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Atom Documentation Index

Last Updated: April 10, 2026 Purpose: Comprehensive index of all Atom documentation with quick links and descriptions

📚 Back to Documentation Hub - Browse by category (Agents, Intelligence, Integration, Platform)


🚀 Recent Updates (June 2026)

  • 2026 Enhancement Plan: ✅ COMPLETE - All 5 phases delivered with validation metrics
    • ARBOR_FRAMEWORK.md - ✨ NEW: Arbor Hypothesis Tree Refinement (HTR) - Tree-based LLM code generation with cumulative learning
    • Phase 1: POMDP Memory Framework - Experience-driven agent learning
    • Phase 2: GraphRAG Enhancement - Multi-hop expansion, dynamic graphs
    • Phase 3: Learning-Based LLM Routing - RouteLLM with 15% cost savings
    • Phase 4: Zero-Trust Federation Identity - DID/VC with mTLS
    • Phase 5: Enhanced Orchestration - Conductor Agent, workflow state machine
  • Canvas Integration: ✅ COMPLETE - Canvas system integrated with Phase 1-5 features
  • UI/UX Enhancement: ✅ COMPLETE - User journeys updated with 2026 features

🚀 Recent Updates (April 2026)

  • Documentation Updates: ✨ NEW - Added 7 comprehensive documentation files with verified metrics
  • Commercial Marketplace: ✨ NEW - Mothership architecture with agentagentos.com - Proprietary marketplace for agents, domains, components, skills
  • Phase 234: E2E Testing Infrastructure - 486 E2E test functions with API-first authentication
  • Phase 237: Bug Discovery Infrastructure - AI-enhanced bug discovery (fuzzing, property-based testing, chaos)
  • Phase 236: Cross-Platform & Stress Testing - Load testing with k6, network simulation, failure injection
  • Phase 64: E2E Test Suite - 217+ E2E tests with real services (PostgreSQL, Redis, Docker)
  • Phase 63: Documentation Audit - 98/100 health score, all features documented
  • Phase 61: Skill Marketplace Sync - Bidirectional marketplace sync for skills and ratings
  • Phase 60: Advanced Skill Execution - Marketplace, composition, dynamic loading
  • Phase 36: npm Package Support - 2M+ packages with governance
  • Phase 35: Python Package Support - 350K+ packages with vulnerability scanning

📖 Documentation Guides

Document Description Last Updated
DOCUMENTATION_STRUCTURE_GUIDE.md ✨ NEW: Complete docs structure guide - Navigation, organization, maintenance Apr 7, 2026
DOCS_ATOMAGENTOS_GUIDE.md ✨ NEW: docs.atomagentos.com guide - Commercial platform documentation Apr 7, 2026

🚀 Getting Started

Document Description Last Updated
README.md Project overview and quick start -
PERSONAL_EDITION.md Personal Edition - Run Atom locally Feb 16, 2026
COMMUNITY_SKILLS.md Community Skills Integration (5,000+ skills) Feb 16, 2026
DEVELOPMENT.md Developer setup guide - Security, testing, deployment Feb 6, 2026
ATOM_ARCHITECTURE_SPEC.md High-level system design -
VECTOR_EMBEDDINGS.md Vector embeddings guide (FastEmbed, OpenAI, Cohere) Feb 16, 2026

🔒 Security & Compliance

⚠️ IMPORTANT: Before contributing, read CONTRIBUTING.md for critical security guidelines.

Document Description Last Updated
CONTRIBUTING.md Security guidelines - NEVER commit .claude/, .env, secrets, credentials Apr 23, 2026
security/SECURITY_OVERVIEW.md Security audit report (A- rating) Oct 19, 2025
security/python-packages.md Python package security & vulnerability scanning Feb 19, 2026
security/packages.md Package supply chain security Feb 19, 2026
guides/ADMINISTRATORS/SECURITY_CONFIG.md Security configuration for administrators -

🛒 Commercial Marketplace (atomagentos.com)

⚠️ Commercial Service: The marketplace is a proprietary service requiring connection to atomagentos.com. See LICENSE.md for details.

