diff --git a/bin/codeutil/fix_includes.sh b/bin/codeutil/fix_includes.sh
deleted file mode 100755
index 6ab3cc5216a2547a9d6aa89c2431ff850f84483d..0000000000000000000000000000000000000000
--- a/bin/codeutil/fix_includes.sh
+++ /dev/null
@@ -1,384 +0,0 @@
-#! /bin/bash
-
-if [ $# -eq 0 ]
- then
- echo "No arguments supplied."
- echo "Usage: bash ./fix_includes.sh file1 [file2 ...]"
-fi
-
-for TMP in $@; do
- echo "File: $TMP"
- sed -i \
-"
-s%dumux/implicit/common/implicitassembler.hh%dumux/implicit/assembler.hh%g;
-s%dumux/implicit/common/implicitlocaljacobian.hh%dumux/implicit/localjacobian.hh%g;
-s%dumux/implicit/common/implicitlocalresidual.hh%dumux/implicit/localresidual.hh%g;
-s%dumux/implicit/common/implicitmodel.hh%dumux/implicit/model.hh%g;
-s%dumux/implicit/common/implicitproblem.hh%dumux/implicit/problem.hh%g;
-s%dumux/implicit/common/implicitproperties.hh%dumux/implicit/properties.hh%g;
-s%dumux/implicit/common/implicitpropertydefaults.hh%dumux/implicit/propertydefaults.hh%g;
-s%dumux/implicit/common/implicitvolumevariables.hh%dumux/implicit/volumevariables.hh%g;
-s%dumux/implicit/common/implicitdarcyfluxvariables.hh%dumux/porousmediumflow/implicit/darcyfluxvariables.hh%g;
-s%dumux/implicit/common/implicitforchheimerfluxvariables.hh%dumux/porousmediumflow/implicit/forchheimerfluxvariables.hh%g;
-s%dumux/implicit/common/implicitporousmediaproblem.hh%dumux/porousmediumflow/implicit/problem.hh%g;
-s%dumux/implicit/common/implicitvelocityoutput.hh%dumux/porousmediumflow/implicit/velocityoutput.hh%g;
-s%dumux/implicit/box/boxassembler.hh%dumux/implicit/box/assembler.hh%g;
-s%dumux/implicit/box/boxelementboundarytypes.hh%dumux/implicit/box/elementboundarytypes.hh%g;
-s%dumux/implicit/box/boxelementvolumevariables.hh%dumux/implicit/box/elementvolumevariables.hh%g;
-s%dumux/implicit/box/boxfvelementgeometry.hh%dumux/implicit/box/fvelementgeometry.hh%g;
-s%dumux/implicit/box/boxlocalresidual.hh%dumux/implicit/box/localresidual.hh%g;
-s%dumux/implicit/box/boxproperties.hh%dumux/implicit/box/properties.hh%g;
-s%dumux/implicit/box/boxpropertydefaults.hh%dumux/implicit/box/propertydefaults.hh%g;
-s%dumux/implicit/cellcentered/ccassembler.hh%dumux/implicit/cellcentered/assembler.hh%g;
-s%dumux/implicit/cellcentered/ccelementboundarytypes.hh%dumux/implicit/cellcentered/elementboundarytypes.hh%g;
-s%dumux/implicit/cellcentered/ccelementvolumevariables.hh%dumux/implicit/cellcentered/elementvolumevariables.hh%g;
-s%dumux/implicit/cellcentered/ccfvelementgeometry.hh%dumux/implicit/cellcentered/fvelementgeometry.hh%g;
-s%dumux/implicit/cellcentered/cclocalresidual.hh%dumux/implicit/cellcentered/localresidual.hh%g;
-s%dumux/implicit/cellcentered/ccproperties.hh%dumux/implicit/cellcentered/properties.hh%g;
-s%dumux/implicit/cellcentered/ccpropertydefaults.hh%dumux/implicit/cellcentered/propertydefaults.hh%g;
-s%dumux/implicit/cornerpoint/cpelementvolumevariables.hh%dumux/implicit/cornerpoint/elementvolumevariables.hh%g;
-s%dumux/implicit/cornerpoint/cpfvelementgeometry.hh%dumux/implicit/cornerpoint/fvelementgeometry.hh%g;
-s%dumux/implicit/cornerpoint/cpdarcyfluxvariables.hh%dumux/porousmediumflow/implicit/cpdarcyfluxvariables.hh%g;
-s%dumux/implicit/nonisothermal/nifluxvariables.hh%dumux/porousmediumflow/nonisothermal/implicit/fluxvariables.hh%g;
-s%dumux/implicit/nonisothermal/niindices.hh%dumux/porousmediumflow/nonisothermal/implicit/indices.hh%g;
-s%dumux/implicit/nonisothermal/nilocalresidual.hh%dumux/porousmediumflow/nonisothermal/implicit/localresidual.hh%g;
-s%dumux/implicit/nonisothermal/nimodel.hh%dumux/porousmediumflow/nonisothermal/implicit/model.hh%g;
-s%dumux/implicit/nonisothermal/niproperties.hh%dumux/porousmediumflow/nonisothermal/implicit/properties.hh%g;
-s%dumux/implicit/nonisothermal/nipropertydefaults.hh%dumux/porousmediumflow/nonisothermal/implicit/propertydefaults.hh%g;
-s%dumux/implicit/nonisothermal/nivolumevariables.hh%dumux/porousmediumflow/nonisothermal/implicit/volumevariables.hh%g;
-s%dumux/implicit/1p/1pindices.hh%dumux/porousmediumflow/1p/implicit/indices.hh%g;
-s%dumux/implicit/1p/1plocalresidual.hh%dumux/porousmediumflow/1p/implicit/localresidual.hh%g;
-s%dumux/implicit/1p/1pmodel.hh%dumux/porousmediumflow/1p/implicit/model.hh%g;
-s%dumux/implicit/1p/1pproperties.hh%dumux/porousmediumflow/1p/implicit/properties.hh%g;
-s%dumux/implicit/1p/1ppropertydefaults.hh%dumux/porousmediumflow/1p/implicit/propertydefaults.hh%g;
-s%dumux/implicit/1p/1pvolumevariables.hh%dumux/porousmediumflow/1p/implicit/volumevariables.hh%g;
-s%dumux/implicit/2p/2pgridadaptindicator.hh%dumux/porousmediumflow/2p/implicit/gridadaptindicator.hh%g;
-s%dumux/implicit/2p/2pindices.hh%dumux/porousmediumflow/2p/implicit/indices.hh%g;
-s%dumux/implicit/2p/2plocalresidual.hh%dumux/porousmediumflow/2p/implicit/localresidual.hh%g;
