Improve initializing when files already exist

The various prompts could have defaults, including if you're adding skel to an existing repo, from reading an existing setup.py (or executing it; I only expect this to be run on repos you trust). Would be nice to handle {envdir} workaround as a default at the same time.

Start by locating the prompt initialization flow and the handling of an existing setup.py. Review how skel behaves when files already exist, then define the expected defaults for prompts, trusted setup.py input, and the {envdir} workaround. Done means initialization can use those defaults without unexpectedly overwriting existing repository content.