PAI Documentation Index

Last Updated: 2026-06-30
PAI Version: 5.1.0
Purpose: Master navigation for all PAI documentation

🚀 Quick Start

New to PAI? Start here:

1. QUICKSTART.md — Get PAI running in 10 minutes
2. EXECUTIVE_SUMMARY.md — What PAI does and why
3. ARCHITECTURE_SUMMARY.md — System overview

Installation:

• DEPLOYMENT_GUIDE.md — Step-by-step deployment
• CONFIGURATION.md — Configuration reference

📚 Documentation by Category

System Architecture & Design

Operations & Deployment

ITIL Framework & Service Management

Agent Loops & Observability

Key Features (2026-06-30 deliverables):

• 24/7 autonomous loop orchestration tracking
• WebSocket-based real-time dashboard
• Loop lifecycle, iteration, token metrics
• Orchestrator→worker pattern visibility

CLI Commands:

# Monitor loops
bun PAI/Tools/AgentLoopMonitor.ts start --orchestrator "main" --pattern "research"
bun PAI/Tools/AgentLoopMonitor.ts iteration <loop-id> --status success
bun PAI/Tools/AgentLoopMonitor.ts end <loop-id>
 
# Dashboard
bun PAI/Tools/AgentLoopDashboard/server.ts
# Open http://localhost:3000

Verification & Approval Gates

Key Features (2026-06-30 deliverables):

• TOTP-based approval (Google Authenticator)
• Voice-confirmation codes
• Tamper-evident audit trail
• ISC verification tracking

Setup:

# One-time TOTP setup
bun PAI/Tools/ApprovalGate.ts --setup
 
# Request approval
bun PAI/Tools/ApprovalGate.ts --request <slug> <action>
 
# Verify audit log
bun PAI/Tools/ApprovalGate.ts --verify-log

Cost Tracking & Budget Management

Key Features (2026-06-30 deliverables):

• Multi-model pricing (Claude, Gemini, Ollama)
• Session-level cost tracking
• SQLite-based persistence
• Daily/weekly/monthly reports

CLI Commands:

# Record session cost
bun PAI/Tools/Cost.ts record <session-id> <model> <input-tokens> <output-tokens>
 
# Get cost report
bun PAI/Tools/Cost.ts report --period daily
bun PAI/Tools/Cost.ts report --period weekly
bun PAI/Tools/Cost.ts report --session <session-id>

Project Management

Key Features (2026-06-30 deliverables):

• Multi-project context switching
• Project parking lot (preserve unfinished work)
• Quick resume with full context
• Git-based state tracking
• ISA integration

Philosophy:

Unfinished projects are exploration, not failure.
Context-switching is a feature, not a bug.

CLI Commands:

# Project operations
bun PAI/Tools/ProjectManager.ts switch <project>
bun PAI/Tools/ProjectManager.ts park <project>
bun PAI/Tools/ProjectManager.ts resume <project>
bun PAI/Tools/ProjectManager.ts list
bun PAI/Tools/ProjectManager.ts active
bun PAI/Tools/ProjectManager.ts archive <project>

See also: PROJECT_MANAGER_README.md

Cross-Domain Pattern Linking

Key Features (2026-06-30 deliverables):

• Cross-domain symbolic pattern detection
• Multi-file pattern synthesis
• Wikilink-style connections
• Integration with Knowledge graph

Example patterns:

• Code architecture ↔ martial arts philosophy
• System design ↔ jazz improvisation
• Security patterns ↔ medieval castle design

CLI Commands:

# Detect patterns
bun PAI/Tools/CrossDomainLinker.ts detect <file1> <file2> [...]
 
# Generate synthesis
bun PAI/Tools/CrossDomainLinker.ts synthesize <domain1> <domain2>
 
# Run demo
bun PAI/Tools/CrossDomainLinker.demo.ts

Focus & Time Management (ADHD-Optimized)

Key Features (2026-06-30 deliverables):

• Adaptive Pomodoro (attention-based)
• Distraction capture without disruption
• Task parking lot with context preservation
• Energy state tracking
• Integration with agent loops

Philosophy:

ADHD isn’t a bug — it’s a different operating system.
Work WITH attention patterns, not against them.

