Do not auto-index <bids-root>/derivatives/

[effigies]

If I understand the situation correctly, <bids-root>/derivatives is currently indexed as if it were a standard BIDS directory. While potentially convenient, this presents some order-of-operations ambiguities for users or downstream programs that don't want to automatically include everything.

Under the recently proposed syntax, auto-indexing derivatives could be easily added by a user/developer like so:

derivs_dir = op.join(bids_dir, 'derivatives')
layout = BIDSLayout([bids_dir,
                     (derivs_dir, ['bids', 'derivatives'])])

[adelavega]

This would require adding exclude: ['derivatives/'] to bids.json. I think it's reasonable, because the "derivatives" folder is supposed to be special, and currently it's just treated as any other sub-folder of a bids_dir.

I don't think users would expect derivatives to be indexed by default, and in any case if they were, the derivatives rule set should be applied to those files.