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/UNIFIED_CONFIG_QUICKSTART.md

@@ -0,0 +1,92 @@
+# AtomizerSpec v2.0 - Quick Start Guide
+
+## TL;DR
+
+**Goal**: Replace 4+ config formats with one unified `atomizer_spec.json` that Canvas, Backend, Claude, and Optimization Engine all use.
+
+**Effort**: ~50 tasks across 4 phases (~12 weeks)
+
+**Key Files**:
+- Design: `docs/plans/UNIFIED_CONFIGURATION_ARCHITECTURE.md`
+- Tasks: `docs/plans/UNIFIED_CONFIG_EXECUTION_PLAN.md`
+- Schema: `optimization_engine/schemas/atomizer_spec_v2.json`
+- Prompts: `docs/plans/UNIFIED_CONFIG_RALPH_PROMPT.md`
+
+---
+
+## Start Autonomous Implementation
+
+### 1. Open Claude CLI
+```bash
+claude --dangerously-skip-permissions
+```
+
+### 2. Paste Initial Prompt
+```
+You are implementing the AtomizerSpec v2.0 Unified Configuration Architecture for Atomizer.
+
+Read these documents before starting:
+1. `docs/plans/UNIFIED_CONFIGURATION_ARCHITECTURE.md` - Master design
+2. `docs/plans/UNIFIED_CONFIG_EXECUTION_PLAN.md` - Task list (50+ tasks)
+3. `optimization_engine/schemas/atomizer_spec_v2.json` - JSON Schema
+
+Implement tasks in order (P1.1 → P4.12). Use TodoWrite to track progress. Commit after each logical group. Reference the design document for code examples.
+
+Begin by reading the documents and loading tasks into TodoWrite. Start with P1.1.
+```
+
+### 3. Let It Run
+Claude will work through the task list autonomously, committing as it goes.
+
+---
+
+## Phase Summary
+
+| Phase | Tasks | Focus | Key Deliverables |
+|-------|-------|-------|------------------|
+| **1** | P1.1-P1.17 | Backend | SpecManager, REST API, Migration |
+| **2** | P2.1-P2.16 | Frontend | SpecRenderer, WebSocket Sync |
+| **3** | P3.1-P3.14 | Claude | MCP Tools, Custom Functions |
+| **4** | P4.1-P4.12 | Polish | Tests, Migration, Docs |
+
+---
+
+## Key Concepts
+
+**AtomizerSpec**: Single JSON file containing everything needed for optimization AND canvas display.
+
+**SpecManager**: Backend service that validates, saves, and broadcasts spec changes.
+
+**SpecRenderer**: Frontend component that renders canvas directly from spec.
+
+**Real-time Sync**: WebSocket broadcasts changes to all connected clients.
+
+**Custom Functions**: Python code stored in spec, loaded dynamically during optimization.
+
+---
+
+## Success Metrics
+
+- [ ] Canvas loads/saves without data loss
+- [ ] Claude can modify specs via MCP tools
+- [ ] All existing studies migrated
+- [ ] WebSocket sync works between clients
+- [ ] Custom extractors execute in optimization
+- [ ] All tests pass
+
+---
+
+## If Resuming
+
+```
+Continue implementing AtomizerSpec v2.0.
+
+Reference:
+- `docs/plans/UNIFIED_CONFIG_EXECUTION_PLAN.md`
+
+Check current todo list, find last completed task, continue from there.
+```
+
+---
+
+*Full details in the referenced documents.*