diff --git a/CITATION b/CITATION old mode 100755 new mode 100644 diff --git a/LICENSE b/LICENSE old mode 100755 new mode 100644 diff --git a/README.md b/README.md old mode 100755 new mode 100644 diff --git a/ROOTS b/ROOTS old mode 100755 new mode 100644 diff --git a/examples/CENELEC_50128/ROOTS b/examples/CENELEC_50128/ROOTS old mode 100755 new mode 100644 diff --git a/examples/CENELEC_50128/mini_odo/ROOT b/examples/CENELEC_50128/mini_odo/ROOT old mode 100755 new mode 100644 diff --git a/examples/CENELEC_50128/mini_odo/document/figures/df-numerics-encshaft.png b/examples/CENELEC_50128/mini_odo/document/figures/df-numerics-encshaft.png old mode 100755 new mode 100644 diff --git a/examples/CENELEC_50128/mini_odo/document/figures/odometer.jpeg b/examples/CENELEC_50128/mini_odo/document/figures/odometer.jpeg old mode 100755 new mode 100644 diff --git a/examples/CENELEC_50128/mini_odo/document/figures/three-phase-odo.pdf b/examples/CENELEC_50128/mini_odo/document/figures/three-phase-odo.pdf old mode 100755 new mode 100644 diff --git a/examples/CENELEC_50128/mini_odo/document/figures/wheel-df.png b/examples/CENELEC_50128/mini_odo/document/figures/wheel-df.png old mode 100755 new mode 100644 diff --git a/examples/CENELEC_50128/mini_odo/document/isadof.cfg b/examples/CENELEC_50128/mini_odo/document/isadof.cfg old mode 100755 new mode 100644 diff --git a/examples/CENELEC_50128/mini_odo/document/lstisadof.sty b/examples/CENELEC_50128/mini_odo/document/lstisadof.sty old mode 100755 new mode 100644 diff --git a/examples/CENELEC_50128/mini_odo/document/preamble.tex b/examples/CENELEC_50128/mini_odo/document/preamble.tex old mode 100755 new mode 100644 diff --git a/examples/CENELEC_50128/mini_odo/document/root.bib b/examples/CENELEC_50128/mini_odo/document/root.bib old mode 100755 new mode 100644 diff --git a/examples/CENELEC_50128/mini_odo/document/root.mst b/examples/CENELEC_50128/mini_odo/document/root.mst old mode 100755 new mode 100644 diff --git a/examples/CENELEC_50128/mini_odo/mini_odo.thy b/examples/CENELEC_50128/mini_odo/mini_odo.thy old mode 100755 new mode 100644 diff --git a/examples/README.md b/examples/README.md old mode 100755 new mode 100644 diff --git a/examples/ROOTS b/examples/ROOTS old mode 100755 new mode 100644 diff --git a/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/IsaDofApplications.thy b/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/IsaDofApplications.thy old mode 100755 new mode 100644 diff --git a/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/ROOT b/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/ROOT old mode 100755 new mode 100644 diff --git a/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/figures/Dogfood-II-bgnd1.png b/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/figures/Dogfood-II-bgnd1.png old mode 100755 new mode 100644 diff --git a/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/figures/Dogfood-III-bgnd-text_section.png b/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/figures/Dogfood-III-bgnd-text_section.png old mode 100755 new mode 100644 diff --git a/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/figures/Dogfood-IV-jumpInDocCLass.png b/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/figures/Dogfood-IV-jumpInDocCLass.png old mode 100755 new mode 100644 diff --git a/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/figures/Dogfood-Intro.png b/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/figures/Dogfood-Intro.png old mode 100755 new mode 100644 diff --git a/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/figures/Dogfood-V-attribute.png b/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/figures/Dogfood-V-attribute.png old mode 100755 new mode 100644 diff --git a/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/figures/Dogfood-figures.png b/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/figures/Dogfood-figures.png old mode 100755 new mode 100644 diff --git a/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/figures/InteractiveMathSheet.png b/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/figures/InteractiveMathSheet.png old mode 100755 new mode 100644 diff --git a/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/figures/antiquotations-PIDE.png b/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/figures/antiquotations-PIDE.png old mode 100755 new mode 100644 diff --git a/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/figures/isabelle-architecture.pdf b/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/figures/isabelle-architecture.pdf old mode 100755 new mode 100644 diff --git a/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/figures/isabelle-architecture.svg b/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/figures/isabelle-architecture.svg old mode 100755 new mode 100644 diff --git a/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/figures/srac-as-es-application.png b/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/figures/srac-as-es-application.png old mode 100755 new mode 100644 diff --git a/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/figures/srac-definition.png