# Atom Documentation Index

> **Last Updated**: July 12, 2026
> **Purpose**: Comprehensive index of all Atom documentation with quick links and descriptions

**📚 [Back to Documentation Hub](README.md)** - Browse by category (Agents, Intelligence, Integration, Platform)

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## 🚀 Recent Updates (July 2026)

- **Swarm Coordination & Stigmergic Field Guide**: ✨ NEW - Three advanced multi-agent coordination patterns from Cursor swarm research (2026), implemented in production:
  - **Stigmergic Field Guide** (`core/field_guide_service.py`): Agent-curated shared Markdown ops manual auto-injected into system prompts. 50-line budget, per-workspace, deduplicated. See [SWARM_COORDINATION.md](architecture/SWARM_COORDINATION.md).
  - **Parallel Branch Reconciler** (`conductor_agent._reconcile_branch_conflicts`): Neutral third-party mediator that merges per-key output from diverging parallel branches instead of discarding minority work.
  - **Megafile & Bloat Tripwire** (`sandbox_tripwire.MegafileDetector`): Tracks file edits per loop; blocks hotspot megafiles (>800 LOC or ≥5 edits/loop) and emits `HarnessEvolutionService`-compatible patch proposals for auto-modularization.
- **Bugs Found and Fixed via User-Journey Testing**: ✨ NEW - catalog of the real defects the end-to-end suite uncovered (router double-prefixes, async/await bugs, frontend response-shape mismatches, RBAC gaps, CI/Docker flakiness), each with symptom → root cause → fix → commit. Read before debugging a regression. See [BUGS_FOUND_AND_FIXED.md](architecture/BUGS_FOUND_AND_FIXED.md).

- **Workbook Runtime**: ✨ NEW - Excel engine replaced openpyxl-as-parser with a formula-evaluating runtime (`core/workbook_runtime.py`). LibreOffice headless primary (recalc + pixel-accurate HTML render + structural edits), `formulas` library fallback, openpyxl cached-values last resort. `office_service.py` write_cell now recalculates and returns computed values; render_to_html produces evaluated output with conditional formatting. See [WORKBOOK_RUNTIME.md](architecture/WORKBOOK_RUNTIME.md).
- **Integration Resilience Layer**: ✨ NEW - Universal HTTP wrapper (`core/integration_http.py`) for all third-party API calls: circuit breaker, rate limiting, 429 Retry-After parsing, exponential backoff, 401 token refresh, health monitoring. 89 calls across 13 services wired.
- **Phase 2/4/5 Integration Complete**: ✨ All five enhancement phases are now genuinely delivered end-to-end, not just committed libraries:
  - **Phase 2 (GraphRAG)**: Multi-hop scored expansion wired into `local_search`; `build_communities` populates the community table; `leidenalg` dependency added (with Louvain fallback).
  - **Phase 4 (Federation)**: New `api/routes/federation_routes.py` exposes DIDs, verifiable credentials, zero-trust verification, and security health/stats at `/api/federation/...` (the previously broken import in `main_api_app.py` now resolves).
  - **Phase 5 (Orchestration)**: EventBus lifecycle events published by every live workflow; Conductor Agent endpoint at `POST /api/v1/workflows/conductor/execute` with 5 execution strategies; state-machine + rollback integrated.
  - **Phase 1 (Memory)**: POMDP-backed consolidation service now wired correctly (was importing the legacy class) and scheduled on a 6-hour background loop (was never invoked).
  - **Bug fix**: Word-doc canvas→file sync was crashing (`office_sync_service.py` missing `import docx`).
- **Learning LLM Router**: ✨ NEW - Per-model satisfaction predictors that re-rank BPC candidates from observed outcomes. A genuine end-to-end learning loop: the router observes response quality (truncation, schema failures, refusals), collects user feedback (thumbs up/down + regenerate), and re-ranks model candidates as data accumulates. Flag-gated (`ATOM_LEARNING_ROUTER`, default off). DB-persisted feedback (`llm_routing_feedback` table, migration `20260711`). Live `POST /api/chat/feedback` + `GET /api/chat/routing-stats` endpoints. Model visibility badge on chat messages + routing dashboard at `/settings/routing`.
  - [LEARNING_LLM_ROUTER.md](architecture/LEARNING_LLM_ROUTER.md) - Architecture, the singleton registry, per-model predictors, quality assessment, the flag, the user journey, and honest limitations.
- **Office Automation & Canvas Co-Editing**: ✨ NEW - Direct python-based manipulation (read/write/render) and live co-editing of Word (`.docx`), Excel (`.xlsx`), and PowerPoint (`.pptx`) documents. Excel workbooks run through a formula-evaluating workbook runtime (LibreOffice headless → `formulas` library → openpyxl fallback) so agents see computed values, not unevaluated formula strings.
  - [ATOM_OFFICE_AUTOMATION_GUIDE.md](guides/ATOM_OFFICE_AUTOMATION_GUIDE.md) - Covers: (a) DOM-like sheet coordinate paths, (b) Word & PowerPoint modifiers, (c) Interactive Canvas co-editing with real-time sync, (d) CLI commands and API endpoints, (e) formula evaluation + pixel-accurate rendering via the workbook runtime.
  - [WORKBOOK_RUNTIME.md](architecture/WORKBOOK_RUNTIME.md) - Excel engine architecture: LibreOffice headless (recalc + render + structural edits) → `formulas` library → openpyxl cached values.
  - Integrates directly with frontend `CanvasHost.tsx` for real-time bi-directional collaboration.

