Merge branch 'master' into parmetis-perm

configure.ac

doc/Doxyfile.in

doc/RTD/source/GettingStarted/parameter_file.rst

doc/RTD/source/InitialConditions/index.rst

examples/AgoraDisk/agora_disk.yml

examples/AgoraDisk/changeType.py

examples/AgoraDisk/cleanupSwift.py

examples/AgoraDisk/getIC.sh

examples/AgoraDisk/getSolution.sh

examples/AgoraDisk/plotSolution.py

examples/AgoraDisk/run.sh

examples/CoolingBox/run.sh

examples/KeplerianRing/README.md

examples/KeplerianRing/run.sh

examples/Makefile.am

examples/ZeldovichPancake_3D/makeIC.py

examples/getCoolingTable.sh

examples/plot_gravity_checks.py

src/hydro/Shadowswift/hydro.h

src/hydro/Shadowswift/hydro_gradients.h