docs: fix plumbing docstring gaps + add plumbing reference doc

pack-objects: add missing Exit 3 (I/O error) to plumbing contract. ls-remote: add default_branch field and * marker to output examples in the module docstring, matching actual command behaviour.

Add docs/reference/plumbing.md — a shareable, high-level plumbing reference covering all 12 commands with flags tables, JSON output examples, exit code contracts, composability patterns, and an object ID quick reference. Aimed at scripters, operators, and agent authors rather than developers reading source.