Restructured the folders, other misc renamings.

README.md

cp2kparser/cp2kparser/old/__init__.py

cp2kparser/cp2kparser/old/csvengine/tests.py

cp2kparser/cp2kparser/old/csvengine/xyz/10.xyz

cp2kparser/cp2kparser/old/csvengine/xyz/100.xyz

cp2kparser/cp2kparser/old/csvengine/xyz/1000.xyz

cp2kparser/cp2kparser/old/csvengine/xyz/10000.xyz

cp2kparser/cp2kparser/old/regexengine.py

cp2kparser/cp2kparser/old/xmlengine.py

cp2kparser/cp2kparser/utils/parser.py

cp2kparser/library.md

nomadtoolkit/README.md

nomadtoolkit/nomadtoolkit/__init__.py

nomadtoolkit/nomadtoolkit/__main__.py

nomadtoolkit/nomadtoolkit/analysis/__init__.py

nomadtoolkit/nomadtoolkit/analysis/analyzer.py

nomadtoolkit/nomadtoolkit/analysis/local_backend.py

nomadtoolkit/nomadtoolkit/examples/1_basics.py

nomadtoolkit/nomadtoolkit/metaviewer/README.md

nomadtoolkit/nomadtoolkit/metaviewer/__init__.py