Document Description Last Updated
marketplace/connection.md ✨ NEW: Marketplace connection guide - Setup, configuration, troubleshooting Apr 7, 2026
GUIDES/MARKETPLACE_QUICKSTART.md ✨ NEW: Marketplace quick start - 5-minute setup Apr 10, 2026
marketplace/canvas-components.md ✨ NEW: Canvas component marketplace - Browse, install, use components Apr 7, 2026
marketplace/domains.md ✨ NEW: Domain marketplace - Specialist knowledge domains Apr 7, 2026
marketplace/skills.md Skills marketplace - Agent capabilities and integrations Apr 6, 2026
marketplace/analytics.md Marketplace analytics and usage tracking Apr 6, 2026

🌐 Community Skills & Package Support

Document Description Last Updated
Marketplace Documentation ✨ NEW: Complete marketplace guide (connection, skills, analytics) Apr 7, 2026
MARKETPLACE_CONNECTION_GUIDE.md ✨ NEW: Connect to Atom SaaS marketplace Apr 6, 2026
COMMUNITY_SKILLS.md 5,000+ OpenClaw/ClawHub skills guide Feb 19, 2026
PYTHON_PACKAGES.md Python Package Support (NumPy, Pandas, 350K+ packages) Apr 7, 2026
PACKAGE_GOVERNANCE.md Maturity-based access control and approval workflow Feb 19, 2026
PACKAGE_SECURITY.md Vulnerability scanning and supply chain security Feb 19, 2026
PYTHON_PACKAGES_DEPLOYMENT.md Production deployment and monitoring Feb 19, 2026
NPM_PACKAGE_SUPPORT.md npm Package Support (Lodash, Express, 2M+ packages) Feb 19, 2026
ADVANCED_SKILL_EXECUTION.md Phase 60: Marketplace, composition, dynamic loading Feb 19, 2026
SKILL_MARKETPLACE_GUIDE.md PostgreSQL-based skill marketplace guide Feb 19, 2026
SKILL_COMPOSITION_PATTERNS.md DAG workflows and skill composition Feb 19, 2026
PERFORMANCE_TUNING.md Performance optimization and benchmarks Feb 19, 2026
ATOM_CLI_SKILLS_GUIDE.md Built-in CLI skills (daemon, status, start, stop, execute, config) Apr 7, 2026

🌐 Federation & Multi-Instance

Document Description Last Updated
GUIDES/FEDERATION_INSTANCE_IDENTITY.md ✨ NEW: Federation & Instance Identity - Multi-instance communication Apr 10, 2026

🔒 Security

Document Description Last Updated
[AUTHENTICATION.md]# OAuth 2.0, session management, request validation Feb 6, 2026
[DATA_PROTECTION.md]# Fernet encryption, secrets management, migration Feb 6, 2026
WEBHOOK_VERIFICATION.md Slack, Teams, Gmail webhook signature verification Feb 6, 2026
COMPLIANCE.md GDPR, SOC2, HIPAA considerations -
SECURITY_OVERVIEW.md Security architecture overview -

🤖 Agent Systems

Core Agent Features

Document Description Last Updated
AGENT_GOVERNANCE_LEARNING_INTEGRATION.md Agent governance and learning integration Feb 2, 2026
AGENT_GRADUATION_GUIDE.md Agent promotion criteria and validation Feb 3, 2026
STUDENT_AGENT_TRAINING_IMPLEMENTATION.md Agent maturity system (STUDENT → AUTONOMOUS) Feb 2, 2026
agents/guidance-system.md Real-time agent operation tracking Feb 2, 2026

Multi-Agent Coordination

Document Description Last Updated
QUEEN_AGENT.md Queen Agent (Queen Hive) - Structured workflow automation Apr 7, 2026
GUIDES/QUEEN_AGENT_USER_GUIDE.md ✨ NEW: Queen Agent user guide - Blueprints, scheduling, monitoring Apr 10, 2026
agents/unstructured-tasks.md Intent classification & dynamic routing (CHAT/WORKFLOW/TASK) Apr 7, 2026
agents/fleet-admiral.md Multi-agent fleet coordination for unstructured long-horizon tasks Apr 7, 2026
agents/overview.md Agent system overview and intent classification Apr 7, 2026
GUIDES/QUEEN_VS_FLEET_ADMIRAL.md ✨ NEW: Queen Agent vs Fleet Admiral - Which orchestrator to use? Apr 10, 2026
GUIDES/AUTO_DEV_USER_GUIDE.md ✨ Auto-Dev Module - Self-evolving agent capabilities Apr 10, 2026
intelligence/self-evolution.md ✨ NEW: Self-Evolution & Reflection Pool - Complete guide Apr 12, 2026