-s%dumux/implicit/2p/2pmodel.hh%dumux/porousmediumflow/2p/implicit/model.hh%g;
-s%dumux/implicit/2p/2pproperties.hh%dumux/porousmediumflow/2p/implicit/properties.hh%g;
-s%dumux/implicit/2p/2ppropertydefaults.hh%dumux/porousmediumflow/2p/implicit/propertydefaults.hh%g;
-s%dumux/implicit/2p/2pvolumevariables.hh%dumux/porousmediumflow/2p/implicit/volumevariables.hh%g;
-s%dumux/implicit/3p/3pindices.hh%dumux/porousmediumflow/3p/implicit/indices.hh%g;
-s%dumux/implicit/3p/3plocalresidual.hh%dumux/porousmediumflow/3p/implicit/localresidual.hh%g;
-s%dumux/implicit/3p/3pmodel.hh%dumux/porousmediumflow/3p/implicit/model.hh%g;
-s%dumux/implicit/3p/3pproperties.hh%dumux/porousmediumflow/3p/implicit/properties.hh%g;
-s%dumux/implicit/3p/3ppropertydefaults.hh%dumux/porousmediumflow/3p/implicit/propertydefaults.hh%g;
-s%dumux/implicit/3p/3pvolumevariables.hh%dumux/porousmediumflow/3p/implicit/volumevariables.hh%g;
-s%dumux/implicit/1p2c/1p2cfluxvariables.hh%dumux/porousmediumflow/1p2c/implicit/fluxvariables.hh%g;
-s%dumux/implicit/1p2c/1p2cindices.hh%dumux/porousmediumflow/1p2c/implicit/indices.hh%g;
-s%dumux/implicit/1p2c/1p2clocalresidual.hh%dumux/porousmediumflow/1p2c/implicit/localresidual.hh%g;
-s%dumux/implicit/1p2c/1p2cmodel.hh%dumux/porousmediumflow/1p2c/implicit/model.hh%g;
-s%dumux/implicit/1p2c/1p2cproperties.hh%dumux/porousmediumflow/1p2c/implicit/properties.hh%g;
-s%dumux/implicit/1p2c/1p2cpropertydefaults.hh%dumux/porousmediumflow/1p2c/implicit/propertydefaults.hh%g;
-s%dumux/implicit/1p2c/1p2cvolumevariables.hh%dumux/porousmediumflow/1p2c/implicit/volumevariables.hh%g;
-s%dumux/implicit/2p2c/2p2cfluxvariables.hh%dumux/porousmediumflow/2p2c/implicit/fluxvariables.hh%g;
-s%dumux/implicit/2p2c/2p2cindices.hh%dumux/porousmediumflow/2p2c/implicit/indices.hh%g;
-s%dumux/implicit/2p2c/2p2clocalresidual.hh%dumux/porousmediumflow/2p2c/implicit/localresidual.hh%g;
-s%dumux/implicit/2p2c/2p2cmodel.hh%dumux/porousmediumflow/2p2c/implicit/model.hh%g;
-s%dumux/implicit/2p2c/2p2cnewtoncontroller.hh%dumux/porousmediumflow/2p2c/implicit/newtoncontroller.hh%g;
-s%dumux/implicit/2p2c/2p2cproperties.hh%dumux/porousmediumflow/2p2c/implicit/properties.hh%g;
-s%dumux/implicit/2p2c/2p2cpropertydefaults.hh%dumux/porousmediumflow/2p2c/implicit/propertydefaults.hh%g;
-s%dumux/implicit/2p2c/2p2cvolumevariables.hh%dumux/porousmediumflow/2p2c/implicit/volumevariables.hh%g;
-s%dumux/implicit/3p3c/3p3cfluxvariables.hh%dumux/porousmediumflow/3p3c/implicit/fluxvariables.hh%g;
-s%dumux/implicit/3p3c/3p3cindices.hh%dumux/porousmediumflow/3p3c/implicit/indices.hh%g;
-s%dumux/implicit/3p3c/3p3clocalresidual.hh%dumux/porousmediumflow/3p3c/implicit/localresidual.hh%g;
-s%dumux/implicit/3p3c/3p3cmodel.hh%dumux/porousmediumflow/3p3c/implicit/model.hh%g;
-s%dumux/implicit/3p3c/3p3cnewtoncontroller.hh%dumux/porousmediumflow/3p3c/implicit/newtoncontroller.hh%g;
-s%dumux/implicit/3p3c/3p3cproperties.hh%dumux/porousmediumflow/3p3c/implicit/properties.hh%g;
-s%dumux/implicit/3p3c/3p3cpropertydefaults.hh%dumux/porousmediumflow/3p3c/implicit/propertydefaults.hh%g;
-s%dumux/implicit/3p3c/3p3cvolumevariables.hh%dumux/porousmediumflow/3p3c/implicit/volumevariables.hh%g;
-s%dumux/implicit/2pnc/2pncfluxvariables.hh%dumux/porousmediumflow/2pnc/implicit/fluxvariables.hh%g;
-s%dumux/implicit/2pnc/2pncindices.hh%dumux/porousmediumflow/2pnc/implicit/indices.hh%g;
-s%dumux/implicit/2pnc/2pnclocalresidual.hh%dumux/porousmediumflow/2pnc/implicit/localresidual.hh%g;
-s%dumux/implicit/2pnc/2pncmodel.hh%dumux/porousmediumflow/2pnc/implicit/model.hh%g;
-s%dumux/implicit/2pnc/2pncnewtoncontroller.hh%dumux/porousmediumflow/2pnc/implicit/newtoncontroller.hh%g;
-s%dumux/implicit/2pnc/2pncproperties.hh%dumux/porousmediumflow/2pnc/implicit/properties.hh%g;
-s%dumux/implicit/2pnc/2pncpropertydefaults.hh%dumux/porousmediumflow/2pnc/implicit/propertydefaults.hh%g;
-s%dumux/implicit/2pnc/2pncvolumevariables.hh%dumux/porousmediumflow/2pnc/implicit/volumevariables.hh%g;
-s%dumux/implicit/2pncmin/2pncminfluxvariables.hh%dumux/porousmediumflow/2pncmin/implicit/fluxvariables.hh%g;
-s%dumux/implicit/2pncmin/2pncminindices.hh%dumux/porousmediumflow/2pncmin/implicit/indices.hh%g;
-s%dumux/implicit/2pncmin/2pncminlocalresidual.hh%dumux/porousmediumflow/2pncmin/implicit/localresidual.hh%g;
-s%dumux/implicit/2pncmin/2pncminmodel.hh%dumux/porousmediumflow/2pncmin/implicit/model.hh%g;
-s%dumux/implicit/2pncmin/2pncminproperties.hh%dumux/porousmediumflow/2pncmin/implicit/properties.hh%g;
-s%dumux/implicit/2pncmin/2pncminpropertydefaults.hh%dumux/porousmediumflow/2pncmin/implicit/propertydefaults.hh%g;
-s%dumux/implicit/2pncmin/2pncminvolumevariables.hh%dumux/porousmediumflow/2pncmin/implicit/volumevariables.hh%g;
