Use canonical domain names in the persisted graph

agentctl will use canonical domain names in SurrealDB even when shorter names are tempting: repository and checkout instead of ambiguous repo path language, changeset for a unit of work, and precise snake_case names such as file_memory, code_ir, code_finding, has_checkout, and has_ir where single-word names would become unclear. Node tables store durable identity, while edge tables store relationship-specific evidence such as edit paths, diff stats, import specifiers, and derivation links.