docs(research): add comprehensive API reference manual v1.0 (#415)

- Complete CLI tools documentation (tri commands)
- Core libraries reference (VSA, Ternary, Sacred Math, VM)
- Research frameworks (Ablation, Benchmark, Hyperparameter)
- MCP server tools and session examples
- Build system configuration
- Error handling patterns
- Configuration loading and JSON schema
- Quick reference appendix

824 lines of detailed API documentation

φ² + 1/φ² = 3 | TRINITY

Author: Antigravity Agent