-s%dumux/implicit/2pdfm/2pdfmfluxvariables.hh%dumux/porousmediumflow/2pdfm/implicit/fluxvariables.hh%g;
-s%dumux/implicit/2pdfm/2pdfmindices.hh%dumux/porousmediumflow/2pdfm/implicit/indices.hh%g;
-s%dumux/implicit/2pdfm/2pdfmlocalresidual.hh%dumux/porousmediumflow/2pdfm/implicit/localresidual.hh%g;
-s%dumux/implicit/2pdfm/2pdfmmodel.hh%dumux/porousmediumflow/2pdfm/implicit/model.hh%g;
-s%dumux/implicit/2pdfm/2pdfmproblem.hh%dumux/porousmediumflow/2pdfm/implicit/problem.hh%g;
-s%dumux/implicit/2pdfm/2pdfmproperties.hh%dumux/porousmediumflow/2pdfm/implicit/properties.hh%g;
-s%dumux/implicit/2pdfm/2pdfmpropertydefaults.hh%dumux/porousmediumflow/2pdfm/implicit/propertydefaults.hh%g;
-s%dumux/implicit/2pdfm/2pdfmvolumevariables.hh%dumux/porousmediumflow/2pdfm/implicit/volumevariables.hh%g;
-s%dumux/implicit/2pminc/2pmincfluxvariables.hh%dumux/porousmediumflow/2pminc/implicit/fluxvariables.hh%g;
-s%dumux/implicit/2pminc/2pmincindices.hh%dumux/porousmediumflow/2pminc/implicit/indices.hh%g;
-s%dumux/implicit/2pminc/2pminclocalresidual.hh%dumux/porousmediumflow/2pminc/implicit/localresidual.hh%g;
-s%dumux/implicit/2pminc/2pmincmodel.hh%dumux/porousmediumflow/2pminc/implicit/model.hh%g;
-s%dumux/implicit/2pminc/2pmincproperties.hh%dumux/porousmediumflow/2pminc/implicit/properties.hh%g;
-s%dumux/implicit/2pminc/2pmincpropertydefaults.hh%dumux/porousmediumflow/2pminc/implicit/propertydefaults.hh%g;
-s%dumux/implicit/2pminc/2pmincvolumevariables.hh%dumux/porousmediumflow/2pminc/implicit/volumevariables.hh%g;
-s%dumux/implicit/co2/co2model.hh%dumux/porousmediumflow/co2/implicit/model.hh%g;
-s%dumux/implicit/co2/co2volumevariables.hh%dumux/porousmediumflow/co2/implicit/volumevariables.hh%g;
-s%dumux/implicit/richards/richardsfluxvariables.hh%dumux/porousmediumflow/richards/implicit/fluxvariables.hh%g;
-s%dumux/implicit/richards/richardsindices.hh%dumux/porousmediumflow/richards/implicit/indices.hh%g;
-s%dumux/implicit/richards/richardslocalresidual.hh%dumux/porousmediumflow/richards/implicit/localresidual.hh%g;
-s%dumux/implicit/richards/richardsmodel.hh%dumux/porousmediumflow/richards/implicit/model.hh%g;
-s%dumux/implicit/richards/richardsnewtoncontroller.hh%dumux/porousmediumflow/richards/implicit/newtoncontroller.hh%g;
-s%dumux/implicit/richards/richardsproblem.hh%dumux/porousmediumflow/richards/implicit/problem.hh%g;
-s%dumux/implicit/richards/richardsproperties.hh%dumux/porousmediumflow/richards/implicit/properties.hh%g;
-s%dumux/implicit/richards/richardspropertydefaults.hh%dumux/porousmediumflow/richards/implicit/propertydefaults.hh%g;
-s%dumux/implicit/richards/richardsvolumevariables.hh%dumux/porousmediumflow/richards/implicit/volumevariables.hh%g;
-s%dumux/implicit/mpnc/mpncfluxvariables.hh%dumux/porousmediumflow/mpnc/implicit/fluxvariables.hh%g;
-s%dumux/implicit/mpnc/mpncindices.hh%dumux/porousmediumflow/mpnc/implicit/indices.hh%g;
-s%dumux/implicit/mpnc/mpnclocalresidual.hh%dumux/porousmediumflow/mpnc/implicit/localresidual.hh%g;
-s%dumux/implicit/mpnc/mpncmodel.hh%dumux/porousmediumflow/mpnc/implicit/model.hh%g;
-s%dumux/implicit/mpnc/mpncmodelkinetic.hh%dumux/porousmediumflow/mpnc/implicit/modelkinetic.hh%g;
-s%dumux/implicit/mpnc/mpncnewtoncontroller.hh%dumux/porousmediumflow/mpnc/implicit/newtoncontroller.hh%g;
-s%dumux/implicit/mpnc/mpncproperties.hh%dumux/porousmediumflow/mpnc/implicit/properties.hh%g;
-s%dumux/implicit/mpnc/mpncpropertieskinetic.hh%dumux/porousmediumflow/mpnc/implicit/propertieskinetic.hh%g;
-s%dumux/implicit/mpnc/mpncpropertydefaults.hh%dumux/porousmediumflow/mpnc/implicit/propertydefaults.hh%g;
-s%dumux/implicit/mpnc/mpncpropertydefaultskinetic.hh%dumux/porousmediumflow/mpnc/implicit/propertydefaultskinetic.hh%g;
-s%dumux/implicit/mpnc/mpncvolumevariables%dumux/porousmediumflow/mpnc/implicit/volumevariables%g;
-s%dumux/implicit/mpnc/mpncvtkwriter%dumux/porousmediumflow/mpnc/implicit/vtkwriter%g;
-s%dumux/implicit/mpnc/velomodelnewtoncontroller.hh%dumux/porousmediumflow/mpnc/implicit/velomodelnewtoncontroller.hh%g;
-s%dumux/implicit/mpnc/diffusion%dumux/porousmediumflow/mpnc/implicit/diffusion%g;
-s%dumux/implicit/mpnc/energy/mpncfluxvariablesenergy%dumux/porousmediumflow/mpnc/implicit/energy/fluxvariables%g;
-s%dumux/implicit/mpnc/energy/mpncindicesenergy%dumux/porousmediumflow/mpnc/implicit/energy/indices%g;
-s%dumux/implicit/mpnc/energy/mpnclocalresidualenergy%dumux/porousmediumflow/mpnc/implicit/energy/localresidual%g;
-s%dumux/implicit/mpnc/energy/mpncvolumevariablesenergy%dumux/porousmediumflow/mpnc/implicit/energy/volumevariables%g;
-s%dumux/implicit/mpnc/energy/mpncvtkwriterenergy%dumux/porousmediumflow/mpnc/implicit/energy/vtkwriter%g;
-s%dumux/implicit/mpnc/mass/mpncindicesmass%dumux/porousmediumflow/mpnc/implicit/mass/indices%g;
-s%dumux/implicit/mpnc/mass/mpnclocalresidualmass%dumux/porousmediumflow/mpnc/implicit/mass/localresidual%g;
