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POLLN Documentation Index

Last Updated: 2026-03-10 Purpose: Complete inventory of all documentation across the project

Documentation by Category

PROJECT OVERVIEW & GUIDES

Quick Start Documents:

  • NEXT_SESSION_GUIDE.md - Step-by-step continuation guide
  • README.md - Main project README
  • ONBOARD_ROADMAP.md - Project roadmap and phases
  • OVERVIEW.md - Use cases and vision

Project Status:

  • PROJECT_AUDIT.md - Complete project audit
  • STATE_ASSESSMENT.md - Current completion status
  • TYPESCRIPT_FIX_PLAN.md - TypeScript error patterns and solutions

Documentation Guides:

  • CODE_GUIDE.md - Code style and patterns
  • CHANGELOG.md - Version history

ARCHITECTURE & DESIGN

System Architecture:

  • ARCHITECTURE.md - Complete system architecture
  • docs/ARCHITECTURE.md - Architecture deep dive (docs folder)
  • PROJECT_INTEGRATION.md - Integration patterns and standards

Component Analysis:

  • EXTRACTABLE_COMPONENTS.md - Reusable components
  • NOVELTY_REPORT.md - Novel implementations and patterns
  • TILE_SYSTEM_ANALYSIS.md - Deep dive into tile system

Specialized Systems:

  • docs/MICROBIOME_ARCHITECTURE.md - Microbiome ecosystem
  • docs/MICROBIOME_ORCHESTRATION.md - Microbiome operations
  • docs/LORA_SYSTEM_SUMMARY.md - LoRA system overview
  • docs/EMERGENT_INTELLIGENCE.md - Emergence patterns

INFRASTRUCTURE & DEPLOYMENT

Infrastructure Planning:

  • BACKEND_INFRASTRUCTURE.md - Backend systems overview
  • docs/DEPLOYMENT.md - Deployment guide
  • docs/SECURITY_AUDIT.md - Complete security audit
  • docs/SECURITY_IMPLEMENTATION.md - Security implementation guide

Operational Guides:

  • docs/BENCHMARK_GUIDE.md - Benchmarking methodology
  • docs/BENCHMARK_QUICKSTART.md - Quick start for benchmarks
  • docs/PERFORMANCE.md - Performance optimization

SECURITY & OPERATIONS

Security Documentation:

  • docs/SECURITY_AUDIT.md - Comprehensive audit
  • docs/SECURITY_CHECKLIST.md - Pre-deployment checklist
  • docs/SECURITY_USAGE_GUIDE.md - Using security features
  • docs/SECURITY_GUIDE.md - General security guidelines

Operational Procedures:

  • docs/SECURITY_IMPLEMENTATION.md - Implementation details
  • docs/INTEGRATION_ROADMAP.md - Integration planning

PHASE REPORTS

Completion Reports:

  • docs/PHASE12_COMPLETION_REPORT.md - Phases 1-2 completion
  • docs/phase4-sprint5-guardian-angel.md - Guardian system report
  • docs/phase4-sprint5-meta-tiles-simulations.md - Meta-tiles report
  • docs/phase5-benchmarks.md - Phase 5 benchmarks
  • docs/phase5-completion.md - Phase 5 completion status
  • docs/phase9-milestone3-report.md - Phase 9 milestone report

ADVANCED TOPICS

Research & Theory:

  • docs/ADVANCED_FEDERATED_LEARNING.md - Advanced federation
  • docs/DISTRIBUTED_MEMORY.md - Distributed memory systems
  • docs/EMERGENT_INTELLIGENCE.md - Emergence and complexity

Specialized Systems:

  • docs/LORA_SYSTEM_SUMMARY.md - LoRA overview
  • docs/MICROBIOME_ARCHITECTURE.md - Microbiome design
  • docs/MICROBIOME_ORCHESTRATION.md - Microbiome operations

Planning & Strategy:

  • docs/NAMING_WORKSHOP.md - Terminology and naming
  • docs/GLM47_PLAN.md - Advanced planning document
  • docs/graph-evolution-simulations.md - Graph evolution research

API DOCUMENTATION

API Reference:

  • docs/api/ - Complete API documentation
  • docs/api/examples/ - API usage examples
  • docs/api/endpoints/ - Endpoint reference

SDK Documentation:

  • docs/sdk/ - SDK usage guide
  • Published types in distributed packages

USER & DEVELOPER GUIDES

User Documentation:

  • docs/USER_GUIDE.md - End-user guide
  • docs/CLI_GUIDE.md - CLI usage guide
  • docs/ROADMAP.md - Feature roadmap

