Merge branch 'tlc/remove-unused-packages-bump-up-versions' into 'develop'

nomad/app/resources/routers/resources.py

nomad/atomutils.py

nomad/datamodel/metainfo/simulation/legacy_workflows.py

nomad/datamodel/metainfo/simulation/workflow.py

nomad/files.py

nomad/normalizing/common.py

nomad/normalizing/material.py

pyproject.toml

requirements-dev.txt

requirements-plugins.txt

requirements.txt

scripts/generate_python_dependencies.sh

test_plugins.txt

tests/test_config.py