Atomizer/docs/protocols

Atomizer Protocol Operating System (POS)

Version: 1.1 Last Updated: 2026-01-06

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Overview

This directory contains the Protocol Operating System (POS) - a 4-layer documentation architecture optimized for LLM consumption.

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Directory Structure

protocols/
├── README.md                    # This file
├── operations/                  # Layer 2: How-to guides
│   ├── OP_01_CREATE_STUDY.md
│   ├── OP_02_RUN_OPTIMIZATION.md
│   ├── OP_03_MONITOR_PROGRESS.md
│   ├── OP_04_ANALYZE_RESULTS.md
│   ├── OP_05_EXPORT_TRAINING_DATA.md
│   ├── OP_06_TROUBLESHOOT.md
│   ├── OP_07_DISK_OPTIMIZATION.md
│   └── OP_08_GENERATE_REPORT.md
├── system/                      # Layer 3: Core specifications
│   ├── SYS_10_IMSO.md
│   ├── SYS_11_MULTI_OBJECTIVE.md
│   ├── SYS_12_EXTRACTOR_LIBRARY.md
│   ├── SYS_13_DASHBOARD_TRACKING.md
│   ├── SYS_14_NEURAL_ACCELERATION.md
│   ├── SYS_15_METHOD_SELECTOR.md
│   ├── SYS_16_SELF_AWARE_TURBO.md
│   ├── SYS_17_STUDY_INSIGHTS.md
│   └── SYS_18_CONTEXT_ENGINEERING.md
└── extensions/                  # Layer 4: Extensibility guides
    ├── EXT_01_CREATE_EXTRACTOR.md
    ├── EXT_02_CREATE_HOOK.md
    ├── EXT_03_CREATE_PROTOCOL.md
    ├── EXT_04_CREATE_SKILL.md
    └── templates/

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Layer Descriptions

Layer 1: Bootstrap (.claude/skills/)

Entry point for LLM sessions. Contains:

• 00_BOOTSTRAP.md - Quick orientation and task routing
• 01_CHEATSHEET.md - "I want X → Use Y" lookup
• 02_CONTEXT_LOADER.md - What to load per task
• PROTOCOL_EXECUTION.md - Meta-protocol for execution

Layer 2: Operations (operations/)

Day-to-day how-to guides:

• OP_01: Create optimization study
• OP_02: Run optimization
• OP_03: Monitor progress
• OP_04: Analyze results
• OP_05: Export training data
• OP_06: Troubleshoot issues
• OP_07: Disk optimization (free space)
• OP_08: Generate study report

Layer 3: System (system/)

Core technical specifications:

• SYS_10: Intelligent Multi-Strategy Optimization (IMSO)
• SYS_11: Multi-Objective Support (MANDATORY)
• SYS_12: Extractor Library
• SYS_13: Real-Time Dashboard Tracking
• SYS_14: Neural Network Acceleration
• SYS_15: Method Selector
• SYS_16: Self-Aware Turbo (SAT) Method
• SYS_17: Study Insights (Physics Visualization)
• SYS_18: Context Engineering (ACE Framework)

Layer 4: Extensions (extensions/)

Guides for extending Atomizer:

• EXT_01: Create new extractor
• EXT_02: Create lifecycle hook
• EXT_03: Create new protocol
• EXT_04: Create new skill

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Protocol Template

All protocols follow this structure:

# {LAYER}_{NUMBER}_{NAME}.md

<!--
PROTOCOL: {Full Name}
LAYER: {Operations|System|Extensions}
VERSION: {Major.Minor}
STATUS: {Active|Draft|Deprecated}
LAST_UPDATED: {YYYY-MM-DD}
PRIVILEGE: {user|power_user|admin}
LOAD_WITH: [{dependencies}]
-->

## Overview
{1-3 sentence description}

## When to Use
| Trigger | Action |
|---------|--------|

## Quick Reference
{Tables, key parameters}

## Detailed Specification
{Full content}

## Examples
{Working examples}

## Troubleshooting
| Symptom | Cause | Solution |

## Cross-References
- Depends On: []
- Used By: []

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Quick Navigation

By Task

I want to...	Protocol
Create a study	OP_01
Run optimization	OP_02
Check progress	OP_03
Analyze results	OP_04
Export neural data	OP_05
Fix errors	OP_06
Free disk space	OP_07
Generate report	OP_08
Add extractor	EXT_01

By Protocol Number

#	Name	Layer
10	IMSO	System
11	Multi-Objective	System
12	Extractors	System
13	Dashboard	System
14	Neural	System
15	Method Selector	System
16	Self-Aware Turbo	System
17	Study Insights	System
18	Context Engineering	System

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Privilege Levels

Level	Operations	System	Extensions
user	All OP_*	Read SYS_*	None
power_user	All OP_*	Read SYS_*	EXT_01, EXT_02
admin	All	All	All

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Version History

Version	Date	Changes
1.0	2025-12-05	Initial Protocol Operating System
1.1	2026-01-06	Added OP_07, OP_08; SYS_16, SYS_17, SYS_18; Fixed SYS_16 duplication