-s%dumux/implicit/mpnc/mass/mpncvolumevariablesmass%dumux/porousmediumflow/mpnc/implicit/mass/volumevariables%g;
-s%dumux/implicit/mpnc/mass/mpncvtkwritermass%dumux/porousmediumflow/mpnc/implicit/mass/vtkwriter%g;
-s%dumux/freeflow/stokes/stokesfluxvariables.hh%dumux/freeflow/stokes/fluxvariables.hh%g;
-s%dumux/freeflow/stokes/stokesindices.hh%dumux/freeflow/stokes/indices.hh%g;
-s%dumux/freeflow/stokes/stokeslocaljacobian.hh%dumux/freeflow/stokes/localjacobian.hh%g;
-s%dumux/freeflow/stokes/stokeslocalresidual.hh%dumux/freeflow/stokes/localresidual.hh%g;
-s%dumux/freeflow/stokes/stokesmodel.hh%dumux/freeflow/stokes/model.hh%g;
-s%dumux/freeflow/stokes/stokesnewtoncontroller.hh%dumux/freeflow/stokes/newtoncontroller.hh%g;
-s%dumux/freeflow/stokes/stokesproblem.hh%dumux/freeflow/stokes/problem.hh%g;
-s%dumux/freeflow/stokes/stokesproperties.hh%dumux/freeflow/stokes/properties.hh%g;
-s%dumux/freeflow/stokes/stokespropertydefaults.hh%dumux/freeflow/stokes/propertydefaults.hh%g;
-s%dumux/freeflow/stokes/stokesvolumevariables.hh%dumux/freeflow/stokes/volumevariables.hh%g;
-s%dumux/freeflow/stokesnc/stokesncfluxvariables.hh%dumux/freeflow/stokesnc/fluxvariables.hh%g;
-s%dumux/freeflow/stokesnc/stokesncindices.hh%dumux/freeflow/stokesnc/indices.hh%g;
-s%dumux/freeflow/stokesnc/stokesnclocalresidual.hh%dumux/freeflow/stokesnc/localresidual.hh%g;
-s%dumux/freeflow/stokesnc/stokesncmodel.hh%dumux/freeflow/stokesnc/model.hh%g;
-s%dumux/freeflow/stokesnc/stokesncproperties.hh%dumux/freeflow/stokesnc/properties.hh%g;
-s%dumux/freeflow/stokesnc/stokesncpropertydefaults.hh%dumux/freeflow/stokesnc/propertydefaults.hh%g;
-s%dumux/freeflow/stokesnc/stokesncvolumevariables.hh%dumux/freeflow/stokesnc/volumevariables.hh%g;
-s%dumux/freeflow/stokesncni/stokesncnifluxvariables.hh%dumux/freeflow/stokesncni/fluxvariables.hh%g;
-s%dumux/freeflow/stokesncni/stokesncniindices.hh%dumux/freeflow/stokesncni/indices.hh%g;
-s%dumux/freeflow/stokesncni/stokesncnilocalresidual.hh%dumux/freeflow/stokesncni/localresidual.hh%g;
-s%dumux/freeflow/stokesncni/stokesncnimodel.hh%dumux/freeflow/stokesncni/model.hh%g;
-s%dumux/freeflow/stokesncni/stokesncniproperties.hh%dumux/freeflow/stokesncni/properties.hh%g;
-s%dumux/freeflow/stokesncni/stokesncnipropertydefaults.hh%dumux/freeflow/stokesncni/propertydefaults.hh%g;
-s%dumux/freeflow/stokesncni/stokesncnivolumevariables.hh%dumux/freeflow/stokesncni/volumevariables.hh%g;
-s%dumux/freeflow/zeroeq/zeroeqfluxvariables.hh%dumux/freeflow/zeroeq/fluxvariables.hh%g;
-s%dumux/freeflow/zeroeq/zeroeqindices.hh%dumux/freeflow/zeroeq/indices.hh%g;
-s%dumux/freeflow/zeroeq/zeroeqmodel.hh%dumux/freeflow/zeroeq/model.hh%g;
-s%dumux/freeflow/zeroeq/zeroeqproblem.hh%dumux/freeflow/zeroeq/problem.hh%g;
-s%dumux/freeflow/zeroeq/zeroeqproperties.hh%dumux/freeflow/zeroeq/properties.hh%g;
-s%dumux/freeflow/zeroeq/zeroeqpropertydefaults.hh%dumux/freeflow/zeroeq/propertydefaults.hh%g;
-s%dumux/freeflow/zeroeqnc/zeroeqncfluxvariables.hh%dumux/freeflow/zeroeqnc/fluxvariables.hh%g;
-s%dumux/freeflow/zeroeqnc/zeroeqncindices.hh%dumux/freeflow/zeroeqnc/indices.hh%g;
-s%dumux/freeflow/zeroeqnc/zeroeqncmodel.hh%dumux/freeflow/zeroeqnc/model.hh%g;
-s%dumux/freeflow/zeroeqnc/zeroeqncproperties.hh%dumux/freeflow/zeroeqnc/properties.hh%g;
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-s%dumux/decoupled/2p/diffusion/fvmpfa/lmethod/fvmpfal3dtransmissibilitycalculator.hh%dumux/porousmediumflow/2p/sequential/diffusion/mpfa/lmethod/3dtransmissibilitycalculator.hh%g;
-s%dumux/decoupled/2p/diffusion/fvmpfa/lmethod/fvmpfal3dvelocity2p%dumux/porousmediumflow/2p/sequential/diffusion/mpfa/lmethod/3dvelocity%g;
-s%dumux/decoupled/2p/diffusion/fvmpfa/omethod/fvmpfao2dpressure2p.hh%dumux/porousmediumflow/2p/sequential/diffusion/mpfa/omethod/2dpressure.hh%g;
-s%dumux/decoupled/2p/diffusion/fvmpfa/omethod/fvmpfao2dpressureproperties2p.hh%dumux/porousmediumflow/2p/sequential/diffusion/mpfa/omethod/2dpressureproperties.hh%g;
-s%dumux/decoupled/2p/diffusion/fvmpfa/omethod/fvmpfao2dpressurevelocity2p.hh%dumux/porousmediumflow/2p/sequential/diffusion/mpfa/omethod/2dpressurevelocity.hh%g;
-s%dumux/decoupled/2p/diffusion/fvmpfa/omethod/fvmpfao2dvelocity2p.hh%dumux/porousmediumflow/2p/sequential/diffusion/mpfa/omethod/2dvelocity.hh%g;
-s%dumux/decoupled/2p/diffusion/mimetic/croperator2p%dumux/porousmediumflow/2p/sequential/diffusion/mimetic/croperator%g;
-s%dumux/decoupled/2p/diffusion/mimetic/localstiffness.hh%dumux/porousmediumflow/2p/sequential/diffusion/mimetic/localstiffness.hh%g;
-s%dumux/decoupled/2p/diffusion/mimetic/mimetic2p%dumux/porousmediumflow/2p/sequential/diffusion/mimetic/mimetic%g;
-s%dumux/decoupled/2p/diffusion/mimetic/mimeticoperator2p%dumux/porousmediumflow/2p/sequential/diffusion/mimetic/operator%g;
