ai-collaboration-reference-guide

AI Collaboration System: Comprehensive Reference Guide

Purpose: Complete implementation guide for sustainable long-term AI collaboration in doctoral research and professional projects.

System Requirements & Context

Designed For:

Important: This system was developed specifically for Claude Sonnet 4.5 with Pro/Teams/Enterprise features (Projects, custom instructions, file upload). It may be adaptable to other AI models or Claude tiers, but functionality may vary. The protocols assume access to Claude’s Project system and persistent file storage.

Document Information

Version: 1.0 (Living Document)

Status: Active - This is a living document that evolves with implementation experience and methodological refinement.

Research Context: This system is part of an EdD dissertation methodology examining AI-human collaboration in doctoral research at Northeastern University’s Graduate School of Education.

Related Resources:

Contribution Ratio: H50-C50 (Equal collaboration between human design and AI implementation)

Table of Contents

  1. System Overview
  2. Architecture: Where Everything Goes
  3. Naming Conventions
  4. Two-Tier Chat System
  5. Decision Frameworks
  6. Session Protocols
  7. File Management
  8. Chat Retirement Protocol
  9. META Chat Maintenance
  10. Human/AI Responsibility Matrix
  11. Implementation Guide
  12. Troubleshooting Guide
  13. Quick Reference

System Overview

Core Principles

Discovery vs. Execution Modes:

Progressive Autonomy:

Resource Management:

Transparency & Integrity:

System Goals

Architecture: Where Everything Goes

CRITICAL DISTINCTION

Understanding where things live prevents confusion and ensures the system works correctly.

Account-Level Custom Instructions

Location: Settings → Personalization → Custom Instructions

What Lives Here:

Purpose: Universal “how David works with Claude” protocols that apply everywhere

When to Update: Rarely - only when universal work patterns change

Project-Level Instructions

Location: Project Settings → Custom Instructions (within specific project)

What Lives Here:

Purpose: “How this specific project works” configuration

When to Update: When project structure changes significantly

Project Files

Location: Project → Files (uploaded documents within project)

What Lives Here:

System Files (Required):

Content Files:

Purpose: Searchable knowledge base accessible to all chats in project

When to Update: Continuously as project evolves; Project Overview every 2-4 weeks

Individual Chat Context

Location: Within specific chat conversations

What Lives Here:

What Does NOT Live Here:

Purpose: Focused workspace for specific deliverable or ongoing dialogue

Visual Summary

ACCOUNT LEVEL (Universal)
└── Custom Instructions: How David works with Claude always

PROJECT LEVEL
├── Project Instructions: How THIS project works
├── Project Files
│   ├── Project Overview - Current.md (auto-read by all chats)
│   ├── Project Overview Template.md (reference for META)
│   └── All other project documents
└── Individual Chats
    ├── Home Base Chat (long-running dialogue)
    └── Work Unit Chats (specific deliverables)

Naming Conventions

1. Chat Naming Convention

Home Base Format

[Project Name] - Home Base [Month Year]

Example: EdD Research - Home Base (Nov 2025)

When retired: EdD Research - Home Base (Aug-Nov 2025)

Purpose: Long-running exploratory and accountability chat

Work Unit Format

[Category] - [Specific Deliverable] - [YYYY-MM-DD] - [Status]

Examples:
- DEV - Dissertation Website - 2025-10-15 - Active
- DATA - Cycle 1 Coding Framework - 2025-11-01 - Active
- THEORY - Hall-Savickas Integration - 2025-09-20 - Complete
- WRITING - Methodology Chapter - 2026-02-10 - Active
- META - Project Overview Maintenance - 2025-11-07 - Active

Category Codes:

Status Options:

Purpose: Time-stamped, scannable identification of focused work

2. Artifact Naming Convention

[Descriptive Title] - [Contribution Ratio]

Examples:
- Account-Level Custom Instructions - H30-C70
- Project Overview Template - H20-C80
- Dissertation Timeline Dashboard - H95-C5
- Career Conversation Toolkit - H60-C40
- Website Homepage Code - H10-C90

Components:

Purpose: Scannable artifact menu with transparent contribution tracking

3. File Naming Convention

yyyy-mm-dd_[Type]_[Document Title]_[H/C Ratio]_[Version]

Examples:
- 2025-11-07_META_System-Design-Session_H50-C50_v1.0.md
- 2025-10-15_DEV_Website-Structure-Specs_H40-C60_v2.0.md
- 2025-11-01_DATA_Interview-Protocol_H90-C10_v1.0.md
- 2025-09-20_THEORY_Framework-Synthesis_H70-C30_v1.5.md
- 2025-12-01_WRITING_Methodology-Draft_H85-C15_v1.0.md