## 🚀 Recent Updates (June 2026)

- **Execution Sandbox Layer**: ✨ NEW (Rounds 43-47) - Deterministic blast-radius layer that closes the "tier is routing, not security" gap
  - [SANDBOX_LAYER.md](architecture/SANDBOX_LAYER.md) - Five-phase design: (A) policy + audit table, (B) filesystem scope, (C) tripwires + resource caps + KillRun, (D) Firecracker microVM + dual-proxy egress, (E) provenance tagging + LLM ActionJudge
  - Closes the gap documented in [TRUST_VS_SANDBOX.md](security/TRUST_VS_SANDBOX.md) and [PROMPT_INJECTION_DEFENSE_PLAN.md](security/PROMPT_INJECTION_DEFENSE_PLAN.md)
  - Migration `20260630_add_sandbox_tables` (chains on Round 42, guarded per SQLite hybrid-DB pattern)
  - Shadow mode default — compute + audit always on, enforcement off (`ATOM_SANDBOX_FORCE_ENFORCE=false`)
  - 166 tests across 5 files in `tests/unit/core/test_sandbox_*.py`
- **Self-Consistency Voter**: ✨ NEW (Round 42) - N-sample majority vote on structured plans (Wang et al. 2022)
  - [SELF_CONSISTENCY_VOTER.md](architecture/SELF_CONSISTENCY_VOTER.md) - VoteResult tri-state mirroring match-confidence; shadow + audit extensions on PR #548 base
  - Migration `20260629_add_self_consistency_votes` (guarded)
- **Pre-Action Match-Confidence Layer**: ✨ NEW (Round 41) - Selector-certainty scorer mirroring the post-action `VerifiedOutcome` tri-state
  - [MATCH_CONFIDENCE.md](architecture/MATCH_CONFIDENCE.md) - Pre-action `high/partial/ambiguous` gating through ProposalService (including AUTONOMOUS)
  - [SELECTOR_CONFIDENCE_THRESHOLDS.md](architecture/SELECTOR_CONFIDENCE_THRESHOLDS.md) - Tuning env vars + score curve
  - Migration `20260628_add_match_confidence_gating_flag` (per-agent opt-out column)
  - Shadow mode default — computation + audit always on, gating off (`MATCH_CONFIDENCE_FORCE_PROPOSAL=false`)
- **2026 Enhancement Plan**: ✅ COMPLETE - All 5 phases delivered with validation metrics
  - [ARBOR_FRAMEWORK.md](architecture/ARBOR_FRAMEWORK.md) - **✨ NEW: Arbor Hypothesis Tree Refinement (HTR)** - Tree-based LLM code generation with cumulative learning
  - [HARNESS_EVOLUTION.md](architecture/HARNESS_EVOLUTION.md) - **✨ NEW: Self-Evolving Harness & Weakness Mining** - Offline trace analysis, weakness mining, and auto-mutation patches
  - Phase 1: POMDP Memory Framework - Experience-driven agent learning
  - Phase 2: GraphRAG Enhancement - Multi-hop expansion, dynamic graphs
  - Phase 3: Learning-Based LLM Routing - per-model predictors, DB persistence, live feedback, quality signals, re-ranking. See [LEARNING_LLM_ROUTER.md](architecture/LEARNING_LLM_ROUTER.md). Flag-gated (`ATOM_LEARNING_ROUTER`).
  - 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
  - [canvas/README.md](canvas/README.md) - Canvas with POMDP memory, GraphRAG, orchestration
  - [canvas/feedback-memory.md](canvas/feedback-memory.md) - Canvas feedback with experience-driven graduation
  - [canvas/agent-learning.md](canvas/agent-learning.md) - Canvas learning with Conductor Agent
- **UI/UX Enhancement**: ✅ COMPLETE - User journeys updated with 2026 features
  - [guides/USER_PERSONAS_AND_JOURNEYS.md](guides/USER_PERSONAS_AND_JOURNEYS.md) - Enhanced personas with Phase 1-5
  - [guides/USER_GUIDE.md](guides/USER_GUIDE.md) - Multi-agent governance and memory sections
  - [guides/QUICKSTART.md](guides/QUICKSTART.md) - Phase 1-5 quick examples

