docs: trim appendix, add SSH setup

- Remove command quick reference (~290 lines) — redundant with
  playbook and git help
- Add SSH key setup section (generate, agent, GitHub, test, switch URL)
  to close cross-reference from chapter 4
- Convert Git clients list to table with platform/notes
- Reorganize references into books, troubleshooting, visualization,
  workflows
- Clean up notes wording

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: braboj