Restructure entity model: separate types, rename SkillGroup to SkillBundle

Split the single Skill entity (with kind field) into three separate
entity types: Skill, Subagent, Hook. Rename SkillGroup to SkillBundle
with typed member lists (skills, subagents, hooks, mcp_servers) replacing
the SkillGroupVersionMember entity. Use "subagent" to avoid collision
with a future agent registry.

Updates span both RFCs: entity definitions, DB schema, store interface,
REST API, SDK convenience functions, CLI, and harness adapter interfaces.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: jwm4