Restructure output

.gitlab-ci.yml

README.md

docs/source/calibrator.rst

docs/source/calibrator_old.rst

docs/source/parset.rst

docs/source/parset_old.rst

docs/source/pipelineoverview.rst

docs/source/pipelineoverview_old.rst

docs/source/running.rst

docs/source/running_old.rst

docs/source/target.rst

docs/source/target_old.rst

steps/collectfiles.cwl

test_jobs/HBA_target.json

test_jobs/check_workflow_results.py

workflows/HBA_calibrator.cwl

workflows/HBA_target.cwl