Scaffolds a Fleet project in the current directory: creates .fleet/config.yaml and .fleet/prompts/ with a starter agent set, picked either from repo signals (interactively or auto in non-TTY shells) or from a named template. With --org <name> it scaffolds ~/.fleet/orgs/
If a config already exists, init refuses unless you pass --force (which snapshots the old config to .fleet/.backup/ first, unless --no-backup). It does not write .mcp.json and does not run skills install.