docs: Major documentation overhaul - restructure folders, update tagline, add Getting Started guide

- Restructure docs/ folder (remove numeric prefixes):
  - 04_USER_GUIDES -> guides/
  - 05_API_REFERENCE -> api/
  - 06_PHYSICS -> physics/
  - 07_DEVELOPMENT -> development/
  - 08_ARCHIVE -> archive/
  - 09_DIAGRAMS -> diagrams/

- Replace tagline 'Talk, don't click' with 'LLM-driven optimization framework' in 9 files

- Create comprehensive docs/GETTING_STARTED.md:
  - Prerequisites and quick setup
  - Project structure overview
  - First study tutorial (Claude or manual)
  - Dashboard usage guide
  - Neural acceleration introduction

- Rewrite docs/00_INDEX.md with correct paths and modern structure

- Archive obsolete files:
  - 01_PROTOCOLS.md -> archive/historical/01_PROTOCOLS_legacy.md
  - 03_GETTING_STARTED.md -> archive/historical/
  - ATOMIZER_PODCAST_BRIEFING.md -> archive/marketing/

- Update timestamps to 2026-01-20 across all key files

- Update .gitignore to exclude docs/generated/

- Version bump: ATOMIZER_CONTEXT v1.8 -> v2.0

docs/plans/ATOMIZER_CONTEXT_ENGINEERING_PLAN.md

@@ -750,7 +750,7 @@ The system prompt is structured to maximize KV-cache hits:
 ```
 [SECTION 1: STABLE - Never changes]
 - Atomizer identity and capabilities
-- Core principles (talk don't click)
+- Core principles (LLM-driven optimization)
 - Tool schemas and definitions
 - Base protocol routing table
 
@@ -780,7 +780,7 @@ You are assisting with **Atomizer**, an LLM-first FEA optimization framework.
 - Neural acceleration (600-1000x speedup)
 
 ## Principles
-1. Talk, don't click - users describe goals in plain language
+1. LLM-driven - users describe goals in plain language
 2. Never modify master models - work on copies
 3. Always validate before running
 4. Document everything