Fixed issues with method information not being correctly written for phonon calculations in case the referenced calculation had failed to be processed by encyclopedia.

Updated phonopy processing so that the smaller subsystem is used as representative one and that calculation references are specified relative to the upload root.

Completely removed the 'joined' field from Uploads as it is not needed, removed redis persistence on development docker-compose, made sure that results are not kept for celery tasks.

Refactored re-processing to use pipelines, fixed issue with calculation processes not being updated.

Added PipelineContext object and corresponding custom serializer to make working with pipelines easier.