Intelligence & Learning Systems

Document Description Last Updated
ARBOR_FRAMEWORK.md ✨ Arbor Framework - Hypothesis Tree Refinement (HTR) - LLM code generation with tree search Jun 18, 2026
intelligence/overview.md Intelligence systems overview - Memory, knowledge, and reasoning Apr 7, 2026
intelligence/episodic-memory.md Episodic Memory - Agent learning framework Feb 3, 2026
intelligence/self-evolution.md ✨ Self-Evolution & Reflection Pool - Critique-based learning and Auto-Dev Apr 12, 2026
intelligence/graphrag.md GraphRAG & Entity Types - Knowledge graph and entity extraction Mar 24, 2026
intelligence/world-model-guide.md World Model & Business Facts - Knowledge management and JIT provision Apr 7, 2026
intelligence/jit-facts.md JIT Fact Provision - Real-time fact verification with citations Apr 7, 2026
intelligence/vector-embeddings.md Vector Embeddings - Semantic search infrastructure (FastEmbed, OpenAI) Feb 16, 2026
intelligence/memory-integration.md Memory integration guide Feb 4, 2026
EPISODIC_MEMORY_QUICK_START.md Episodic memory quick start guide Feb 4, 2026
CANVAS_FEEDBACK_EPISODIC_MEMORY.md Canvas presentations in episodes Feb 4, 2026

🎨 Canvas System

Core Canvas

Document Description Last Updated
CANVAS_IMPLEMENTATION_COMPLETE.md Canvas presentation system Feb 1, 2026
CANVAS_QUICK_REFERENCE.md Canvas types and usage Feb 1, 2026
SPECIALIZED_CANVAS_TYPES_IMPLEMENTATION_COMPLETE.md Specialized canvas types Feb 2, 2026

Canvas AI & State

Document Description Last Updated
canvas/ai-accessibility.md AI agent accessibility with dual representation Apr 2026
CANVAS_STATE_API.md JavaScript API for real-time canvas state Feb 2026
canvas/llm-summaries.md LLM-powered semantic summaries Apr 2026

Canvas Collaboration

Document Description Last Updated
archive/COLLABORATION_PHASE_4_COMPLETE.md Multi-agent canvas coordination Feb 1, 2026
CANVAS_RECORDING_IMPLEMENTATION.md Canvas recording and replay Feb 2, 2026
CANVAS_AGENT_LEARNING_INTEGRATION.md Canvas and agent learning Feb 2, 2026

🔧 Integrations

Integration Guides

Document Description Last Updated
API.md Build custom integrations -
[CONTRIBUTING_INTEGRATIONS.md]# Integration contribution guide -
[BYOK_LLM_INTEGRATION_COMPLETE.md]# Multi-provider LLM setup Feb 5, 2026

Workflow Automation

Document Description Last Updated
INTEGRATIONS.md Complete workflow guide -
INTEGRATIONS.md AI-powered workflow optimization -
MONITORING_GUIDE.md Track workflow performance -
MULTI_INTEGRATION_WORKFLOW_ENGINE.md Multi-integration workflows -

📱 Mobile

Document Description Last Updated
REACT_NATIVE_ARCHITECTURE.md React Native architecture Feb 1, 2026
MOBILE_QUICK_START.md Mobile development quick start Feb 1, 2026
MOBILE_DEPLOYMENT.md Mobile deployment guide Feb 1, 2026
archive/MOBILE_SCREENS_IMPLEMENTATION_COMPLETE.md Mobile screens implementation Feb 5, 2026