## 🚀 Recent Updates (April 2026)

- **Documentation Updates**: ✨ NEW - Added 7 comprehensive documentation files with verified metrics
  - [PYTHON_PACKAGES.md](security/python-packages.md) - Python Package Support system (350K+ PyPI packages)
  - [FLEET_ADMIRAL.md](agents/fleet-admiral.md) - Multi-agent fleet coordination
  - CANVAS_AI_ACCESSIBILITY.md - Canvas AI accessibility and state API
  - LLM_CANVAS_SUMMARIES.md - LLM-generated canvas summaries
  - [agents/unstructured-tasks.md](agents/unstructured-tasks.md) - Intent classification and fleet recruitment
  - [STUDENT_AGENT_TRAINING_IMPLEMENTATION.md](archive/legacy/STUDENT_AGENT_TRAINING_IMPLEMENTATION.md) - Agent maturity system
  - [ATOM_CLI_SKILLS_GUIDE.md](guides/ATOM_CLI_SKILLS_GUIDE.md) - Built-in CLI skills
- **Commercial Marketplace**: ✨ NEW - Mothership architecture with atomagentos.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](reference/DOCUMENTATION_STRUCTURE_GUIDE.md) | **✨ NEW: Complete docs structure guide** - Navigation, organization, maintenance | Apr 7, 2026 |
| [DOCS_ATOMAGENTOS_GUIDE.md](guides/DOCS_ATOMAGENTOS_GUIDE.md) | **✨ NEW: docs.atomagentos.com guide** - Commercial platform documentation | Apr 7, 2026 |

---

## 🚀 Getting Started

| Document | Description | Last Updated |
|----------|-------------|--------------|
| [README.md](../README.md) | Project overview and quick start | - |
| [PERSONAL_EDITION.md](operations/personal-edition.md) | **Personal Edition - Run Atom locally** | Feb 16, 2026 |
| [COMMUNITY_SKILLS.md](integrations/community-skills.md) | **Community Skills Integration (5,000+ skills)** | Feb 16, 2026 |
| [DEVELOPMENT.md](development/overview.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](../CONTRIBUTING.md#security-guidelines) for critical security guidelines.

