From the docs:

CLAUDE_CODE_NEW_INIT

Set to 1 to make /init run an interactive setup flow. The flow asks which files to generate, including CLAUDE.md, skills, and hooks, before exploring the codebase and writing them. Without this variable, /init generates a CLAUDE.md automatically without prompting.

Probably. It does seem to have a built-in tool for exploring its own docs, and it has a special mode for working in a .claude/ directory. It's probably intended that users do this.

Yeah I'd love to see a cookie cutter project with all of the best practices of the boilerplate files

There’s a slash command that’ll look through your conversation history to add allow permissions.

Yes, absolutely. Claude is very good at modifying itself