UW-504 - Allow YAML as supplemental config always

[WeirAE]

Description
From user stories:
I'd like to update a namelist file (or INI or shell) with supplemental files in YAML format
Continues #414

Requirements
config.update() must allow YAML regardless of input/output files

Acceptance Criteria (Definition of Done)
Ability to use YAML-formatted files as supplemental file format is restored
Documentation Updated
Tests Updated

[WeirAE]

Closing to clear room in issues for new user concerns