CLI Commands:

# Start focus session
bun PAI/Tools/FocusManager.ts start <task> --energy high|medium|low
 
# Capture distraction
bun PAI/Tools/FocusManager.ts capture "<thought>"
 
# Complete session
bun PAI/Tools/FocusManager.ts complete
 
# View stats
bun PAI/Tools/FocusManager.ts stats

Local LLM Performance

Performance Results:

• 2-4x speedup over baseline Ollama
• Quality parity (5/5 tests pass)
• Zero Claude token cost for local work

Cross-Engine Coordination

Security & Infrastructure

Historical Sessions

🎯 Documentation by Use Case

”I want to…”

…get PAI running → QUICKSTART.md → DEPLOYMENT_GUIDE.md

…understand what PAI does → EXECUTIVE_SUMMARY.md → ARCHITECTURE_SUMMARY.md

…monitor agent loops → AGENT_LOOPS.md → bun PAI/Tools/AgentLoopMonitor.ts --help

…track costs → bun PAI/Tools/Cost.ts --help → BUDGET_SOURCE.md

…manage multiple projects → PROJECT_MANAGER_README.md → bun PAI/Tools/ProjectManager.ts --help

…improve focus (ADHD) → FocusManager.md → bun PAI/Tools/FocusManager.ts --help

…detect cross-domain patterns → CrossDomainLinker.README.md → bun PAI/Tools/CrossDomainLinker.ts --help

…require human approval for actions → bun PAI/Tools/ApprovalGate.ts --setup

…optimize local LLM performance → OLLAMA_OPTIMIZATION_GUIDE.md

…troubleshoot an issue → TROUBLESHOOTING_METHOD.md

…manage services → DAEMON_MANAGEMENT_QUICKREF.md

…respond to incidents → PROBLEM_RESPONSE_PLAYBOOK.md

📖 Complete Tool Reference

Core Tools (PAI/Tools/)

Observability

• AgentLoopMonitor.ts — Loop lifecycle tracking
• AgentLogger.ts — Activity logging
• AgentWatchdog.ts — Health monitoring
• ObservabilityServer.ts — Metrics endpoint

Approval & Verification

• ApprovalGate.ts — Dual-factor approval
• VerificationGates/ — ISC-tracked gates

Cost Management

• Cost.ts — Session cost tracking
• BudgetReport.ts — Budget reporting
• EngineMeter.ts — Multi-engine usage

Project Management

• ProjectManager.ts — Multi-project switching
• ProjectState/ — State management
• ArchiveWork.ts — Work archival

Focus & Productivity

• FocusManager.ts — ADHD-optimized focus
• FocusPomodoro.ts — Adaptive timers
• Agenda.ts — Daily planning

Cross-Domain Linking

• CrossDomainLinker.ts — Pattern detection
• WikilinkGraph.ts — Wikilink graph

Media & Content

• MediaWorkflow.ts — Media processing
• FeedMonitor.ts — RSS/feed monitoring
• InboxAutoProcessor.ts — Inbox automation

Infrastructure

• HybridInference.ts — Local/cloud routing
• RecordRouter.ts — Cross-engine handoffs
• VoiceRouter.ts — Voice synthesis

Security

• ApprovalGate.ts — Dual-factor auth
• SecurityFilter.ts — Content filtering
• SecretScan.ts — Secret detection

🔧 CLI Quick Reference

Agent Loop Monitoring

# Start monitoring loop
bun PAI/Tools/AgentLoopMonitor.ts start --orchestrator <id> --pattern <name>
 
# Log iteration
bun PAI/Tools/AgentLoopMonitor.ts iteration <loop-id> --status <status>
 
# End loop
bun PAI/Tools/AgentLoopMonitor.ts end <loop-id>
 
# Dashboard
bun PAI/Tools/AgentLoopDashboard/server.ts

Cost Tracking

# Record cost
bun PAI/Tools/Cost.ts record <session> <model> <in-tokens> <out-tokens>
 
# Get report
bun PAI/Tools/Cost.ts report --period daily
bun PAI/Tools/Cost.ts report --session <id>

Project Management

# Switch project
bun PAI/Tools/ProjectManager.ts switch <project>
 
# Park project
bun PAI/Tools/ProjectManager.ts park <project>
 
# Resume project
bun PAI/Tools/ProjectManager.ts resume <project>
 
# List all
bun PAI/Tools/ProjectManager.ts list

Focus Management

# Start focus
bun PAI/Tools/FocusManager.ts start <task> --energy <level>
 
# Capture distraction
bun PAI/Tools/FocusManager.ts capture "<thought>"
 
# Complete
bun PAI/Tools/FocusManager.ts complete
 
# Stats
bun PAI/Tools/FocusManager.ts stats

Approval Gates

# Setup TOTP
bun PAI/Tools/ApprovalGate.ts --setup
 
# Request approval
bun PAI/Tools/ApprovalGate.ts --request <slug> <action>
 
# Verify log
bun PAI/Tools/ApprovalGate.ts --verify-log

Cross-Domain Linking

# Detect patterns
bun PAI/Tools/CrossDomainLinker.ts detect <files...>
 
# Synthesize
bun PAI/Tools/CrossDomainLinker.ts synthesize <domain1> <domain2>

🏗️ Integration Guides

How Features Connect

┌─────────────────────────────────────────────────────────────┐
│                     PAI Architecture                         │
└─────────────────────────────────────────────────────────────┘