Developer Resources:

  • docs/CODE_GUIDE.md - Code patterns and conventions
  • docs/DEPLOYMENT.md - Deployment procedures
  • /examples/ - Comprehensive examples

Integration Guides:

  • docs/INTEGRATION_ROADMAP.md - Integration planning
  • PROJECT_INTEGRATION.md - Integration patterns

RESEARCH DOCUMENTATION

Research Guides:

  • docs/research/smp-paper/README.md - Research index
  • docs/research/smp-paper/EXECUTIVE_SUMMARY.md - Executive summary
  • docs/research/smp-paper/FUTURE_RESEARCH_DIRECTIONS.md - Future work

Research Synthesis:

  • RESEARCH_SYNTHESIS.md - Research findings synthesis
  • R&D_PHASE_ONBOARDING.md - R&D phase directions

Simulation Documentation:

  • simulations/README.md - Simulation framework
  • simulations/SIMULATION_GUIDE.md - How to run simulations
  • simulations/INTEGRATION_GUIDE.md - Integrating with code

SPECIALIZED DOCUMENTATION

Strategic Documents:

  • PHASE_2_EXECUTION_PLAN.md - Phase 2 execution plan
  • KILLER_APP_VISION.md - Product vision and goals
  • R&D_PHASE_ONBOARDING.md - R&D research directions

Index & Catalog Documents:

  • docs/DOCUMENTATION_SUMMARY.md - Documentation overview
  • docs/RESEARCH_ARCHIVE_INDEX.md - Research archive index
  • docs/AGENT_SYNTHESIS_REPORT.md - Agent coordination report

Project Planning:

  • ONBOARD_ROADMAP.md - Project roadmap
  • NEXT_SESSION_GUIDE.md - Session continuation
  • TYPESCRIPT_FIX_PLAN.md - TypeScript error fixing

CI/CD & TESTING

Testing Documentation:

  • TEST_PLAN.md - Testing strategy
  • docs/cicd/ - CI/CD pipeline docs
  • Test files throughout /src/

Benchmarking:

  • docs/BENCHMARK_GUIDE.md - Comprehensive guide
  • docs/BENCHMARK_QUICKSTART.md - Quick start
  • src/benchmarks/ - Benchmark suite

AGENT & TEAM COORDINATION

Agent System:

  • /.agents/ - Agent role definitions
  • /agent-messages/ - Inter-agent communications
  • README.md in /agent-messages/ - Coordination protocol

Research Agent Documentation:

  • /.agents/round1/ - Round 1 research teams
  • /.agents/round2/ - Round 2 research teams
  • /.agents/round4/ - Round 4 research teams

Synthesis Reports:

  • docs/AGENT_SYNTHESIS_REPORT.md - Overall synthesis
  • docs/round*-synthesis/ - Round synthesis documents
  • docs/SPRINT7_SUMMARY.md - Sprint summaries

EXAMPLES & TEMPLATES

Code Examples:

  • /examples/ directory - 20+ example projects
  • docs/api/examples/ - API usage examples
  • Test files as reference implementations

Project Templates:

  • Example plugins
  • Template configurations
  • Starter projects

Documentation Organization by Topic

TILE SYSTEM

  • TILE_SYSTEM_ANALYSIS.md - Complete analysis
  • /src/spreadsheet/tiles/ - Implementation
  • /docs/research/smp-paper/ - Research
  • /examples/ - Examples

CONFIDENCE MODEL

  • ARCHITECTURE.md - Zone definitions
  • INDEX_FEATURES.md - Feature overview
  • /docs/research/smp-paper/concepts/ - Theoretical foundation
  • Test files - Validation

DISTRIBUTED SYSTEMS

  • docs/DISTRIBUTED_MEMORY.md - Memory management
  • docs/ADVANCED_FEDERATED_LEARNING.md - Federation
  • docs/MICROBIOME_ARCHITECTURE.md - Ecosystem
  • docs/research/smp-paper/distributed/ - Research

SECURITY

  • docs/SECURITY_AUDIT.md - Complete audit
  • docs/SECURITY_IMPLEMENTATION.md - Implementation
  • docs/SECURITY_CHECKLIST.md - Pre-deployment
  • src/core/security/ - Code implementation

PERFORMANCE

  • docs/PERFORMANCE.md - Optimization guide
  • docs/BENCHMARK_GUIDE.md - Benchmarking
  • src/benchmarks/ - Benchmark suites
  • src/spreadsheet/performance/ - Optimization code

DEPLOYMENT

  • docs/DEPLOYMENT.md - Deploy procedures
  • Docker files at root - Containerization
  • deployment/ directory - Deploy configs
  • k8s/ directory - Kubernetes manifests

