feat: prompt before overwriting existing or invalid repos during batch clone

[masonlet]

Summary

Mono/batch cloning previously silently skipped any repo directory that already
existed on disk, no update, no prompt, regardless of --yes, and didn't
distinguish a real git repo from a stale/invalid leftover directory. This adds:

• A prompt before updating an existing repo during batch clone, with a/s
  shortcuts (update-all / skip-all) once a batch reaches 5+ repos.
• Detection of directories that exist but aren't actually git repos (no .git),
  with an explicit "remove and re-clone?" prompt. This destructive action is
  never auto-confirmed by --yes, destructive actions should be explicitly set.

Also includes some structural cleanup: splitting repository.rs and prompts.rs into per-concern modules, replacing clone_repo's on_exists_skip/yes bool pair with a pluggable on_exists callback (so both single- and batch-clone modes can supply their own decision without duplicating the clone/pull mechanics).