phenotype/ is a bit of an outlier in BIDS terms. Other folders at the top level are either entities (sub-<label>) or their contents are opaque to BIDS. phenotype/, on the other hand, is a collection of .tsv/.json files that are to be validated on the same terms as participants.tsv/participants.json.

I would suggest classifying phenotype as a datatype, distinct from other datatypes only in that it spans multiple subjects, and so the subject and session entities do not apply. BEP036 seems to go some way in a similar direction, permitting a pheno/ datatype within subjects/sessions.

In the (unmerged) PR #1672, I suggest using phenotype as a datatype for the purposes of filename validation, and then carve out some exceptions that allow us to use it that way without it being an official datatype. If we make it a datatype, then the exception can be removed. That it fits with very little modification to the schema and validation (https://github.com/bids-standard/bids-validator/pull/1957), seems to me to be an argument for this classification.

The alternative, as I see it, is to consider phenotype a completely unique category of thing, and all implementations will need to have special code for handling it.