🌐 Browser & Device

Document Description Last Updated
BROWSER_AUTOMATION.md Browser automation (Playwright CDP) Jan 31, 2026
BROWSER_QUICK_START.md Browser automation quick start Jan 31, 2026
DEVICE_CAPABILITIES.md Camera, screen recording, location Feb 1, 2026
DEEPLINK_IMPLEMENTATION.md External app integration via atom:// URLs Feb 1, 2026

📊 Data & Performance

Database

Document Description Last Updated
DATABASE_MIGRATION_GUIDE.md Database migration guide Feb 4, 2026
DATABASE_MODEL_AUDIT.md Database model audit Feb 4, 2026
DATABASE_MODEL_BEST_PRACTICES.md Database best practices Feb 4, 2026

Performance

Document Description Last Updated
PERFORMANCE_MONITORING_SETUP.md Performance monitoring setup -
CODE_QUALITY_GUIDE.md Code quality guidelines Feb 4, 2026
CODEBASE_HEALTH_CHECK.md Codebase health check Feb 3, 2026

🚢 Deployment

Document Description Last Updated
Production Readiness Production deployment checklist Feb 5, 2026
DEPLOYMENT_GUIDE.md AWS, GCP, Azure deployment -
PERSONAL_EDITION.md Docker deployment guide -

✨ Phase 15: Production Readiness (Feb 16, 2026)

Document Description Last Updated
API_DOCUMENTATION.md Comprehensive API documentation (26,299 lines) Feb 16, 2026
DEPLOYMENT_RUNBOOK.md Deployment procedures with rollback Feb 16, 2026
OPERATIONS_GUIDE.md Daily operations & common tasks Feb 16, 2026
TROUBLESHOOTING.md Production troubleshooting guide Feb 16, 2026
API_TESTING_GUIDE.md API testing guide (18,288 lines) Feb 16, 2026
CODE_QUALITY_STANDARDS.md Type hints, MyPy, code quality (9,412 lines) Feb 16, 2026

Monitoring & Observability

Document Description Last Updated
MONITORING_SETUP.md Health checks, Prometheus metrics, logging Feb 16, 2026
HEALTH_MONITORING_SYSTEM.md Health monitoring system Feb 2, 2026
MONITORING_GUIDE.md Monitoring guide Feb 2, 2026

CI/CD Pipeline

Document Description Last Updated
.github/workflows/deploy.yml CI/CD pipeline (test, build, deploy) Feb 16, 2026
.github/workflows/ci.yml CI pipeline with type checking Feb 16, 2026


🧪 Testing

E2E Testing ✨ NEW (March 2026)

Document Description Last Updated
E2E_TESTING_GUIDE.md E2E testing guide (91+ comprehensive tests) Mar 28, 2026
Phase 234: Authentication & Agent E2E E2E test infrastructure (AUTH-01 to AUTH-07, AGNT-01 to AGNT-08) Mar 24, 2026

E2E Test Infrastructure (Phase 234):

  • 91+ comprehensive E2E tests with Playwright Python 1.58.0
  • API-first authentication (10-100x faster than UI login)
  • Worker-based database isolation for parallel execution
  • Page Object Model for maintainable UI abstractions
  • Comprehensive fixture suite (auth, database, API, factory)
  • Tests complete in under 10 minutes with parallel execution

Bug Discovery ✨ NEW (March 2026)

Document Description Last Updated
[docs/testing/BUG_DISCOVERY_INFRASTRUCTURE.md]# AI-enhanced bug discovery infrastructure Mar 28, 2026
[docs/testing/BUG_DISCOVERY.md]# Bug discovery guide Mar 28, 2026
Phase 237: Bug Discovery Infrastructure Bug discovery foundation (fuzzing, property-based testing, chaos) Mar 24, 2026

Bug Discovery Features (Phase 237):

  • Automated fuzzing with atheris (coverage-guided fuzzing)
  • Mutation testing with mutmut for test quality validation
  • Property-based testing with Hypothesis framework (66+ invariants)
  • Chaos engineering with locust for load testing
  • Automated bug filing with GitHub Issues API integration
  • CI pipeline separation (fast PR tests <10min, weekly bug discovery ~2 hours)

Stress Testing ✨ NEW (March 2026)

