Restructuring logic for setting the metadata

Simplifying the logic for setting the metadata. There should be three ways of setting user metadata:

1. via json/yaml files defined by the user, included in the upload files
2. via the entry api/entry methods,
3. via the upload api/upload methods.

The upload api/methods should be used if and only if the field in question is defined on the upload level. This currently includes the attributes embargo_length, upload_name, uploader, upload_time (changing the last two requires admin privileges). The upload api/method should also ensure that the fields that are mirrored to entry metadata are consistently copied to all entries (which was not ensured previously). Old storage of compressed metadata in pickled files is removed.