Merge branch release-2021

Merge branch release-2021

Resolved conflicts:

        admin/gitlab-ci/gromacs.gitlab-ci.yml
        admin/gitlab-ci/python-gmxapi01.gitlab-ci.yml
        api/nblib/gmxsetup.cpp
        api/nblib/listed_forces/gmxcalculator.cpp
        api/nblib/listed_forces/tests/calculator.cpp
        api/nblib/molecules.cpp
        api/nblib/molecules.h
        api/nblib/ppmap.h
        api/nblib/tests/integrator.cpp
        api/nblib/topologyhelpers.cpp
        docs/install-guide/index.rst
        python_packaging/src/setup.py
        src/gromacs/gmxpreprocess/pdb2gmx.cpp
        src/gromacs/gmxpreprocess/readir.cpp
        src/gromacs/gmxpreprocess/topdirs.cpp
        src/gromacs/math/densityfit.cpp
        src/gromacs/mdrun/md.cpp
        src/gromacs/mdrunutility/handlerestart.cpp
        src/gromacs/modularsimulator/simulatoralgorithm.cpp
        src/gromacs/nbnxm/cuda/nbnxm_cuda_data_mgmt.cu
        src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp
        src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.h
        src/gromacs/nbnxm/opencl/nbnxm_ocl_data_mgmt.cpp
        src/gromacs/pulling/pull.cpp

Mostly from refactoring in master that clashed with fixes in
release-2021. Preserved the functionality from the latter in the form
of the former.

Some changes are simply due to the change to clang-format
configuration.

One CI configuration change for mdrun-only build is adapted, since
mdrun-only build has been removed.