Updated and fixed sphynx documentation.

docs/components.graffle/data.plist

docs/reference.md

nomad/api/__init__.py

nomad/api/__main__.py

nomad/api/app.py

nomad/api/archive.py

nomad/api/repository.py

nomad/api/upload.py

nomad/files.py

nomad/patch.py

nomad/user.py

nomad/utils.py