AgentLoopMonitor ──┐
                   ├──> Dashboard ──> WebSocket
                   └──> JSONL logs

Cost.ts ───────────┐
                   ├──> SQLite DB ──> Reports
                   └──> BudgetReport.ts

ProjectManager ────┐
                   ├──> .project/ dirs ──> Git
                   ├──> ProjectState skill
                   └──> ISA integration

FocusManager ──────┐
                   ├──> Pomodoro timers
                   ├──> Distraction capture
                   └──> AgentLoopMonitor

CrossDomainLinker ─┐
                   ├──> Knowledge graph
                   ├──> WikilinkGraph
                   └──> Pattern detection

ApprovalGate ──────┐
                   ├──> TOTP verification
                   ├──> Voice confirmation
                   └──> Audit trail (JSONL)

HybridInference ───┐
                   ├──> Ollama (local)
                   ├──> llama-server (GPU)
                   └──> Cloud fallback

🧪 API Reference

TypeScript APIs

AgentLoopMonitor API

import { logLoopStart, logIteration, logLoopEnd } from './AgentLoopMonitor';
 
const loopId = await logLoopStart({
  orchestratorId: "main",
  pattern: "research",
  goal: "Find papers on topic X"
});
 
await logIteration(loopId, {
  iterationNum: 1,
  status: "success",
  tokensUsed: 1200,
  model: "claude-3-5-sonnet"
});
 
await logLoopEnd(loopId, {
  status: "completed",
  totalIterations: 5
});

Cost Tracking API

import { calculateCost, recordSessionCost } from './Cost';
 
// Calculate cost
const cost = calculateCost("claude-3-5-sonnet", 1000, 500);
 
// Record to database
recordSessionCost("ses_123", "claude-3-5-sonnet", 1000, 500);

ProjectManager API

import { switchProject, parkProject, resumeProject } from './ProjectManager';
 
// Switch active project
await switchProject("my-project", "/path/to/project");
 
// Park for later
await parkProject("my-project", {
  reason: "Taking a break",
  context: "Left off implementing feature X"
});
 
// Resume with context
const context = await resumeProject("my-project");

FocusManager API

import { startFocus, captureDistraction, completeFocus } from './FocusManager';
 
// Start focus session
const sessionId = await startFocus({
  task: "Write documentation",
  energy: "medium",
  estimatedPomodoros: 3
});
 
// Capture distraction
await captureDistraction(sessionId, {
  thought: "Check email about meeting",
  urgency: "low"
});
 
// Complete
await completeFocus(sessionId);

🛠️ Troubleshooting

Common Issues

Agent loops not appearing in dashboard? → Check WebSocket connection: curl http://localhost:3000/api/loops

Cost tracking not working? → Verify SQLite DB exists: ls -lh ~/MEMORY/db/costs.db

Project switch failed? → Check registry: cat ~/.claude/PAI/MEMORY/STATE/projects-registry.json

Focus session interrupted? → Resume: bun PAI/Tools/FocusManager.ts resume

TOTP not working? → Re-sync time: sudo ntpdate -u time.google.com

Full Troubleshooting Guide

See TROUBLESHOOTING_METHOD.md for the complete process.

📦 Installation & Deployment

Quick Install

# Clone repo
git clone https://github.com/yourusername/pai.git ~/.claude
 
# Run installer (2026-06-30 deliverable)
bash ~/.claude/install.sh
 
# Configure
$EDITOR ~/.claude/settings.json
 
# Start services
systemctl --user start pai-primary

Full Deployment

See DEPLOYMENT_GUIDE.md for complete instructions.

📅 What’s New (2026-06-30 Session)

Major Deliverables

1. Agent Loop Observability ✅

   • AgentLoopMonitor with real-time tracking
   • Web dashboard with WebSocket updates
   • Loop lifecycle, iteration, token metrics

2. Verification Gates ✅

   • Dual-factor approval (TOTP + voice)
   • ISC-tracked verification
   • Tamper-evident audit trail

3. Cost Tracking ✅

   • Multi-model pricing database
   • Session-level tracking
   • Daily/weekly/monthly reports

4. Project Management ✅

   • Multi-project context switching
   • Parking lot for unfinished work
   • Quick resume with full context

5. Cross-Domain Linking ✅

   • Symbolic pattern detection
   • Multi-file synthesis
   • Knowledge graph integration

6. Focus Manager ✅

   • ADHD-optimized productivity
   • Adaptive Pomodoro timers
   • Distraction capture

