docs(cytoplasm): comprehensive tri-cell guide

- Added complete command reference with 40+ commands
- Quick start section for immediate use
- Cell anatomy with manifest structure explanation
- Recipes for common workflows (add cell, fix broken, health, graph)
- Permission levels table and version constraints
- Health scoring formula explanation

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

Author: Antigravity Agent