deleted file mode 100644
index 52343f0f..00000000
--- a/examples/math_exam/MathExam/document/root.inf
+++ /dev/null
@@ -1 +0,0 @@
-scrartcl
diff --git a/examples/scholarly_paper/2018_cicm/ROOT b/examples/scholarly_paper/2018_cicm/ROOT
index fac0be9a..0ea790b9 100644
--- a/examples/scholarly_paper/2018_cicm/ROOT
+++ b/examples/scholarly_paper/2018_cicm/ROOT
@@ -3,12 +3,11 @@ session "IsaDofApplications" = "Isabelle_DOF" +
   theories
     IsaDofApplications
   document_files
-    "root.inf"
+    "isadof.cfg"
     "root.bib"
     "preamble.tex"
     "build"
     "lstisadof.sty"
-    "ontologies.tex"
     "figures/isabelle-architecture.pdf"
     "figures/Dogfood-Intro.png"
     "figures/InteractiveMathSheet.png"
diff --git a/examples/scholarly_paper/2018_cicm/document/isadof.cfg b/examples/scholarly_paper/2018_cicm/document/isadof.cfg
new file mode 100644
index 00000000..dbf4a8e6
--- /dev/null
+++ b/examples/scholarly_paper/2018_cicm/document/isadof.cfg
@@ -0,0 +1,2 @@
+Template: scrartcl
+Ontology: scholarly_paper
diff --git a/examples/scholarly_paper/2018_cicm/document/ontologies.tex b/examples/scholarly_paper/2018_cicm/document/ontologies.tex
deleted file mode 100644
index 33e9548e..00000000
--- a/examples/scholarly_paper/2018_cicm/document/ontologies.tex
+++ /dev/null
@@ -1,17 +0,0 @@
-% This file was modified by the DOF LaTeX converter, version 0.0.3
-%% Copyright (C) 2018 The University of Sheffield
-%%               2018 The University of Paris-Sud
-%%
-%% License:
-%%   This program can be redistributed and/or modified under the terms
-%%   of the LaTeX Project Public License Distributed from CTAN
-%%   archives in directory macros/latex/base/lppl.txt; either
-%%   version 1 of the License, or any later version.
-%%   OR
-%%   The 2-clause BSD-style license.
-%%  
-%%   SPDX-License-Identifier: LPPL-1.0+ OR BSD-2-Clause
-
-%% This file is used for including the LaTeX ontology mappings. 
-\usepackage{DOF-core}
-\usepackage{DOF-scholarly_paper}
\ No newline at end of file
diff --git a/examples/scholarly_paper/2018_cicm/document/root.inf b/examples/scholarly_paper/2018_cicm/document/root.inf
deleted file mode 100644
index 52343f0f..00000000
--- a/examples/scholarly_paper/2018_cicm/document/root.inf
+++ /dev/null
@@ -1 +0,0 @@
-scrartcl
diff --git a/examples/technical_report/IsaDof_Manual/ROOT b/examples/technical_report/IsaDof_Manual/ROOT
index 1a0b5fd8..fbbd4391 100644
--- a/examples/technical_report/IsaDof_Manual/ROOT
+++ b/examples/technical_report/IsaDof_Manual/ROOT
@@ -3,12 +3,11 @@ session "IsaDof_Manual" = "Isabelle_DOF" +
   theories
     IsaDofManual
   document_files
-    "root.inf"
+    "isadof.cfg"
     "root.bib"
     "preamble.tex"
     "build"
     "lstisadof.sty"
-    "ontologies.tex"
     "figures/isabelle-architecture.pdf"
     "figures/Dogfood-Intro.png"
     "figures/InteractiveMathSheet.png"
diff --git a/examples/technical_report/IsaDof_Manual/document/isadof.cfg b/examples/technical_report/IsaDof_Manual/document/isadof.cfg
new file mode 100644
index 00000000..849fad5e
--- /dev/null
+++ b/examples/technical_report/IsaDof_Manual/document/isadof.cfg
@@ -0,0 +1,2 @@
+Template: scrreprt
+Ontology: technical_report
diff --git a/examples/technical_report/IsaDof_Manual/document/ontologies.tex b/examples/technical_report/IsaDof_Manual/document/ontologies.tex
deleted file mode 100644
index 47fcfd6c..00000000
--- a/examples/technical_report/IsaDof_Manual/document/ontologies.tex
+++ /dev/null
@@ -1,16 +0,0 @@
-%% Copyright (C) 2018 The University of Sheffield
-%%               2018 The University of Paris-Sud
-%%
-%% License:
-%%   This program can be redistributed and/or modified under the terms
-%%   of the LaTeX Project Public License Distributed from CTAN
-%%   archives in directory macros/latex/base/lppl.txt; either
-%%   version 1 of the License, or any later version.