-s%dumux/decoupled/2p/diffusion/mimetic/mimeticpressure2p%dumux/porousmediumflow/2p/sequential/diffusion/mimetic/pressure%g;
-s%dumux/decoupled/2p/diffusion/mimetic/mimeticpressureproperties2p%dumux/porousmediumflow/2p/sequential/diffusion/mimetic/pressureproperties%g;
-s%dumux/decoupled/2p/impes/gridadaptionindicator2p.hh%dumux/porousmediumflow/2p/sequential/impes/gridadaptionindicator.hh%g;
-s%dumux/decoupled/2p/impes/gridadaptionindicator2plocalflux.hh%dumux/porousmediumflow/2p/sequential/impes/gridadaptionindicatorlocalflux.hh%g;
-s%dumux/decoupled/2p/impes/gridadaptionindicator2plocal.hh%dumux/porousmediumflow/2p/sequential/impes/gridadaptionindicatorlocal.hh%g;
-s%dumux/decoupled/2p/impes/impesproblem2p.hh%dumux/porousmediumflow/2p/sequential/impes/problem.hh%g;
-s%dumux/decoupled/2p/impes/impesproperties2padaptive.hh%dumux/porousmediumflow/2p/sequential/impes/propertiesadaptive.hh%g;
-s%dumux/decoupled/2p/impes/impesproperties2p.hh%dumux/porousmediumflow/2p/sequential/impes/properties.hh%g;
-s%dumux/decoupled/2p/transport/transportproblem2p.hh%dumux/porousmediumflow/2p/sequential/transport/problem.hh%g;
-s%dumux/decoupled/2p/transport/transportproperties2p.hh%dumux/porousmediumflow/2p/sequential/transport/properties.hh%g;
-s%dumux/decoupled/2p/transport/fv/capillarydiffusion.hh%dumux/porousmediumflow/2p/sequential/transport/cellcentered/capillarydiffusion.hh%g;
-s%dumux/decoupled/2p/transport/fv/convectivepart.hh%dumux/porousmediumflow/2p/sequential/transport/cellcentered/convectivepart.hh%g;
-s%dumux/decoupled/2p/transport/fv/diffusivepart.hh%dumux/porousmediumflow/2p/sequential/transport/cellcentered/diffusivepart.hh%g;
-s%dumux/decoupled/2p/transport/fv/evalcflfluxcoats.hh%dumux/porousmediumflow/2p/sequential/transport/cellcentered/evalcflfluxcoats.hh%g;
-s%dumux/decoupled/2p/transport/fv/evalcflfluxdefault.hh%dumux/porousmediumflow/2p/sequential/transport/cellcentered/evalcflfluxdefault.hh%g;
-s%dumux/decoupled/2p/transport/fv/evalcflflux.hh%dumux/porousmediumflow/2p/sequential/transport/cellcentered/evalcflflux.hh%g;
-s%dumux/decoupled/2p/transport/fv/fvsaturation2p.hh%dumux/porousmediumflow/2p/sequential/transport/cellcentered/saturation.hh%g;
-s%dumux/decoupled/2p/transport/fv/fvtransportproperties2p.hh%dumux/porousmediumflow/2p/sequential/transport/cellcentered/properties.hh%g;
-s%dumux/decoupled/2p/transport/fv/gravitypart.hh%dumux/porousmediumflow/2p/sequential/transport/cellcentered/gravitypart.hh%g;
-" \
-$TMP
-done
diff --git a/bin/moduleutil/extractmodulepart.sh b/bin/moduleutil/extractmodulepart.sh
new file mode 100755
index 0000000000000000000000000000000000000000..0ee074e126266bb3318937c4b7eff1de9227a88c
--- /dev/null
+++ b/bin/moduleutil/extractmodulepart.sh
@@ -0,0 +1,417 @@
+#! /bin/bash
+
+# check if help is needed
+if test "$1" = "--help" || test "$1" = "-help" \
+ || test "$1" = "help" || test "$1" = ""; then
+ echo ""
+ echo "USAGE: $0 MODULE_DIR PATH_1 [PATH_2 ...]"
+ echo ""
+ echo "MODULE_DIR is the folder containing the DUNE module from which you"
+ echo "want to extract. The script has to be called one level above it."
+ echo ""
+ echo "The PATHs need to indicate subfolders of MODULE_DIR. At least one"
+ echo "of them has to contain a source file *.cc of an executable for which"
+ echo "you would like to timber a table in dumux-pub."
+ exit 0
+fi
+
+MODULE_DIR=$1
+# if MODULE_DIR contains a slash as last character, delete it
+MODULE_DIR=$(echo $MODULE_DIR | sed s'/\/$//')
+# check if we are above MODULE_DIR
+if (! [ -d $MODULE_DIR ]); then
+ echo "ERROR: you need to run the script one level above the folder $MODULE_DIR."
+ echo "Run \"$0 --help\" for details."
+ exit 1
+fi
+
+# determine all source files in the paths passed as arguments
+cd $MODULE_DIR
+MODULE_FULL_PATH=$(pwd)
+ALL_SOURCES=""
+ALL_DIRECTORIES=""
+for DIR_PATH in ${*:2}; do
+ STRIPPED_PATH=$(sed 's%.*'"$MODULE_DIR"'/%%g' <(echo "$DIR_PATH"))
+ ALL_DIRECTORIES="$ALL_DIRECTORIES $STRIPPED_PATH"
+ ALL_SOURCES="$ALL_SOURCES $(find $STRIPPED_PATH -name '*.cc' 2>/dev/null)"
+done
+cd ..
+
+# check if sources have been obtained
+CONTRACTED="$(echo "$ALL_SOURCES" | tr -d " \t\n\r")"
+if test "$CONTRACTED" = ""; then
+ echo "ERROR: no source files *.cc found in the directories ${*:2}."
+ echo "Be sure to provide a list of paths as arguments to this script."
+ echo "Run \"$0 --help\" for details."
+ exit 1;
+fi
+
+# try to find the duneproject script
+if hash duneproject 2>/dev/null; then
+ DUNE_PROJECT="duneproject"
+else
+ DUNE_PROJECT=$(find . -name 'duneproject')
+fi
+if test "$DUNE_PROJECT" = ""; then
+ echo "ERROR: Could not find duneproject."
+ echo "Be sure to either have duneproject in your search path"
+ echo "or to run this script from a directory that contains duneproject."
