DOC/ENH: Update docs ⚠️ not ready for merge⚠️

I took a pass through all the rst files in the doc directory and it seems like
I've changed all mentions to JSON and the old format, except for the
add_metadata.rst file which I've left unomodified as I don't know how to
translate the metadata representations to HDF5, anyone has any ideas.

Should fix #383.