b/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/figures/srac-definition.png old mode 100755 new mode 100644 diff --git a/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/isadof.cfg b/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/isadof.cfg old mode 100755 new mode 100644 diff --git a/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/lstisadof.sty b/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/lstisadof.sty old mode 100755 new mode 100644 diff --git a/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/preamble.tex b/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/preamble.tex old mode 100755 new mode 100644 diff --git a/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/root.bib b/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/root.bib old mode 100755 new mode 100644 diff --git a/examples/scholarly_paper/ROOTS b/examples/scholarly_paper/ROOTS old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/00_Frontmatter.thy b/examples/technical_report/Isabelle_DOF-Manual/00_Frontmatter.thy old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/01_Introduction.thy b/examples/technical_report/Isabelle_DOF-Manual/01_Introduction.thy old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/02_Background.thy b/examples/technical_report/Isabelle_DOF-Manual/02_Background.thy old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/03_GuidedTour.thy b/examples/technical_report/Isabelle_DOF-Manual/03_GuidedTour.thy old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/04_RefMan.thy b/examples/technical_report/Isabelle_DOF-Manual/04_RefMan.thy old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/05_Implementation.thy b/examples/technical_report/Isabelle_DOF-Manual/05_Implementation.thy old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/Isabelle_DOF-Manual.thy b/examples/technical_report/Isabelle_DOF-Manual/Isabelle_DOF-Manual.thy old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/ROOT b/examples/technical_report/Isabelle_DOF-Manual/ROOT old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/document/figures/Dogfood-II-bgnd1.png b/examples/technical_report/Isabelle_DOF-Manual/document/figures/Dogfood-II-bgnd1.png old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/document/figures/Dogfood-III-bgnd-text_section.png b/examples/technical_report/Isabelle_DOF-Manual/document/figures/Dogfood-III-bgnd-text_section.png old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/document/figures/Dogfood-IV-jumpInDocCLass.png b/examples/technical_report/Isabelle_DOF-Manual/document/figures/Dogfood-IV-jumpInDocCLass.png old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/document/figures/Dogfood-Intro.png b/examples/technical_report/Isabelle_DOF-Manual/document/figures/Dogfood-Intro.png old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/document/figures/Dogfood-V-attribute.png b/examples/technical_report/Isabelle_DOF-Manual/document/figures/Dogfood-V-attribute.png old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/document/figures/Dogfood-figures.png b/examples/technical_report/Isabelle_DOF-Manual/document/figures/Dogfood-figures.png old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/document/figures/Isabelle_DOF-logo.pdf b/examples/technical_report/Isabelle_DOF-Manual/document/figures/Isabelle_DOF-logo.pdf old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/document/figures/MyCommentedIsabelle.png b/examples/technical_report/Isabelle_DOF-Manual/document/figures/MyCommentedIsabelle.png old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/document/figures/antiquotations-PIDE.png b/examples/technical_report/Isabelle_DOF-Manual/document/figures/antiquotations-PIDE.png old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/document/figures/cicm2018-combined.png b/examples/technical_report/Isabelle_DOF-Manual/document/figures/cicm2018-combined.png old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/document/figures/cicm2018-dof.png b/examples/technical_report/Isabelle_DOF-Manual/document/figures/cicm2018-dof.png old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/document/figures/cicm2018-pdf.png b/examples/technical_report/Isabelle_DOF-Manual/document/figures/cicm2018-pdf.png old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/document/figures/definition-use-CSP-pdf.png b/examples/technical_report/Isabelle_DOF-Manual/document/figures/definition-use-CSP-pdf.png old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/document/figures/document-hierarchy.pdf b/examples/technical_report/Isabelle_DOF-Manual/document/figures/document-hierarchy.pdf old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/document/figures/document-hierarchy.svg b/examples/technical_report/Isabelle_DOF-Manual/document/figures/document-hierarchy.svg old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/document/figures/header_CSP_pdf.png b/examples/technical_report/Isabelle_DOF-Manual/document/figures/header_CSP_pdf.png old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/document/figures/isabelle-architecture.pdf