Update `iidda::iidda_from_single_file` to match folder organization specs

[stevencarlislewalker]

Specs are getting more stable:

• https://github.com/canmod/iidda/blob/main/docs/data-folder-organization.md
• https://github.com/canmod/iidda/blob/main/docs/data-format-standards.md

But iidda::iidda_from_single_file has not caught up