Move use of `puts` in Runner to IO management

Right now most of these tasks just do `puts "message"`. Then they have a `quiet` flag set to silence this output. We should move this to IO management so we can just set the IO to whatever we want instead of passing around a flag all over

Start by locating the Runner tasks that call puts and pass the quiet flag, then trace the existing IO management entry point. Identify all affected output paths and determine how configurable IO should replace quiet handling; done means Runner output is routed through IO management without passing quiet flags around.

Written by the indexing model from the issue text.