# Atomizer Protocol Operating System (POS)

**Version**: 1.1
**Last Updated**: 2026-01-06

---

## Overview

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

---

## 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/
```

---

## 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

---

## Protocol Template

All protocols follow this structure:

```markdown
# {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: []
```

---

## Quick Navigation

### By Task

| I want to... | Protocol |
|--------------|----------|
| Create a study | [OP_01](operations/OP_01_CREATE_STUDY.md) |
| Run optimization | [OP_02](operations/OP_02_RUN_OPTIMIZATION.md) |
| Check progress | [OP_03](operations/OP_03_MONITOR_PROGRESS.md) |
| Analyze results | [OP_04](operations/OP_04_ANALYZE_RESULTS.md) |
| Export neural data | [OP_05](operations/OP_05_EXPORT_TRAINING_DATA.md) |
| Fix errors | [OP_06](operations/OP_06_TROUBLESHOOT.md) |
| Free disk space | [OP_07](operations/OP_07_DISK_OPTIMIZATION.md) |
| Generate report | [OP_08](operations/OP_08_GENERATE_REPORT.md) |
| Add extractor | [EXT_01](extensions/EXT_01_CREATE_EXTRACTOR.md) |

### By Protocol Number

| # | Name | Layer |
|---|------|-------|
| 10 | IMSO | [System](system/SYS_10_IMSO.md) |
| 11 | Multi-Objective | [System](system/SYS_11_MULTI_OBJECTIVE.md) |
| 12 | Extractors | [System](system/SYS_12_EXTRACTOR_LIBRARY.md) |
| 13 | Dashboard | [System](system/SYS_13_DASHBOARD_TRACKING.md) |
| 14 | Neural | [System](system/SYS_14_NEURAL_ACCELERATION.md) |
| 15 | Method Selector | [System](system/SYS_15_METHOD_SELECTOR.md) |
| 16 | Self-Aware Turbo | [System](system/SYS_16_SELF_AWARE_TURBO.md) |
| 17 | Study Insights | [System](system/SYS_17_STUDY_INSIGHTS.md) |
| 18 | Context Engineering | [System](system/SYS_18_CONTEXT_ENGINEERING.md) |

---

## 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 |

---

## 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 |