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Anto01 ea437d360e 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

2026-01-20 10:03:45 -05:00

2.6 KiB

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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

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.

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