cleanup

find . -name \*~ -exec rm {} \;
find . -name \*.o -exec rm {} \;
find . -name \*.so -exec rm {} \;
find . -name "#*#" -exec rm {} \;

rm -rf ./inst/lib

# prepare inst folder
# copy over all sources from Shark!
rm -rf ./inst/include/shark
mkdir -p ./inst/include
cp -R ./src/shark ./inst/include/shark

# this one hurts
mv ./inst/include/shark/Algorithms/DirectSearch/Operators/Recombination/SimulatedBinaryCrossover.h  ./inst/include/shark/Algorithms/DirectSearch/Operators/Recombination/BinaryCrossover.h

# as do those for too long a path name
mv ./inst/include/shark/Algorithms/DirectSearch/Operators/Hypervolume/HypervolumeContribution2D.h ./inst/include/shark/Algorithms/DirectSearch/Operators/Hypervolume/HVContribution2D.h
mv ./inst/include/shark/Algorithms/DirectSearch/Operators/Hypervolume/HypervolumeContribution3D.h ./inst/include/shark/Algorithms/DirectSearch/Operators/Hypervolume/HVContribution3D.h
#mv ./inst/include/shark/Algorithms/DirectSearch/Operators/Hypervolume/HypervolumeContributionApproximator.h ./inst/include/shark/Algorithms/DirectSearch/Operators/Hypervolume/HVContributionApproximator.h
mv ./inst/include/shark/Algorithms/DirectSearch/Operators/Hypervolume/HypervolumeContributionMD.h ./inst/include/shark/Algorithms/DirectSearch/Operators/Hypervolume/HVContributionMD.h
mv ./inst/include/shark/Algorithms/DirectSearch/Operators/Hypervolume/HypervolumeSubsetSelection2D.h ./inst/include/shark/Algorithms/DirectSearch/Operators/Hypervolume/HVSubsetSelection2D.h
mv ./inst/include/shark/Algorithms/DirectSearch/Operators/Recombination/PartiallyMappedCrossover.h ./inst/include/shark/Algorithms/DirectSearch/Operators/Recombination/PMXCrossover.h

mv ./inst/include/shark/Algorithms/DirectSearch/Operators/Hypervolume/HypervolumeCalculatorMDHOY.h ./inst/include/shark/Algorithms/DirectSearch/Operators/Hypervolume/HVCalculatorMDHOY.h
mv ./inst/include/shark/Algorithms/DirectSearch/Operators/Hypervolume/HypervolumeCalculatorMDWFG.h ./inst/include/shark/Algorithms/DirectSearch/Operators/Hypervolume/HVCalculatorMDWFG.h


# copy over utils
cp ./src/utils.h ./inst/skeleton
cp ./src/utils.cpp ./inst/skeleton