[examples] Use Dumux::initialize and regenerate docs

examples/1protationsymmetry/doc/main.md

examples/1protationsymmetry/main.cc

examples/1ptracer/doc/main.md

examples/1ptracer/main.cc

examples/2pinfiltration/doc/main.md

examples/2pinfiltration/main.cc

examples/biomineralization/doc/fluidmaterial.md

examples/biomineralization/doc/mainfile.md

examples/biomineralization/main.cc

examples/biomineralization/material/co2tableslaboratory.hh

...ralization/material/fluidsystems/biominsimplechemistry.hh

examples/freeflowchannel/README.md

examples/freeflowchannel/main.cc

examples/liddrivencavity/doc/problem.md

examples/liddrivencavity/main.cc

examples/porenetwork_upscaling/doc/main.md

examples/porenetwork_upscaling/doc/problem.md

examples/porenetwork_upscaling/main.cc

examples/shallowwaterfriction/README.md

examples/shallowwaterfriction/doc/main.md