By default, leave modules as-is, user will explicitly choose modules?

Right now the init step asked about every module + their dependencies. Maybe we should make it easy to skip that step, or even remove that step so users can explicitly put their module into the config, or use `tinker on`

Start by reading the init step and the `tinker on` entry point, then trace how modules and their dependencies are written to the config. Clarify whether initialization should be skippable or removed, and define done as allowing users to leave modules unchanged while explicitly selecting modules in the config.

Written by the indexing model from the issue text.