+ exit 1;
+fi
+
+# give explanations
+echo ""
+echo "This script will"
+echo "- extract the following sub-folders of $MODULE_DIR:"
+echo ""
+for DIR_PATH in $ALL_DIRECTORIES; do
+ echo " $DIR_PATH,"
+done
+echo ""
+echo " and all headers in $MODULE_DIR that are required to build the"
+echo " executables from the sources"
+echo ""
+for SOURCE in $ALL_SOURCES; do
+ echo " $SOURCE,"
+done
+echo ""
+echo "- copy the extracted files into a freshly created DUNE module, retaining the"
+echo " directory structure,"
+echo ""
+echo "- update/create all required files like CMakeLists.txt,"
+echo ""
+echo "- store the versions of all used Dune module"
+echo ""
+echo "- and extract their modifications as patches."
+echo ""
+echo "Thus, you receive a fully-working DUNE module containing the subset of"
+echo "$MODULE_DIR that is required to run your application."
+echo ""
+echo "duneproject will be run now. The new module should NOT depend on the"
+echo "module in $MODULE_DIR."
+echo ""
+read -p "Read the above and press [Enter] to proceed..."
+
+# run duneproject
+OLD_LS="$(ls)"
+$DUNE_PROJECT
+NEW_LS="$(ls)"
+
+# determine the new module/directory name
+DIFF_OUTPUT=$(diff <(echo "$OLD_LS" ) <(echo "$NEW_LS"))
+FOUND="0"
+MODULE_NAME=""
+for WORD in $DIFF_OUTPUT; do
+ if test "$FOUND" = "1"; then
+ MODULE_NAME=$WORD
+ fi
+ if test "$WORD" = ">"; then
+ FOUND="1"
+ fi
+done
+if test "$MODULE_NAME" = ""; then
+ echo "ERROR: could not find new module. Aborting."
+ exit 1
+else
+ echo ""
+ echo "$(basename $0): Found new module $MODULE_NAME"
+fi
+
+echo -n "Determining required headers..."
+cd $MODULE_DIR
+
+# initialize lists to hold required headers
+LAST_REQUIRED_HEADERS=""
+REQUIRED_HEADERS="$ALL_SOURCES"
+
+while test "$LAST_REQUIRED_HEADERS" != "$REQUIRED_HEADERS"; do
+ echo -n "."
+ LAST_REQUIRED_HEADERS="$REQUIRED_HEADERS"
+
+ # remove the file that stores all required headers line by line
+ rm -f tmp_header_file
+
+ for HEADER in $REQUIRED_HEADERS; do
+ # if tmp_header_file does not exist, create it
+ if test "$(ls tmp_header_file 2>/dev/null)" = ""; then
+ touch tmp_header_file
+ fi
+
+ # append header name to tmp_header_file
+ echo "$HEADER" >> tmp_header_file
+
+ # obtain the base name and the directory name of the header that is considered
+ HEADER_BASE_NAME=$(basename $HEADER)
+ HEADER_DIR_NAME=$(dirname $HEADER)
+
+ # create a list of all files that are included from the header
+ sed -i 's/#include/#include /' $HEADER
+ INCLUDE_LIST=$(tr -s " " < $HEADER | tr -d '><"' | awk '/#include/{print $2}')
+ sed -i 's/#include /#include/' $HEADER
+
+ # look at each of the included files
+ for INCLUDED_HEADER in $INCLUDE_LIST; do
+ # don't include config.h
+ if test "$INCLUDED_HEADER" = "config.h"; then
+ continue
+ fi
+
+ INCLUDED_BASE_NAME=$(basename $INCLUDED_HEADER)
+ INCLUDED_DIR_NAME=$(dirname $INCLUDED_HEADER)
+
+ # if the header file exists, add it
+ if test "$(ls $INCLUDED_HEADER 2>/dev/null)" = "$INCLUDED_HEADER"; then
+ echo "$INCLUDED_HEADER" >> tmp_header_file
+ continue
+ fi
+
+ # try the header preceded by its path
+ INCLUDED_HEADER_WITH_PATH="${HEADER_DIR_NAME}/${INCLUDED_HEADER}"
+
+ # if the header file actually exists, add it
+ if test "$(ls $INCLUDED_HEADER_WITH_PATH 2>/dev/null)" = "$INCLUDED_HEADER_WITH_PATH"; then
+ # remove "../" from the path
+ cd $(dirname $INCLUDED_HEADER_WITH_PATH)
+ HEADER_FULL_PATH=$(pwd)
+ HEADER_RELATIVE_PATH=${HEADER_FULL_PATH#$MODULE_FULL_PATH}
+ HEADER_RELATIVE_PATH=$(echo $HEADER_RELATIVE_PATH | sed 's/^.//')
+ INCLUDED_HEADER_WITH_PATH="${HEADER_RELATIVE_PATH}/${INCLUDED_BASE_NAME}"
+ cd $MODULE_FULL_PATH
+ echo "$INCLUDED_HEADER_WITH_PATH" >> tmp_header_file
+ fi
+ done
+ done
+
+ # sort the required headers, eliminate copies
+ REQUIRED_HEADERS=$(sort -u tmp_header_file)
+done
+
+# remove the file that stores all required headers line by line
+rm -f tmp_header_file
+
+# provide some output and copy everything to the new module
+echo ""
+echo -n "Number of required headers: "
+echo "$REQUIRED_HEADERS" | wc -w
+for HEADER in $REQUIRED_HEADERS; do
+ echo $HEADER
+ rsync -R $HEADER ../$MODULE_NAME
+done
+for DIR_PATH in $ALL_DIRECTORIES; do
+ rsync -rR $DIR_PATH ../$MODULE_NAME
+done
+
+# delete all architecture-dependent files
+cd ../$MODULE_NAME
+find . -name Makefile.in -delete
+find . -name Makefile -delete
+find . -name '*.o' -delete
+find . -wholename '*.deps/*' -delete
+find . -path '*.deps' -delete
+echo "Removed architecture-dependent files."
+
+# remove directories that are not required
+sed -i '/"dune"/d' CMakeLists.txt
+sed -i '/"src"/d' CMakeLists.txt
+sed -i '/"m4"/d' CMakeLists.txt
+rm -rf dune/
+rm -rf src/
+rm -rf m4/
+
+# create a list of the subfolders
+EMPTY_DIR_NAME="."