| Document | Description | Last Updated |
|----------|-------------|--------------|
| [architecture/SANDBOX_LAYER.md](architecture/SANDBOX_LAYER.md) | **Execution Sandbox Layer** - 5-phase blast-radius defense (Rounds 43-47) | Jun 30, 2026 |
| [security/TRUST_VS_SANDBOX.md](security/TRUST_VS_SANDBOX.md) | **Trust tier ≠ security boundary** - Why maturity routing needs a sandbox | Jun 27, 2026 |
| [security/PROMPT_INJECTION_DEFENSE_PLAN.md](security/PROMPT_INJECTION_DEFENSE_PLAN.md) | **Prompt injection defense plan** - ✅ Implemented (Rounds 43-47) | Jun 30, 2026 |
| [CONTRIBUTING.md](../CONTRIBUTING.md) | **Security guidelines** - NEVER commit .claude/, .env, secrets, credentials | Apr 23, 2026 |
| [security/packages.md](security/packages.md) | Package security, Python package scanning, & vulnerability checks | July 19, 2026 |
| [guides/ADMINISTRATORS/SECURITY_CONFIG.md](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](../LICENSE.md#marketplace-commercial-appendix) for details.

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

---

## 🌐 Community Skills & Package Support

| Document | Description | Last Updated |
|----------|-------------|--------------|
| [**Marketplace Documentation**](marketplace/) | **✨ 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](integrations/community-skills.md) | **5,000+ OpenClaw/ClawHub skills guide** | Feb 19, 2026 |
| [security/packages.md](security/packages.md) | **Package Governance & Security (Vulnerability scanning & sandbox controls)** | July 19, 2026 |
| [NPM_PACKAGE_SUPPORT.md](security/npm-packages.md) | **npm Package Support (Lodash, Express, 2M+ packages)** | Feb 19, 2026 |
| [ADVANCED_SKILL_EXECUTION.md](integrations/advanced-skills.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](operations/performance.md) | Performance optimization and benchmarks | Feb 19, 2026 |
| [ATOM_CLI_SKILLS_GUIDE.md](guides/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](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](security/WEBHOOK_VERIFICATION.md) | **Slack, Teams, Gmail webhook signature verification** | Feb 6, 2026 |
| [COMPLIANCE.md](security/COMPLIANCE.md) | GDPR, SOC2, HIPAA considerations | - |
| [SECURITY_OVERVIEW.md](security/SECURITY_OVERVIEW.md) | Security architecture overview | - |

---

## 🤖 Agent Systems

### Core Agent Features
| Document | Description | Last Updated |
|----------|-------------|--------------|
| [AGENT_GOVERNANCE_LEARNING_INTEGRATION.md](agents/governance.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](archive/legacy/STUDENT_AGENT_TRAINING_IMPLEMENTATION.md) | **Agent maturity system (STUDENT → AUTONOMOUS)** | Feb 2, 2026 |
| [agents/guidance-system.md](agents/guidance-system.md) | **Real-time agent operation tracking** | Feb 2, 2026 |

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

### Intelligence & Learning Systems
| Document | Description | Last Updated |
|----------|-------------|--------------|
| [ARBOR_FRAMEWORK.md](architecture/ARBOR_FRAMEWORK.md) | **✨ Arbor Framework - Hypothesis Tree Refinement (HTR)** - LLM code generation with tree search | Jun 18, 2026 |
| [intelligence/overview.md](intelligence/overview.md) | **Intelligence systems overview** - Memory, knowledge, and reasoning | Apr 7, 2026 |
| [intelligence/episodic-memory.md](intelligence/episodic-memory.md) | **Episodic Memory - Agent learning framework** | Feb 3, 2026 |
| [architecture/CONTEXT_MEMORY.md](architecture/CONTEXT_MEMORY.md) | **Context Memory - Per-turn fact extraction** - Hermes-style durable-fact layer, two-tier recall, embedded LanceDB | Jun 24, 2026 |
| [architecture/HERMES_COMPARISON.md](architecture/HERMES_COMPARISON.md) | **Atom vs. Hermes Agent** - Capability matrix, decision log, what was deliberately deferred | Jun 24, 2026 |
| [intelligence/self-evolution.md](intelligence/self-evolution.md) | **✨ Self-Evolution & Reflection Pool** - Critique-based learning and Auto-Dev | Apr 12, 2026 |
| [intelligence/graphrag.md](intelligence/graphrag.md) | **GraphRAG & Entity Types** - Knowledge graph and entity extraction | Mar 24, 2026 |
| [intelligence/episodic-memory.md](intelligence/episodic-memory.md) | **Episodic Memory, Embeddings & World Model** - Semantic memory & FastEmbed search | July 19, 2026 |
| [intelligence/jit-facts.md](intelligence/jit-facts.md) | **JIT Fact Provision** - Real-time fact verification with citations | Apr 7, 2026 |
| [intelligence/memory-integration.md](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](archive/implementation/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](archive/implementation/SPECIALIZED_CANVAS_TYPES_IMPLEMENTATION_COMPLETE.md) | Specialized canvas types | Feb 2, 2026 |

