Your idea

• Custom prefix (X-) for arbitrary metadata in .json files bids-2-devel#80 (comment)

and reflecting on

• [ENH] introduce GeneratedBy to "core" BIDS #440

for GeneratedBy to be universally adopted at the Dataset level.

To accommodate provenance "per file", e.g. for dcm2niix and alike, we better allow for GeneratedBy at individual file level.