Move AnnotateRuntime* into cli/runtimeannotate and the Cobra-keyed
ContractFinal store into cli/contractfinal so corecmd depends on thin
subpackages instead of the cli delivery root. Keep contract as DTO-only,
document Description declare-vs-delivery, and house homology gates under
cli/homology.
Co-authored-by: Cursor <cursoragent@cursor.com>