Components:

Purpose: Chronological organization, scannable by type, transparent contribution tracking, version control

Special Cases:

4. Contribution Ratio System

H[X]-C[Y]

Where:
- H = Human contribution percentage
- C = Claude (AI) contribution percentage
- Total always equals 100

Examples:
- H90-C10: 90% human work, 10% AI assistance
- H50-C50: Equal collaboration
- H10-C90: Primarily AI-generated with human direction
- H100-C0: Fully human-created (no AI involvement)

Application:

Purpose: Transparent contribution tracking for academic integrity and methodological rigor

Two-Tier Chat System

Architecture Overview

PROJECT
├── HOME BASE CHAT (Tier 1)
│   └── Long-running, exploratory, accountability
│
└── WORK UNIT CHATS (Tier 2)
    ├── DEV - Specific Deliverable - Active
    ├── DATA - Specific Deliverable - Active
    ├── WRITING - Specific Deliverable - Complete
    └── META - Project Overview Maintenance - Active

Tier 1: Home Base Chat

Purpose:

Communication Mode: Primarily Discovery Mode

Lifespan: Long-running (months), retired only when:

Characteristics:

Tier 2: Work Unit Chats

Purpose:

Communication Mode: Varies by work type (Discovery for design, Execution for development)

Lifespan: Short (days to weeks), retired when:

Characteristics:

Special Case: META Chat

Purpose: Maintain Project Overview document

Type: Work Unit chat, but long-running

Usage: Revisit every 2-4 weeks for Project Overview updates

Lifespan: Persistent throughout project, used periodically

Decision Frameworks

When to Use Home Base vs. Work Unit Chat

USE HOME BASE IF:

CREATE WORK UNIT CHAT IF:

Mode Transitions: Prototyping to Development

PROTOTYPE IN HOME BASE:

GRADUATE TO WORK UNIT WHEN:

Example: Single HTML page guide (Home Base) → Multi-page website (New Work Unit chat)

Signal to transition: “Am I now committed to building this out?” → Create Work Unit chat

Communication Mode Selection

DISCOVERY MODE Indicators:

EXECUTION MODE Indicators:

MODE SWITCHING:

Can switch within conversation (creative reverb ideas → technical Ableton settings)

When unclear, Claude asks: “Are we exploring possibilities or executing something specific?”

Session Protocols

Opening Protocol: Starting a Session

Your Opening: “I’m ready to start.”

Claude’s Response Prompts:

Welcome back! Let me orient to where we are:

1. What's today's date?
2. When was our last check-in?
3. What have you accomplished since then?
4. What's your focus for today's session?
5. What mode are we working in - Discovery or Execution?

You Provide:

Today is [Day, Date]
Last check-in: [X days ago]
Accomplished since then:
- [bullet list]

Today's focus: [specific goal or question]
Mode: [Discovery/Execution/Will switch between]

Closing Protocol: Ending a Session

Your Closing: “I’m ready to close this session.”

Claude’s Response Prompts:

Let's capture what happened in this session:

1. What did we accomplish today?
2. What artifacts or decisions were created?
3. What's the contribution ratio for today's work?
4. What's your next step or focus for next session?
5. Any open questions or parking lot items?
6. Should anything be documented in Project Overview?

You Provide:

Accomplished:
- [bullet list]

Artifacts created:
- [artifact name - H[X]-C[Y]]

Next session focus:
- [what comes next]

For Project Overview:
- [anything META should know about]

Check-In Protocol (Home Base)

Frequency: Weekly or bi-weekly

Standard Check-In Structure:

  1. Orientation: Date, time since last check-in
  2. Progress Report: What you’ve accomplished
  3. Challenges: What’s blocking or confusing you
  4. Planning: Next steps and priorities
  5. Mode Declaration: Discovery or Execution for this session

Purpose: Maintain momentum, prevent drift, track progress

File Management

Project Files Best Practices

Keep Lean:

Naming Consistency:

Cross-Chat References:

Version Control

Local/Cloud Storage:

Version Incrementing:

Artifacts Inventory:

File Upload Strategy

Rely on Project Files First:

When to Upload New Files:

Avoid Duplication:

Chat Retirement Protocol

Home Base Retirement Triggers

When to retire Home Base:

Rule of Thumb: Every 2-3 months or at major research phase shifts

Process:

