Centralise the binary file saving metadata

[JoeZiminski]

Following on from a discussion at #3245. At present there is a binary.json metadata file written during the saving of binary data. This duplicates the si_folder.json metadata which has caused some problems with failure to propagate metadata and confusing behaviour during debugging #3245. The logic flow for the data-saving is discussed here. It would be nice to completely deprecate binary.json and use only si_folder.json to centralise the metadata.