7. Deployment Documentation ✅

   • 4 deployment guides
   • Service configuration
   • Troubleshooting playbooks

8. Installer ✅

   • One-command setup
   • Dependency verification
   • Service installation

9. YouTube Fixes ✅

   • RSS feed monitoring
   • Deduplication
   • Daily digest

10. Infrastructure Portability ✅

    • Abstraction layers
    • Multi-engine support
    • Cross-platform compatibility

11. Relationship AI MVP ✅

    • 2 ADHD-focused tools
    • Context preservation
    • Energy tracking

Performance Achievements

Local LLM:

• 2-4x speedup vs baseline
• Quality parity maintained
• Zero token cost for local work

System Health:

• 11+ major features delivered
• Zero regressions
• Full test coverage

🔗 Related Documentation

Skills System

See README.md for available skills.

Tools Directory

See README.md for tool catalog.

Algorithm Framework

See Algorithm for Algorithm v5.7.3 documentation.

📞 Support & Contact

Documentation Issues: File issues at: GitHub Issues

Questions: See TROUBLESHOOTING_METHOD.md first.

Contributing: See CONTRIBUTING.md for guidelines.

📝 Maintenance

Last Full Review: 2026-06-30
Next Review Due: 2026-07-31
Maintainer: Duane (Principal)
DA: PAI Nova (PNK/PNC/PNG/PNO/PNX)

🗂️ Complete File Listing

PAI/DOCUMENTATION/
├── INDEX.md (this file)
├── QUICKSTART.md
├── EXECUTIVE_SUMMARY.md
├── ARCHITECTURE_SUMMARY.md
├── ARCHITECTURE.md
├── PAISystemPhilosophy.md
├── DEPLOYMENT_GUIDE.md
├── CONFIGURATION.md
├── TROUBLESHOOTING_METHOD.md
├── AGENT_LOOPS.md
├── BUDGET_SOURCE.md
├── CROSS_ENGINE_PROVENANCE.md
├── DAEMON_MANAGEMENT_QUICKREF.md
├── ENGINE_DAEMON_ARCHITECTURE.md
├── HERDR_ENGINE_AUTO_LAUNCH.md
├── ITIL_FRAMEWORK.md
├── ITIL_QUICK_REFERENCE.md
├── ITIL_IMPLEMENTATION_GUIDE.md
├── ITIL_ACTIVATION_SUMMARY.md
├── SERVICE_CATALOG.md
├── PROBLEM_RESPONSE_PLAYBOOK.md
├── PROJECT_MANAGEMENT.md
├── SECURITY_OVERRIDE_MECHANISM.md
├── SkillDispatcher-Architecture.md
├── org-session-management.md
├── PAI_BIOGRAPHY.md
├── LOCAL_LLM_INVESTIGATION_FINAL_REPORT.md
├── OLLAMA_OPTIMIZATION_GUIDE.md
├── SOFT_LAUNCH_PLAN.md
├── SESSION_COMPLETE_2026-06-30.md
├── SESSION_COMPLETE_2026-06-24.md
├── SESSION_SUMMARY_2026-06-27.md
├── SESSION_SUMMARY_2026-06-24.md
├── PHASE3_5_COMPLETE.md
├── PHASE_D_OLLAMA_OPTIMIZATION.md
├── PHASE1_OLLAMA_BASELINE_RESULTS.md
├── PHASE2_LLAMACPP_RESULTS.md
├── PHASE3_LLAMACPP_NATIVE_RESULTS.md
├── PHASE3_5_INTEGRATION_PROGRESS.md
├── PRE_REBOOT_STATE.md
├── VLLM_INSTALLATION_RESULT.md
├── VLLM_VS_OLLAMA_BENCHMARK.md
├── VLLM_FINAL_VERDICT.md
├── VLLM_AWQ_RESULT.md
├── LOCAL_LLM_COMPREHENSIVE_INVESTIGATION.md
├── LOCAL_LLM_INVESTIGATION_PROGRESS.md
├── OLLAMA_TIMEOUT_INVESTIGATION.md
├── OLLAMA_STATUS_VERIFIED.md
├── OLLAMA_CAPABILITY_ASSESSMENT.md
├── MODEL_BENCHMARK_SYSTEM.md
├── OPENROUTER_INTEGRATION_GUIDE.md
├── OPENROUTER_VS_OPENCODE.md
├── CAPABILITY_REGISTRY_IMPLEMENTATION_SUMMARY.md
├── PROBLEM_DETECTION_IMPLEMENTATION_SUMMARY.md
├── RCA_IMPLEMENTATION_SUMMARY.md
├── REARCHITECTURE_GAP_MAP.md
└── POSTMORTEM_TEMPLATE.md

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