### Canvas AI & State
| Document | Description | Last Updated |
|----------|-------------|--------------|
| [canvas/ai-accessibility.md](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](canvas/llm-summaries.md) | **LLM-powered semantic summaries** | Apr 2026 |

### Canvas Collaboration
| Document | Description | Last Updated |
|----------|-------------|--------------|
| [archive/COLLABORATION_PHASE_4_COMPLETE.md](archive/implementation/COLLABORATION_PHASE_4_COMPLETE.md) | Multi-agent canvas coordination | Feb 1, 2026 |
| [CANVAS_RECORDING_IMPLEMENTATION.md](canvas/recording.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](api/OVERVIEW.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](integrations/OVERVIEW.md) | **Complete workflow guide** | - |
| [INTEGRATIONS.md](integrations/OVERVIEW.md) | AI-powered workflow optimization | - |
| [MONITORING_GUIDE.md](deployment/MONITORING_SETUP.md) | Track workflow performance | - |
| MULTI_INTEGRATION_WORKFLOW_ENGINE.md | Multi-integration workflows | - |

---

## 📱 Mobile

| Document | Description | Last Updated |
|----------|-------------|--------------|
| [REACT_NATIVE_ARCHITECTURE.md](archive/mobile/REACT_NATIVE_ARCHITECTURE.md) | React Native architecture | Feb 1, 2026 |
| [MOBILE_QUICK_START.md](archive/mobile/MOBILE_QUICK_START.md) | Mobile development quick start | Feb 1, 2026 |
| [MOBILE_DEPLOYMENT.md](archive/mobile/MOBILE_DEPLOYMENT.md) | Mobile deployment guide | Feb 1, 2026 |
| [archive/MOBILE_SCREENS_IMPLEMENTATION_COMPLETE.md](archive/implementation/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](archive/legacy/DEEPLINK_IMPLEMENTATION.md) | **External app integration via atom:// URLs** | Feb 1, 2026 |

---

## 📊 Data & Performance

### Database
| Document | Description | Last Updated |
|----------|-------------|--------------|
| [DATABASE_MIGRATION_GUIDE.md](archive/legacy/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](development/code-quality.md) | Code quality guidelines | Feb 4, 2026 |
| [CODEBASE_HEALTH_CHECK.md](archive/legacy/CODEBASE_HEALTH_CHECK.md) | Codebase health check | Feb 3, 2026 |

---

## 🚢 Deployment

| Document | Description | Last Updated |
|----------|-------------|--------------|
| [Production Readiness](operations/production-readiness.md) | **Production deployment checklist** | Feb 5, 2026 |
| DEPLOYMENT_GUIDE.md | AWS, GCP, Azure deployment | - |
| [PERSONAL_EDITION.md](operations/personal-edition.md) | Docker deployment guide | - |

