Change linter and formater to ruff, apply changes
to make ruff happy. This decision was taken, because yapf caused
problems on the CI, i.e could not be installed, etc.

Fix bug in aggregator which caused changes of patches not be
written into derived. So uplifting now works.
But the serialization of the derived data differs from the usual
serialization the data comes in. Because of not support by rdflib
there.

Reorder folder structure for openaire mining examples and add table generator files, mapping for rare, re3data and licenses