Gen 2 Butler init enhancements for modifying the set of input/output repos

Kian-Tat Lim remarks on DM-11500:

It should be possible to change the Butler initialization logic to accept steps that have a subset of input repos in the current output repo config (without changing the latter) in addition to steps that add new input repos to the output repo config (while changing it). That would be a better long-term fix.