+rm -f tmp_subdir_file
+for HEADER in $REQUIRED_HEADERS; do
+
+ # move through every header, cutting off the last folder
+ while test "$HEADER" != $EMPTY_DIR_NAME; do
+ if test "$(dirname $HEADER)" != $EMPTY_DIR_NAME; then
+ dirname $HEADER >> tmp_subdir_file
+ fi
+
+ HEADER=$(dirname $HEADER)
+ done
+
+ # finally add the topmost folder
+ if test "$(basename $HEADER)" != $EMPTY_DIR_NAME; then
+ basename $HEADER >> tmp_subdir_file
+ fi
+done
+SUBDIR_LIST=$(sort -u tmp_subdir_file)
+rm -f tmp_subdir_file
+
+# treat every subfolder
+START_DIR=$PWD
+INITIAL_SUBDIR_LIST=""
+for SUBDIR in $SUBDIR_LIST; do
+ if test "$SUBDIR" = "$(basename $SUBDIR)"; then
+ INITIAL_SUBDIR_LIST="$INITIAL_SUBDIR_LIST $SUBDIR"
+ fi
+
+ cd $SUBDIR
+
+ # create lists of files and folders
+ FILE_LIST=""
+ DIR_LIST=""
+ for FILE_OR_FOLDER in $( ls ); do
+ if ([ -f $FILE_OR_FOLDER ]); then
+ FILE_LIST="$FILE_LIST $FILE_OR_FOLDER"
+ fi
+
+ if ([ -d $FILE_OR_FOLDER ]); then
+ DIR_LIST="$DIR_LIST $FILE_OR_FOLDER"
+ fi
+ done
+
+ # create CMakeLists.txt if not present
+ if ([ ! -f CMakeLists.txt ]); then
+ # add subfolder information
+ for DIR in $DIR_LIST; do
+ echo "add_subdirectory(\"$DIR\")" >> CMakeLists.txt
+ done
+
+ # determine whether to add file information
+ ADD_FILE_INFO="0"
+ for FILE in $FILE_LIST; do
+ if ([ -f $FILE ]); then
+ ADD_FILE_INFO="1"
+ fi
+ done
+
+ # add file information
+ if test "$ADD_FILE_INFO" = "1"; then
+ echo "" >> CMakeLists.txt
+ echo "install(FILES" >> CMakeLists.txt
+
+ for FILE in $FILE_LIST; do
+ echo " $FILE" >> CMakeLists.txt
+ done
+
+ echo " DESTINATION \${CMAKE_INSTALL_INCLUDEDIR}/$SUBDIR)" >> CMakeLists.txt
+ fi
+ fi
+
+ cd $START_DIR
+
+done
+
+# update top CMakeLists.txt
+for INITIAL_SUBDIR in $INITIAL_SUBDIR_LIST; do
+ sed -i '/add_subdirectory("doc")/a add_subdirectory('"$INITIAL_SUBDIR"')' CMakeLists.txt
+done
+echo "Updated and created CMakeLists.txt's."
+cd ..
+
+# add includes to the automatically generated file *Macros.cmake
+MACROS_FILE="$(find $MODULE_NAME -name '*Macros.cmake')"
+if test "$(find $MODULE_NAME -type f -name 'CMakeLists.txt' -exec grep add_csv_file_links {} \; 2>/dev/null)" != ""; then
+ cp dumux-devel/cmake/modules/AddCSVFileLinks.cmake $MODULE_NAME/cmake/modules/.
+ echo "include(AddCSVFileLinks)" >>$MACROS_FILE
+fi
+if test "$(find $MODULE_NAME -type f -name 'CMakeLists.txt' -exec grep add_executable_all {} \; 2>/dev/null)" != ""; then
+ cp dumux-devel/cmake/modules/AddExecutableAll.cmake $MODULE_NAME/cmake/modules/.
+ echo "include(AddExecutableAll)" >>$MACROS_FILE
+fi
+if test "$(find $MODULE_NAME -type f -name 'CMakeLists.txt' -exec grep add_file_link {} \; 2>/dev/null)" != ""; then
+ cp dumux-devel/cmake/modules/AddFileLink.cmake $MODULE_NAME/cmake/modules/.
+ echo "include(AddFileLink)" >>$MACROS_FILE
+fi
+if test "$(find $MODULE_NAME -type f -name 'CMakeLists.txt' -exec grep add_folder_link {} \; 2>/dev/null)" != ""; then
+ cp dumux-devel/cmake/modules/AddFolderLink.cmake $MODULE_NAME/cmake/modules/.
+ echo "include(AddFolderLink)" >>$MACROS_FILE
+fi
+if test "$(find $MODULE_NAME -type f -name 'CMakeLists.txt' -exec grep add_gnuplot_file_links {} \; 2>/dev/null)" != ""; then
+ cp dumux-devel/cmake/modules/AddGnuplotFileLinks.cmake $MODULE_NAME/cmake/modules/.
+ echo "include(AddGnuplotFileLinks)" >>$MACROS_FILE
+fi
+
+# create $README_FILE
+README_FILE="README.md"
+mv $MODULE_NAME/README $MODULE_NAME/$README_FILE
+echo "This file has been created automatically. Please adapt it to your needs." >$MODULE_NAME/$README_FILE
+echo "" >>$MODULE_NAME/$README_FILE
+echo "===============================" >>$MODULE_NAME/$README_FILE
+echo "" >>$MODULE_NAME/$README_FILE
+echo "The content of this DUNE module was extracted from the module $MODULE_DIR." >>$MODULE_NAME/$README_FILE
+echo "In particular, the following subfolders of $MODULE_DIR have been extracted:" >>$MODULE_NAME/$README_FILE
+echo "" >>$MODULE_NAME/$README_FILE
+for DIR_PATH in $ALL_DIRECTORIES; do
+ echo " $DIR_PATH," >>$MODULE_NAME/$README_FILE
+done
+echo "" >>$MODULE_NAME/$README_FILE
+echo "Additionally, all headers in $MODULE_DIR that are required to build the" >>$MODULE_NAME/$README_FILE
+echo "executables from the sources" >>$MODULE_NAME/$README_FILE
+echo "" >>$MODULE_NAME/$README_FILE
+for SOURCE in $ALL_SOURCES; do
+ echo " $SOURCE," >>$MODULE_NAME/$README_FILE
+done
+echo "" >>$MODULE_NAME/$README_FILE
+echo "have been extracted. You can build the module just like any other DUNE" >>$MODULE_NAME/$README_FILE
+echo "module. For building and running the executables, please go to the folders" >>$MODULE_NAME/$README_FILE
+echo "containing the sources listed above." >>$MODULE_NAME/$README_FILE
+echo "" >>$MODULE_NAME/$README_FILE
+echo "" >>$MODULE_NAME/$README_FILE
+echo "" >>$MODULE_NAME/$README_FILE
+echo "" >>$MODULE_NAME/$README_FILE
+
+# get versions from modules we are depeding on
+# create patches for un-pushed commits and uncomitted changes
+
+# try to find the dunecontrol script
+if hash dunecontrol 2>/dev/null; then
+ DUNE_CONTROL="dunecontrol"
+else
+ DUNE_CONTROL=$(find . -type f -executable -name 'dunecontrol')
+fi
+if test "$DUNE_CONTROL" = ""; then
+ echo "ERROR: Could not find dunecontrol."
+ echo "Be sure to either have dunecontrol in your search path"
+ echo "or to run this script from a directory that contains dunecontrol."