RESEARCH & INNOVATION

  • docs/research/smp-paper/ - Complete research
  • INDEX_RESEARCH.md - Research inventory
  • RESEARCH_SYNTHESIS.md - Key findings
  • R&D_PHASE_ONBOARDING.md - R&D focus

Document Status

Up-to-Date & Complete

  • ARCHITECTURE.md
  • STATE_ASSESSMENT.md
  • EXTRACTABLE_COMPONENTS.md
  • NOVELTY_REPORT.md
  • CODE_GUIDE.md
  • NEXT_SESSION_GUIDE.md
  • ONBOARD_ROADMAP.md
  • PROJECT_INTEGRATION.md
  • docs/DEPLOYMENT.md
  • docs/SECURITY_AUDIT.md
  • docs/research/smp-paper/EXECUTIVE_SUMMARY.md
  • docs/research/smp-whitepaper-collection/01-FINAL-PAPER/

Actively Updated

  • PROJECT_AUDIT.md
  • TYPESCRIPT_FIX_PLAN.md
  • RESEARCH_SYNTHESIS.md
  • Phase reports (latest)
  • Agent synthesis reports

Reference & Archive

  • Older phase reports
  • Round synthesis documents
  • Legacy guides

Quick Navigation Guide

For Getting Started:

  1. NEXT_SESSION_GUIDE.md (5 min)
  2. README.md (5 min)
  3. ARCHITECTURE.md (15 min)
  4. ONBOARD_ROADMAP.md (10 min)

For Understanding Systems:

  1. ARCHITECTURE.md - Architecture overview
  2. Component-specific documents (e.g., TILE_SYSTEM_ANALYSIS.md)
  3. /src/ code and implementation
  4. /examples/ for usage patterns

For Production Deployment:

  1. docs/DEPLOYMENT.md - Deployment guide
  2. docs/SECURITY_AUDIT.md - Security review
  3. docs/SECURITY_CHECKLIST.md - Pre-flight
  4. Docker/K8s configs in /deployment/

For Research & Innovation:

  1. INDEX_RESEARCH.md - Research overview
  2. docs/research/smp-paper/EXECUTIVE_SUMMARY.md - Theory
  3. RESEARCH_SYNTHESIS.md - Key findings
  4. R&D_PHASE_ONBOARDING.md - R&D directions

For Benchmarking & Performance:

  1. docs/BENCHMARK_GUIDE.md - Comprehensive guide
  2. docs/BENCHMARK_QUICKSTART.md - Quick start
  3. src/benchmarks/ - Benchmark code
  4. simulations/SIMULATION_GUIDE.md - Simulations

Documentation Statistics

Category Document Count Status
Core Documentation 15 Complete
Architecture & Design 8 Complete
Infrastructure 8 Complete
Security 5 Complete
API & SDK 8 Complete
Research 200+ Complete (White paper)
Examples 20+ Comprehensive
Phase Reports 8 Complete
Advanced Topics 6 In Progress
TOTAL ~280+ Extensive

Technology Documentation

Documented Technologies:

  • TypeScript/JavaScript
  • React (spreadsheet UI)
  • WebSocket (real-time)
  • Yjs (collaboration)
  • TensorFlow.js (ML)
  • Prometheus (monitoring)
  • Docker & Kubernetes
  • AWS/Azure/GCS (cloud)
  • Express.js (API)
  • Jest (testing)

Access Patterns

By Role:

Architects & Designers:

  • ARCHITECTURE.md
  • EXTRACTABLE_COMPONENTS.md
  • docs/MICROBIOME_ARCHITECTURE.md
  • docs/research/smp-paper/

Developers:

  • CODE_GUIDE.md
  • TILE_SYSTEM_ANALYSIS.md
  • /examples/
  • Test files
  • API docs

Researchers:

  • INDEX_RESEARCH.md
  • docs/research/smp-paper/
  • RESEARCH_SYNTHESIS.md
  • simulations/SIMULATION_GUIDE.md

DevOps/SRE:

  • docs/DEPLOYMENT.md
  • docs/SECURITY_AUDIT.md
  • docs/PERFORMANCE.md
  • docs/BENCHMARK_GUIDE.md

Product/Business:

  • README.md
  • KILLER_APP_VISION.md
  • ONBOARD_ROADMAP.md
  • Phase reports

Last Updated: 2026-03-10 Total Documentation: 280+ documents Coverage: Comprehensive (architecture, implementation, research, operations) Status: Production-ready with ongoing enhancement