---

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

| Document | Description | Last Updated |
|----------|-------------|--------------|
| [API_DOCUMENTATION.md](api/OVERVIEW.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](../docs/testing/API_TESTING_GUIDE.md) | **API testing guide (18,288 lines)** | Feb 16, 2026 |
| [CODE_QUALITY_STANDARDS.md](development/code-quality.md) | **Type hints, MyPy, code quality (9,412 lines)** | Feb 16, 2026 |

### Monitoring & Observability

| Document | Description | Last Updated |
|----------|-------------|--------------|
| [MONITORING_SETUP.md](deployment/MONITORING_SETUP.md) | **Health checks, Prometheus metrics, logging** | Feb 16, 2026 |
| HEALTH_MONITORING_SYSTEM.md | Health monitoring system | Feb 2, 2026 |
| [MONITORING_GUIDE.md](deployment/MONITORING_SETUP.md) | Monitoring guide | Feb 2, 2026 |

### CI/CD Pipeline

| Document | Description | Last Updated |
|----------|-------------|--------------|
| [.github/workflows/deploy.yml](../.github/workflows/deploy.yml) | **CI/CD pipeline (test, build, deploy)** | Feb 16, 2026 |
| [.github/workflows/ci.yml](../.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](testing/e2e-guide.md) | **E2E testing guide (91+ comprehensive tests)** | Mar 28, 2026 |
| [Phase 234: Authentication & Agent E2E](../.planning/phases/234-authentication-and-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](../.planning/phases/237-bug-discovery-infrastructure-foundation/) | **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](../.planning/phases/236-cross-platform-and-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](development/code-quality.md) | **Testing best practices (TQ-01 through TQ-05)** | Feb 16, 2026 |
| [CI_FIXES.md](archive/legacy/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](archive/legacy/FUNCTIONALITY_TEST.md) | Functionality testing guide | - |

**Test Suite Summary**:
- 27,000+ test functions (unit, integration, E2E, bug discovery, regression)
- Pass rate: targeted 100% before merge (CI-enforced)
- ~17-27% overall line coverage (expanding; new code requires ≥70%)
- 60-70% coverage for MCP service
- <60min full suite execution time
- <30s per test performance target

---

## 📚 Reference

### Architecture
| Document | Description | Last Updated |
|----------|-------------|--------------|
| [ARCHITECTURE.md](architecture/SYSTEM_OVERVIEW.md) | System architecture overview | Feb 1, 2026 |
| CODE_STRUCTURE_OVERVIEW.md | Code structure overview | - |
| [DATABASE_ARCHITECTURE.md](reference/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/OVERVIEW.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](archive/legacy/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)
- IMPLEMENTATION_SUMMARY.md - General implementation summary
- IMPLEMENTATION_SUMMARY_FEB_2026.md - February 2026 summary
- IMPLEMENTATION_PROGRESS.md - Implementation progress
- IMPLEMENTATION_FIXES_FEB2026.md - February 2026 fixes
- INCOMPLETE_IMPLEMENTATIONS_FIX_SUMMARY.md - Incomplete fixes summary

### Archived Implementation Summaries (2025-12)
- BROWSER_IMPLEMENTATION_SUMMARY.md - Browser automation implementation
- DEVICE_WEBSOCKET_IMPLEMENTATION.md - Device WebSocket implementation
- JAVASCRIPT_EXECUTION_IMPLEMENTATION.md - JavaScript execution implementation
- MENUBAR_IMPLEMENTATION_SUMMARY.md - MenuBar implementation

### Legacy Reports
- [ATOM-Testing-Report.md](archive/legacy-reports/ATOM-Testing-Report.md) - Testing report
- [analytics_dashboard_ui_verification_report.md](archive/legacy-reports/analytics_dashboard_ui_verification_report.md) - Analytics dashboard verification
- [comprehensive_bug_analysis_and_fixes.md](archive/legacy-reports/comprehensive_bug_analysis_and_fixes.md) - Bug analysis
- [comprehensive_workflow_engine_testing_report.md](archive/legacy-reports/comprehensive_workflow_engine_testing_report.md) - Workflow engine testing
- [bug_fixes_and_improvements.md](archive/legacy-reports/bug_fixes_and_improvements.md) - Bug fixes
- [final_workflow_engine_ui_testing_report.md](archive/legacy-reports/final_workflow_engine_ui_testing_report.md) - Final UI testing