  1. Update chat name with date range: “Home Base (Aug-Nov 2025)”
  2. Start new Home Base with current month
  3. Update Project Overview to reflect new Home Base
  4. First session in new Home Base: Brief orientation summary

Work Unit Retirement Triggers

When to retire Work Unit:

Rule of Thumb: When the specific work is done

Process:

  1. Mark status: Active → Complete (or Archived)
  2. Document outcome in Project Overview
  3. List in “Recently Completed Work Units” section
  4. Add artifacts to Artifacts Inventory
  5. Export chat if needed for methodology documentation

Proactive vs. Reactive Retirement

PROACTIVE (Preferred):

REACTIVE (Avoid):

Claude’s Role: Provide token warnings at three levels to enable proactive retirement

META Chat Maintenance

Purpose

Periodic consolidation of project progress into optimized Project Overview document that serves as automatic context for all chats.

Workflow

Frequency: Every 2-4 weeks or after major milestones

Process:

  1. Open META chat
  2. Copy appropriate prompt template from Project Overview Template.md
  3. Fill in updates (completed work, new chats, new files, phase changes, decisions)
  4. META produces updated Project Overview - Current.md
  5. Download artifact
  6. Archive old Project Overview locally with date
  7. Upload new version to project files (replaces old one)

Prompt Templates

Three templates available in Project Overview Template.md:

  1. Initial Creation - First-time setup when no Current file exists
  2. Regular Update - Comprehensive update every 2-4 weeks
  3. Quick Reference Update - Minor changes between major updates

Claude’s Role:

What to Include in Updates

Completed Work:

New Active Work:

Progress on Active Work:

New Files/Artifacts:

Retired/Archived:

Key Decisions:

Human/AI Responsibility Matrix

David’s Responsibilities

Strategic Direction:

Context Provision:

File Management:

Session Structure:

Quality Control:

Claude’s Responsibilities

Communication Adaptation:

Resource Management:

Output Quality:

Context Maintenance:

System Adherence:

Shared Responsibilities

Scope Management:

Learning & Adaptation:

Documentation:

Implementation Guide

Phase 1: Account Setup (15 minutes)

Step 1: Copy Account-Level Custom Instructions

Result: Universal collaboration protocols now active across all Claude use

Phase 2: Project Setup (30 minutes)

Step 2: Create Project (if not exists)

Step 3: Configure Project Instructions

Step 4: Upload Core Files

Result: Project structure configured, ready for chat creation

Phase 3: Initial Project Overview (45 minutes)

Step 5: Create META Chat

Step 6: Generate Initial Project Overview

Step 7: Upload Project Overview

Result: Project Overview system operational

Phase 4: Create Home Base (15 minutes)

Step 8: Create Home Base Chat

Step 9: First Home Base Session

Result: Home Base operational for ongoing work

Phase 5: Create Work Unit Chats as Needed (Ongoing)

Step 10: Identify Need for Work Unit

Step 11: Create Work Unit Chat

Step 12: Conduct Focused Work

Result: Focused work units complete deliverables efficiently

Phase 6: Maintain System (Ongoing)

Step 13: Regular META Updates

Step 14: Monitor and Retire Chats

Step 15: Iterate and Improve

Result: Sustainable long-term collaboration system

Troubleshooting Guide

Known Issues and Solutions

Issue: Chat Shows Incorrect Date

Symptoms:

Causes:

Solutions:

  1. Explicitly provide date at session start (always)
  2. If persists, retire chat proactively
  3. Start fresh chat with clear date context
  4. Update Project Overview with correct timeline

Prevention:

Issue: Batch Creation/Corruption

Symptoms:

Causes:

Solutions:

  1. NEVER update multiple files in one go
  2. Work one file at a time
  3. Wait for confirmation before next file
  4. Test each change before proceeding

Prevention:

Issue: Scope Creep Within Chat

Symptoms:

Causes:

Solutions:

  1. Reassess: Is this still same deliverable?
  2. If scope expanded significantly, consider new Work Unit chat
  3. Explicitly declare mode and focus at session start
  4. Use Home Base for exploration, Work Unit for execution

Prevention:

Issue: Context Loss Across Chats

Symptoms:

Causes:

Solutions:

  1. Update Project Overview more frequently
  2. Document key decisions in Project Overview
  3. Explicitly reference files in Project Files
  4. Provide brief context when referencing other chats

Prevention:

Issue: Token Warnings Ignored

Symptoms:

Causes:

Solutions:

  1. Treat Level 2 warnings seriously
  2. Plan retirement at next natural break
  3. Don’t wait for Level 3 (action alert)
  4. Retire proactively, not reactively