Document Description Last Updated
Phase 236: Cross-Platform & Stress Testing Load testing, network simulation, cross-platform validation Mar 24, 2026

Stress Testing Features (Phase 236):

  • k6 load testing (10/50/100 concurrent users)
  • Network simulation (slow 3G, offline mode)
  • Failure injection (database drops, API timeouts)
  • Memory leak detection with CDP heap snapshots
  • Performance regression testing with Lighthouse CI
  • Cross-platform testing (mobile API-level, desktop Tauri)
  • Visual regression testing with Percy
  • Accessibility testing with jest-axe (WCAG 2.1 AA)

Test Quality & Standards

Document Description Last Updated
CODE_QUALITY_GUIDE.md Testing best practices (TQ-01 through TQ-05) Feb 16, 2026
CI_FIXES.md CI pipeline fixes (BYOK typo, dependencies, syntax errors) Feb 16, 2026
TEST_RESULTS_FEB2026.md Test results summary Feb 2026
FUNCTIONALITY_TEST.md Functionality testing guide -

Test Suite Summary:

  • 495+ tests (unit, integration, E2E, bug discovery)
  • 99%+ pass rate (TQ-02 standard)
  • 17-27% overall coverage (expanding to 80%)
  • 60-70% coverage for MCP service
  • <60min full suite execution time
  • <30s per test performance target

📚 Reference

Architecture

Document Description Last Updated
ARCHITECTURE.md System architecture overview Feb 1, 2026
CODE_STRUCTURE_OVERVIEW.md Code structure overview -
DATABASE_ARCHITECTURE.md Database architecture -

API Documentation

Document Description Last Updated
API_DOCUMENTATION_INDEX.md API documentation index Feb 4, 2026
API_STANDARDS.md API standards and conventions Feb 4, 2026
API.md API reference -

Guides

Document Description Last Updated
USER_GUIDE.md User guide -
USER_PERSONAS_AND_JOURNEYS.md User personas and journeys -
MEMORY_INTEGRATION_GUIDE.md Memory integration guide -
ERROR_HANDLING_GUIDELINES.md Error handling guidelines -

📋 Implementation History

Document Description Last Updated
IMPLEMENTATION_HISTORY.md Consolidated implementation timeline Feb 6, 2026
TASK_QUEUE_GUIDE.md Background task queue guide Feb 6, 2026

🗄️ Archive

Archived Implementation Summaries (2026)

Archived Implementation Summaries (2025-12)

Legacy Reports

Old Guides

Archive Index


🔍 Quick Find

By Topic

Security:

  • [AUTHENTICATION.md]# - OAuth and session management
  • [DATA_PROTECTION.md]# - Encryption and secrets
  • WEBHOOK_VERIFICATION.md - Webhook security

Agent Systems:

Canvas:

Integrations:

  • [BYOK_LLM_INTEGRATION_COMPLETE.md]# - LLM providers
  • INTEGRATIONS.md - Workflows

Background Jobs:

By Date (Most Recent)

February 2026:

Canvas & AI Features (Phase 20-23)

Core Development (Feb 6)

January 2026:


📖 Backend Documentation

Document Description Last Updated
[INCOMPLETE_IMPLEMENTATIONS.md]# Recent fixes status (Feb 5, 2026) Feb 5, 2026
Production Readiness Production deployment Feb 5, 2026
API_STANDARDS.md API standards Feb 4, 2026
[BYOK_LLM_INTEGRATION_COMPLETE.md]# LLM integration Feb 5, 2026
[FINAL_IMPLEMENTATION_SUMMARY.md]# Final implementation summary Feb 5, 2026
API_DOCUMENTATION.md Comprehensive API docs Feb 16, 2026
DEPLOYMENT_RUNBOOK.md Deployment runbook Feb 16, 2026
OPERATIONS_GUIDE.md Operations guide Feb 16, 2026
TROUBLESHOOTING.md Troubleshooting guide Feb 16, 2026
MONITORING_SETUP.md Monitoring setup Feb 16, 2026
CODE_QUALITY_STANDARDS.md Code quality standards Feb 16, 2026
API_TESTING_GUIDE.md API testing guide Feb 16, 2026

🔗 External References


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