### Old Guides
- [manual-testing-checklist.md](archive/old-guides/manual-testing-checklist.md) - Manual testing checklist
- [IMMEDIATE_NEXT_STEPS.md](archive/old-guides/IMMEDIATE_NEXT_STEPS.md) - Immediate next steps
- [missing_credentials_guide.md](archive/old-guides/missing_credentials_guide.md) - Legacy credentials guide
- [FOCUSED_DEV_PLAN.md](archive/old-guides/FOCUSED_DEV_PLAN.md) - Development plan
- [CHAT_INTERFACE_QUICK_START.md](archive/old-guides/CHAT_INTERFACE_QUICK_START.md) - Chat interface quick start
- [TESTING-INSTRUCTIONS.md](archive/old-guides/TESTING-INSTRUCTIONS.md) - Testing instructions
- phase24_quickstart.md - Phase 24 quick start
- [ENHANCEMENT_NEXT_STEPS.md](archive/old-guides/ENHANCEMENT_NEXT_STEPS.md) - Enhancement next steps

### Archive Index
- INCOMPLETE_FIXES_COMPLETE.md - Incomplete fixes completion
- INCOMPLETE_IMPLEMENTATION_FIX_SUMMARY.md - Implementation fix summary
- INCOMPLETE_FIXES_SUMMARY.md - Fixes summary
- TODO_FEATURES_IMPLEMENTATION_SUMMARY.md - TODO features implementation
- TODO_FEATURES_QUICK_REFERENCE.md - TODO features reference

---

## 🔍 Quick Find

### By Topic

**Security**:
- [AUTHENTICATION.md]# - OAuth and session management
- [DATA_PROTECTION.md]# - Encryption and secrets
- [WEBHOOK_VERIFICATION.md](security/WEBHOOK_VERIFICATION.md) - Webhook security

**Agent Systems**:
- [STUDENT_AGENT_TRAINING_IMPLEMENTATION.md](archive/legacy/STUDENT_AGENT_TRAINING_IMPLEMENTATION.md) - Agent maturity
- [intelligence/episodic-memory.md](intelligence/episodic-memory.md) - Agent learning
- [agents/guidance-system.md](agents/guidance-system.md) - Real-time guidance

**Canvas**:
- [CANVAS_IMPLEMENTATION_COMPLETE.md](archive/implementation/CANVAS_IMPLEMENTATION_COMPLETE.md) - Canvas system
- CANVAS_FEEDBACK_EPISODIC_MEMORY.md - Canvas in episodes

**Integrations**:
- [BYOK_LLM_INTEGRATION_COMPLETE.md]# - LLM providers
- [INTEGRATIONS.md](integrations/OVERVIEW.md) - Workflows

**Background Jobs**:
- TASK_QUEUE_GUIDE.md - RQ and Redis setup

### By Date (Most Recent)

**February 2026**:
- [COMMUNITY_SKILLS.md](integrations/community-skills.md) - **Community Skills Integration guide** (Feb 16)
- [PERSONAL_EDITION.md](operations/personal-edition.md) - **Personal Edition guide** (Feb 16)
- VECTOR_EMBEDDINGS.md - **Vector embeddings guide** (Feb 16)
- [API_DOCUMENTATION.md](api/OVERVIEW.md) - **Comprehensive API docs** (Feb 16)
- DEPLOYMENT_RUNBOOK.md - **Deployment runbook** (Feb 16)
- OPERATIONS_GUIDE.md - **Operations guide** (Feb 16)
- TROUBLESHOOTING.md - **Troubleshooting** (Feb 16)
- [MONITORING_SETUP.md](deployment/MONITORING_SETUP.md) - **Monitoring setup** (Feb 16)
- [CODE_QUALITY_STANDARDS.md](development/code-quality.md) - **Code quality** (Feb 16)
- [API_TESTING_GUIDE.md](../docs/testing/API_TESTING_GUIDE.md) - **API testing** (Feb 16)