+ exit
+fi
+# get names of all modules we are depeding on
+echo "Extracting dependencies to other Dune modules"
+DEPENDING_MODULE_NAMES=$($DUNE_CONTROL --module=$MODULE_NAME 2>/dev/null | head -n 1)
+DEPENDING_MODULE_NAMES=$(sed 's/--- going to build //' <<< "$DEPENDING_MODULE_NAMES")
+DEPENDING_MODULE_NAMES=$(sed 's/ ---//' <<< "$DEPENDING_MODULE_NAMES")
+# load script
+CALL_FROM_EXTERNAL_SCRIPT="yes"
+SCRIPT_DIR="${BASH_SOURCE%/*}"
+if [[ ! -d "$SCRIPT_DIR" ]]; then
+ SCRIPT_DIR="$PWD";
+fi
+# create install script
+touch $MODULE_NAME/install$MODULE_NAME.sh
+. "$SCRIPT_DIR/getusedversions.sh"
+# execute function from script
+echo "Extracting Git status of dependencies and creating patches"
+for MOD in $DEPENDING_MODULE_NAMES
+do
+ if [ $MOD != $MODULE_NAME ]; then
+ MODULE_DIR=${MOD%*/}
+ getVersionGit $MODULE_DIR $(pwd)/$MODULE_NAME/install$MODULE_NAME.sh >>$MODULE_NAME/$README_FILE
+ fi
+done
+
+# move patches folder into module if existing
+if [[ -d patches ]]; then
+ mv patches $MODULE_NAME
+fi
+
+# output guidence for users
+echo ""
+echo "*************************************************************************"
+echo "The extracted module is contained in the subfolder \"$MODULE_NAME\"."
+echo "You can build it using \"dunecontrol ... --only=$MODULE_NAME all\"."
+echo "*************************************************************************"
+echo "BEFORE building, you can add the module to dumux-pub by something like:"
+echo "(Rename module name if it does not match the AuthorLastNameYearx scheme"
+echo "and commit it to the Git repository dumux-pub)"
+echo "git clone https://git.iws.uni-stuttgart.de/dumux-pub/AuthorLastNameYearx.git"
+echo "sed -i '/Module:/c\Module: AuthorLastNameYearx' $MODULE_NAME/dune.module"
+echo "mv $MODULE_NAME/* dumux-pub/AuthorLastNameYearx/."
+echo "cd AuthorLastNameYearx"
+echo "git commit -a"
+echo "git push"
+
+exit 0
diff --git a/bin/moduleutil/getusedversions.sh b/bin/moduleutil/getusedversions.sh
new file mode 100755
index 0000000000000000000000000000000000000000..6dc2c1d9d4b3593a91eeafe8c3773ebde5e2fb54
--- /dev/null
+++ b/bin/moduleutil/getusedversions.sh
@@ -0,0 +1,105 @@
+# !/bin/bash
+
+# skript to extract Git version information
+# including automating patch extraction and handling of uncommitted changes
+#
+# (c) 2016 Thomas Fetzer
+# (c) 2016 Christoph Grüninger
+#
+
+if [ "${args[1]}" = "-h" ]; then
+ echo "USAGE: ./getDumuxDuneVersions.sh"
+ echo; exit
+fi
+
+OUTFILE=versionNumbers.txt
+
+# create patches from get local commits
+# $1 directory /which is local copy of Git repository to check, assumed to be identical with module name
+# $2 script file to append command for checking out Git repository
+function getPatchesGit
+{
+ # if not yet existing, create common patch directory
+ if [ ! -d ../patches ]; then
+ mkdir ../patches
+ fi
+ # create directory for patches of module
+ mkdir ../patches-$1
+
+ # create patch for local commits
+ git format-patch --output-directory ../patches-$1 @{upstream}
+ # create extra patch for uncommitted changes if necessary
+ if [[ `git status --porcelain | grep -v "build.*"` ]]; then
+ git diff > ../patches-$1/9999-uncommitted-changes.patch
+ fi
+
+ # move and rename all patches to common patch directory
+ MODULE_PWD=$PWD
+ cd ../patches-$1 ;
+ for file in *.patch
+ do
+ mv $file ../patches/$1_$file
+ printf "Created patch %s\n" $1_$file
+ echo "patch -p1 < ../patches/$1_$file" >> $2
+ done
+ cd $MODULE_PWD
+ # remove helper dirctory
+ rm -r ../patches-$1
+}
+
+# get version from Git, output and write to file
+# $1 directory which is local copy of Git repository to check, assumed to be identical with module name
+# $2 script file to append command for checking out Git repository
+function getVersionGit
+{
+ # enter directory
+ cd $1
+ # get URL from remote a.k.a. the repository
+ GIT_REMOTE="$(git ls-remote --get-url)"
+ # get revision, date, author and branch of last remote/upstream commit
+ GIT_UPSTREAM_REVISION="$(git log -n 1 --format=%H @{upstream})"
+ GIT_UPSTREAM_DATE="$(git log -n 1 --format=%ai @{upstream})"
+ GIT_UPSTREAM_AUTHOR="$(git log -n 1 --format=%an @{upstream})"
+ GIT_UPSTREAM_BRANCH="$(git rev-parse --abbrev-ref HEAD)"
+ printf "%-25s %-15s %-15s\n" $1 $GIT_UPSTREAM_BRANCH $GIT_UPSTREAM_REVISION
+ echo "# $1" >> $2
+ echo "# $GIT_UPSTREAM_BRANCH # $GIT_UPSTREAM_REVISION # $GIT_UPSTREAM_DATE # $GIT_UPSTREAM_AUTHOR" >> $2
+ echo "git clone $GIT_REMOTE" >> $2
+ echo "cd $1" >> $2
+ echo "git checkout $GIT_UPSTREAM_BRANCH" >> $2
+ echo "git reset --hard $GIT_UPSTREAM_REVISION" >> $2
+ # check for untracked files and error out if found, but ignore build*
+ if [[ `git ls-files --others --exclude-standard | grep -v "build*" | grep -v "\.[A-Za-z]*"` ]]; then
+ echo "Error: Found untracked files in module $1. Please commit, stash or remove them."
+ echo "You might want to delete the folder patches/ and the module just created."
+ exit
+ fi
+ # create patches if number of commits is not zero
+ if [[ "$(git rev-list HEAD ^@{upstream} --count)" > 0 ]] || [[ `git status --porcelain | grep -v "build.*" | grep -v "\.[A-Za-z]*"` ]]; then
+ getPatchesGit $1 $2
+ fi
+ echo "cd .." >> $2
+ echo "" >> $2
+ cd ..
+}
+
+# run script from comand line
+# suppressed for use of external script when variable set accordingly
+if [ "$CALL_FROM_EXTERNAL_SCRIPT" == "no" ]; then
+ echo "# DUNE/DUMUX VERSIONS" > $OUTFILE
+
+ echo "Creating file containing the version numbers:"
+ for dir in dune-* dumux*
+ do
+ DIR=${dir%*/}
+ # echo $DIR
+ # skip folders that are no Git repository
+ if [ -d $DIR/.git ]; then
+ getVersionGit $DIR ../$OUTFILE
+ fi
+ done
+
+ echo "done"
+
+ exit
+fi