docs: Expand whitepaper with v0.3.1 benchmarks and detailed methodology

[GenesisAeon]

Summary

Significantly expanded the GenesisAeon whitepaper with comprehensive benchmark results, detailed system architecture documentation, and reproducibility instructions. This update documents the completion of Cycle 2 with empirical validation of the UTAC climate model and CosmicWebSimulator.

Key Changes

• Version and metadata updates: Added v0.3.1 version tag, publication date (March 25, 2026), and expanded DOI placeholder
• Enhanced abstract: Added concrete benchmark results showing 37.3% RMSE reduction on ERA5 holdout set (2000–2023) and automatic tipping point detection at ~1998
• New symbol reference table: Added comprehensive table defining all key mathematical symbols (T, V, Φ, Γ, r, σ, K) with their physical meanings
• Expanded core concepts section: Detailed Frame Principle, Mirror-Machine mechanism, and Phase-Transition-Loop with physical explanations
• Detailed benchmark documentation:
  • CosmicWebSimulator: Resonance metric validation against GADGET-4/IllustrisTNG
  • UTAC ODE: Complete methodology including data source (ERA5 1940–2023), train/test split, calibrated parameters (r=0.12, σ=2.2), and tipping point detection results
• System architecture diagram: Added directory structure showing module organization
• Reproducibility instructions: Added complete bash commands for installation, benchmark execution, and full cycle runs with notes on determinism and data sources
• Updated roadmap: Clarified cycle status (1–2 complete, 3 planned) with specific deliverables
• Formal citation block: Added BibTeX entry for proper academic citation

Implementation Details

• All benchmark results are tied to specific Jupyter notebooks (notebooks/cosmicweb_benchmark.ipynb, notebooks/utac_ode_benchmark.ipynb) for full reproducibility
• Tipping point detection (~1998) is validated against IPCC AR6 Section 9.3.1 and published Arctic amplification studies
• Parameters are explicitly documented as ERA5-calibrated with clear physical interpretation
• Document structure reorganized with numbered sections and horizontal dividers for improved readability

https://claude.ai/code/session_01LdbJ7pRLouWcSfTbjuuWnM

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