### Canvas & AI Features (Phase 20-23)
- CANVAS_AI_ACCESSIBILITY.md - **AI agent accessibility with dual representation** (Feb 2026)
- CANVAS_STATE_API.md - **JavaScript API for real-time canvas state** (Feb 2026)
- LLM_CANVAS_SUMMARIES.md - **LLM-powered semantic summaries** (Feb 2026)

### Core Development (Feb 6)
- [DEVELOPMENT.md](development/overview.md) - Updated with security, testing, task queue (Feb 6)
- [IMPLEMENTATION_HISTORY.md](archive/legacy/IMPLEMENTATION_HISTORY.md) - Consolidated history (Feb 6)
- TASK_QUEUE_GUIDE.md - Background task queue (Feb 6)
- [WEBHOOK_VERIFICATION.md](security/WEBHOOK_VERIFICATION.md) - Webhook security (Feb 6)
- [AUTHENTICATION.md]# - Updated with validation (Feb 6)
- [DATA_PROTECTION.md]# - Updated with encryption (Feb 6)
- CANVAS_FEEDBACK_EPISODIC_MEMORY.md - Canvas integration (Feb 4)
- [DATABASE_MIGRATION_GUIDE.md](archive/legacy/DATABASE_MIGRATION_GUIDE.md) - Migration guide (Feb 4)
- EPISODIC_MEMORY_QUICK_START.md - Quick start (Feb 4)
- AGENT_GRADUATION_GUIDE.md - Graduation criteria (Feb 3)
- [intelligence/episodic-memory.md](intelligence/episodic-memory.md) - Memory framework (Feb 3)

**January 2026**:
- [STUDENT_AGENT_TRAINING_IMPLEMENTATION.md](archive/legacy/STUDENT_AGENT_TRAINING_IMPLEMENTATION.md) - Training system (Feb 2)
- [agents/guidance-system.md](agents/guidance-system.md) - Agent guidance (Feb 2)
- [CANVAS_IMPLEMENTATION_COMPLETE.md](archive/implementation/CANVAS_IMPLEMENTATION_COMPLETE.md) - Canvas system (Feb 1)
- [DEEPLINK_IMPLEMENTATION.md](archive/legacy/DEEPLINK_IMPLEMENTATION.md) - Deep linking (Feb 1)
- BROWSER_AUTOMATION.md - Browser automation (Jan 31)

---

## 📖 Backend Documentation

| Document | Description | Last Updated |
|----------|-------------|--------------|
| [INCOMPLETE_IMPLEMENTATIONS.md]# | **Recent fixes status (Feb 5, 2026)** | Feb 5, 2026 |
| [Production Readiness](operations/production-readiness.md) | 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](api/OVERVIEW.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](deployment/MONITORING_SETUP.md) | **Monitoring setup** | Feb 16, 2026 |
| [CODE_QUALITY_STANDARDS.md](development/code-quality.md) | **Code quality standards** | Feb 16, 2026 |
| [API_TESTING_GUIDE.md](../docs/testing/API_TESTING_GUIDE.md) | **API testing guide** | Feb 16, 2026 |

---

## 🔗 External References

- [FastAPI Documentation](https://fastapi.tiangolo.com/)
- [React Documentation](https://react.dev/)
- [Next.js Documentation](https://nextjs.org/docs)
- [Python Documentation](https://docs.python.org/3/)
- [Redis Queue (RQ)](https://python-rq.org/)
- [Playwright Documentation](https://playwright.dev/)

---

**Need Help?**
- Check [DEVELOPMENT.md](development/overview.md) for setup instructions
- Review [SECURITY/AUTHENTICATION.md]# for authentication issues
- See [IMPLEMENTATION_HISTORY.md](archive/legacy/IMPLEMENTATION_HISTORY.md) for recent changes

**Found an Issue?**
- Report bugs on GitHub
- Contribute improvements via pull requests
- Update documentation to keep it current