b/examples/technical_report/Isabelle_DOF-Manual/document/figures/isabelle-architecture.pdf old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/document/figures/isabelle-architecture.svg b/examples/technical_report/Isabelle_DOF-Manual/document/figures/isabelle-architecture.svg old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/document/figures/isadof.png b/examples/technical_report/Isabelle_DOF-Manual/document/figures/isadof.png old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/document/figures/srac-as-es-application.png b/examples/technical_report/Isabelle_DOF-Manual/document/figures/srac-as-es-application.png old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/document/figures/srac-definition.png b/examples/technical_report/Isabelle_DOF-Manual/document/figures/srac-definition.png old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/document/isadof.cfg b/examples/technical_report/Isabelle_DOF-Manual/document/isadof.cfg old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/document/lstisadof-manual.sty b/examples/technical_report/Isabelle_DOF-Manual/document/lstisadof-manual.sty old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/document/preamble.tex b/examples/technical_report/Isabelle_DOF-Manual/document/preamble.tex old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/document/root.bib b/examples/technical_report/Isabelle_DOF-Manual/document/root.bib old mode 100755 new mode 100644 diff --git a/examples/technical_report/Isabelle_DOF-Manual/document/root.mst b/examples/technical_report/Isabelle_DOF-Manual/document/root.mst old mode 100755 new mode 100644 diff --git a/examples/technical_report/ROOTS b/examples/technical_report/ROOTS old mode 100755 new mode 100644 diff --git a/examples/technical_report/TR_my_commented_isabelle/ROOT b/examples/technical_report/TR_my_commented_isabelle/ROOT old mode 100755 new mode 100644 diff --git a/examples/technical_report/TR_my_commented_isabelle/TR_MyCommentedIsabelle.thy b/examples/technical_report/TR_my_commented_isabelle/TR_MyCommentedIsabelle.thy old mode 100755 new mode 100644 diff --git a/examples/technical_report/TR_my_commented_isabelle/document/figures/document-model.pdf b/examples/technical_report/TR_my_commented_isabelle/document/figures/document-model.pdf old mode 100755 new mode 100644 diff --git a/examples/technical_report/TR_my_commented_isabelle/document/figures/isabelle-architecture.pdf b/examples/technical_report/TR_my_commented_isabelle/document/figures/isabelle-architecture.pdf old mode 100755 new mode 100644 diff --git a/examples/technical_report/TR_my_commented_isabelle/document/figures/markup-demo.png b/examples/technical_report/TR_my_commented_isabelle/document/figures/markup-demo.png old mode 100755 new mode 100644 diff --git a/examples/technical_report/TR_my_commented_isabelle/document/figures/pure-inferences-I.pdf b/examples/technical_report/TR_my_commented_isabelle/document/figures/pure-inferences-I.pdf old mode 100755 new mode 100644 diff --git a/examples/technical_report/TR_my_commented_isabelle/document/figures/pure-inferences-II.pdf b/examples/technical_report/TR_my_commented_isabelle/document/figures/pure-inferences-II.pdf old mode 100755 new mode 100644 diff --git a/examples/technical_report/TR_my_commented_isabelle/document/figures/text-element.pdf b/examples/technical_report/TR_my_commented_isabelle/document/figures/text-element.pdf old mode 100755 new mode 100644 diff --git a/examples/technical_report/TR_my_commented_isabelle/document/isadof.cfg b/examples/technical_report/TR_my_commented_isabelle/document/isadof.cfg old mode 100755 new mode 100644 diff --git a/examples/technical_report/TR_my_commented_isabelle/document/preamble.tex b/examples/technical_report/TR_my_commented_isabelle/document/preamble.tex old mode 100755 new mode 100644 diff --git a/examples/technical_report/TR_my_commented_isabelle/document/prooftree.sty b/examples/technical_report/TR_my_commented_isabelle/document/prooftree.sty old mode 100755 new mode 100644 diff --git a/examples/technical_report/TR_my_commented_isabelle/document/root.bib b/examples/technical_report/TR_my_commented_isabelle/document/root.bib old mode 100755 new mode 100644 diff --git a/src/tests/AssnsLemmaThmEtc.thy b/src/tests/AssnsLemmaThmEtc.thy old mode 100755 new mode 100644 diff --git a/src/tests/Attributes.thy b/src/tests/Attributes.thy old mode 100755 new mode 100644 diff --git a/src/tests/Concept_Example.thy b/src/tests/Concept_Example.thy old mode 100755 new mode 100644 diff --git a/src/tests/Concept_Example_Low_Level_Invariant.thy b/src/tests/Concept_Example_Low_Level_Invariant.thy old mode 100755 new mode 100644 diff --git a/src/tests/ROOT b/src/tests/ROOT old mode 100755 new mode 100644 diff --git a/src/tests/TermAntiquotations.thy b/src/tests/TermAntiquotations.thy old mode 100755 new mode 100644 diff --git a/src/tests/figures/A.png b/src/tests/figures/A.png old mode 100755 new mode 100644 diff --git a/src/tests/figures/AnB.odp b/src/tests/figures/AnB.odp old mode 100755 new mode 100644 diff --git a/src/tests/figures/B.png b/src/tests/figures/B.png old mode 100755 new mode 100644