Prevention:

Issue: Unclear Communication Mode

Symptoms:

Causes:

Solutions:

  1. Explicitly state mode at session start
  2. Signal when switching modes
  3. Claude will ask if unclear

Prevention:

Issue: Artifact Naming Inconsistent

Symptoms:

Causes:

Solutions:

  1. Verify Account-Level instructions saved
  2. Remind: “Use artifact naming convention”
  3. Provide clear title suggestion

Prevention:

When to Seek Help

Contact Anthropic Support if:

Revise System if:

Document in META if:

Quick Reference

Daily Use Checklist

Starting Any Session:

  1. ☑ Say “I’m ready to start”
  2. ☑ Provide date and last check-in
  3. ☑ State today’s focus
  4. ☑ Declare mode (Discovery/Execution)

During Session:

  1. ☑ Stay focused on deliverable (Work Unit) or exploration (Home Base)
  2. ☑ Signal mode switches if needed
  3. ☑ Save artifacts with proper naming
  4. ☑ Note any decisions for Project Overview

Closing Any Session:

  1. ☑ Say “I’m ready to close”
  2. ☑ Document accomplishments
  3. ☑ Note contribution ratios
  4. ☑ Identify next steps

Weekly Maintenance

Home Base Check-In:

  1. ☑ Date and time since last check-in
  2. ☑ Progress report
  3. ☑ Challenges or blocks
  4. ☑ Next steps planning

Bi-Weekly/Monthly Maintenance

META Chat Update:

  1. ☑ Open META chat
  2. ☑ Use update prompt template
  3. ☑ Provide comprehensive updates
  4. ☑ Download new Project Overview
  5. ☑ Archive old version locally
  6. ☑ Upload new version to Project Files

Decision Quick Reference

Home Base or Work Unit?

Discovery or Execution?

New Chat or Continue Current?

Retire Chat or Keep Going?

File Location Quick Reference

Account-Level Instructions: Settings → Personalization → Custom Instructions

Project-Level Instructions: Project Settings → Custom Instructions

Project Files: Project → Files (upload documents)

Project Overview - Current.md: Project Files (auto-read by all chats)

Project Overview Template.md: Project Files (reference for META)

Archived Versions: Local storage (not in Claude project)

Naming Pattern Quick Reference

Chats:

Artifacts:

Files:

Contribution Ratios:

Emergency Protocols

Chat Completely Broken:

  1. Don’t panic
  2. Retire current chat immediately
  3. Start fresh chat with opening protocol
  4. Provide brief context recap
  5. Update Project Overview in META

Lost Important Work:

  1. Check artifact menu in conversation
  2. Check Project Files
  3. Check local archives
  4. Reconstruct from session notes
  5. Document in Project Overview for prevention

System Not Working:

  1. Review this guide
  2. Check Account and Project settings
  3. Verify file locations
  4. Update Project Overview
  5. Revise protocols if needed

Citation

APA Format:

Dawson, D. R., II. (2025). AI collaboration system: Comprehensive reference guide. Northeastern University. https://drdawson2.github.io/dissertation-guide/

Note: Update URL with specific GitHub repository location when published.

Document Version History

v1.0 - November 7, 2025

About This Document

This reference guide was developed through AI-human collaboration following the framework documented herein. The system represents an iterative, action research approach to designing sustainable protocols for long-term AI collaboration in academic research contexts.

Methodology Note: This document serves as both a practical implementation guide and a methodological artifact for examining AI-human collaboration practices in doctoral research. The development process itself demonstrates the protocols it describes.

Copyright & Licensing

© 2025 David R. Dawson II Northeastern University

Licensed under CC BY-NC 4.0

Attribution:

Quick Links: Research Context | Contact | Versions (Coming Soon)

Last Updated: November 7, 2025

END OF REFERENCE GUIDE

Contribution Report

Human Contribution (50%):

Claude Contribution (50%):

Collaboration Type: Equal partnership - human design with AI documentation

Citation & Attribution

Citation (APA 7th Edition): Dawson, D. R., II. (2025). AI collaboration system: Comprehensive reference guide. Northeastern University. https://github.com/drdawson2/ai-collaboration-reference-guide

Author Information:

License: This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License (CC BY-NC 4.0).

You are free to:

Under the following terms:

Suggested Attribution:“Based on [Document Title] by David R. Dawson II (2025), available at https://github.com/drdawson2/ai-collaboration-reference-guide. Licensed under CC BY-NC 4.0.”

Last Updated: 2025-11-09