docs: update README with core features and agent alignment

- Resolve merge conflict in CLI reference section
- Reorder Table of Contents to prioritize core features and extensions
- Add Core Features section highlighting SDD workflow and team-ai-directives
- Add Extensions section documenting architect, levelup, tdd, product, quick
- Update Supported AI Agents table (22 agents, organized by CLI/IDE)
- Remove Jules (not in AGENT_CONFIG), add missing agents (agy, vibe, kimi, bob, qodercli)
- Remove q (Amazon Q) agent references to align with upstream

Author: kanfil