-%%   OR
-%%   The 2-clause BSD-style license.
-%%  
-%%   SPDX-License-Identifier: LPPL-1.0+ OR BSD-2-Clause
-
-%% This file is used for including the LaTeX ontology mappings. 
-\usepackage{DOF-core}
-\usepackage{DOF-technical_report}
diff --git a/examples/technical_report/IsaDof_Manual/document/root.inf b/examples/technical_report/IsaDof_Manual/document/root.inf
deleted file mode 100644
index 234a54b2..00000000
--- a/examples/technical_report/IsaDof_Manual/document/root.inf
+++ /dev/null
@@ -1 +0,0 @@
-scrreprt
diff --git a/examples/technical_report/TR_my_commented_isabelle/ROOT b/examples/technical_report/TR_my_commented_isabelle/ROOT
index e992146a..ce596f76 100644
--- a/examples/technical_report/TR_my_commented_isabelle/ROOT
+++ b/examples/technical_report/TR_my_commented_isabelle/ROOT
@@ -3,9 +3,8 @@ session "TR_mycommentedisabelle" = "Isabelle_DOF" +
   theories
     "MyCommentedIsabelle"
   document_files
-    "root.inf"
+    "isadof.cfg"
     "preamble.tex"
-    "ontologies.tex"
     "prooftree.sty"
     "build"
     "figures/text-element.pdf"
diff --git a/examples/technical_report/TR_my_commented_isabelle/document/isadof.cfg b/examples/technical_report/TR_my_commented_isabelle/document/isadof.cfg
new file mode 100644
index 00000000..849fad5e
--- /dev/null
+++ b/examples/technical_report/TR_my_commented_isabelle/document/isadof.cfg
@@ -0,0 +1,2 @@
+Template: scrreprt
+Ontology: technical_report
diff --git a/examples/technical_report/TR_my_commented_isabelle/document/ontologies.tex b/examples/technical_report/TR_my_commented_isabelle/document/ontologies.tex
deleted file mode 100644
index 47fcfd6c..00000000
--- a/examples/technical_report/TR_my_commented_isabelle/document/ontologies.tex
+++ /dev/null
@@ -1,16 +0,0 @@
-%% Copyright (C) 2018 The University of Sheffield
-%%               2018 The University of Paris-Sud
-%%
-%% License:
-%%   This program can be redistributed and/or modified under the terms
-%%   of the LaTeX Project Public License Distributed from CTAN
-%%   archives in directory macros/latex/base/lppl.txt; either
-%%   version 1 of the License, or any later version.
-%%   OR
-%%   The 2-clause BSD-style license.
-%%  
-%%   SPDX-License-Identifier: LPPL-1.0+ OR BSD-2-Clause
-
-%% This file is used for including the LaTeX ontology mappings. 
-\usepackage{DOF-core}
-\usepackage{DOF-technical_report}
diff --git a/examples/technical_report/TR_my_commented_isabelle/document/root.inf b/examples/technical_report/TR_my_commented_isabelle/document/root.inf
deleted file mode 100644
index 234a54b2..00000000
--- a/examples/technical_report/TR_my_commented_isabelle/document/root.inf
+++ /dev/null
@@ -1 +0,0 @@
-scrreprt