Complete Workflow

This guide covers the full 6-phase workflow for generating professional documentation with AI agents.

Workflow Overview

Phase 1: Source Collection

Objective

Gather all source documents that will inform the generated documentation.

Actions

# Create project from template
cp -r template/ my-project/
cd my-project/

# Add source documents
cp ~/research/*.pdf sources/
cp ~/reports/*.docx sources/

# Verify structure
ls -la sources/

Supported Formats

Format	Extension	Notes
PDF	.pdf	Primary format
Word	.docx	Converted internally
Text	.txt, .md	Direct reading

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Phase 2: Parallel Source Analysis

Objective

Have multiple agents read and summarize source documents simultaneously.

Process

Claude Code Command

> Analyze all documents in sources/.
  For each document, provide:
  - Main topics covered
  - Key findings
  - Relevant data/statistics
  - Research gaps

  Identify overlaps and unique contributions across sources.

Output

The orchestrator produces a merged synthesis:

# Source Analysis Summary

## Document Overview
| Document | Type | Pages | Main Topic |
|----------|------|-------|------------|
| thesis.pdf | Research | 85 | ML attacks |
| report.pdf | Industry | 45 | Threat landscape |

## Thematic Analysis
1. Attack methodologies (all documents)
2. Defense mechanisms (thesis, survey)
3. Industry impact (report)

## Identified Gaps
- Current 2024 statistics needed
- Academic papers on specific defense

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Phase 3: External Research

Objective

Fill research gaps using external AI tools.

Tool Selection

Need	Tool	Output
Synthesize uploaded PDFs	NotebookLM	Structured summaries
Current statistics (2024-2025)	Perplexity	Markdown + URLs
Academic papers	Scopus AI	Papers + BibTeX

Workflow

1. Opus generates prompts based on identified gaps
2. User runs prompts on external platforms
3. Results saved to research-prompts/results/
4. Opus integrates results into context

---

Phase 4: Document Planning

Objective

Create detailed document structure with chapter assignments.

Claude Code Command

> Create a document plan with:
  - Target: [X] pages total
  - Chapters with page budgets
  - Source-to-chapter mapping
  - Style guidelines

  Save to plan/DOCUMENT_PLAN.md

Output Structure

# Document Plan

## Overview
| Property | Value |
|----------|-------|
| Total Pages | ~100 |
| Chapters | 10 |
| Language | English |

## Chapter Assignments

| Ch | Title | Pages | Sources |
|----|-------|-------|---------|
| 01 | Introduction | 4 | - |
| 02 | Background | 8 | thesis.pdf (10-30) |
| 03 | Attack Vectors | 12 | thesis.pdf, perplexity.md |

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Phase 5: Parallel Chapter Writing

Objective

Multiple writer agents create chapters simultaneously.

Process

Claude Code Command

> Write chapters 1-5 following plan/CHAPTER_ASSIGNMENTS.md
  and agents/AGENT_GUIDELINES.md.

  Each chapter should:
  - Stay within page budget
  - Use flowing prose (not bullet lists)
  - Include proper citations
  - Use correct language/accents

What Each Agent Receives

Chapter Assignment:
├── File: latex/chapters/XX-name.tex
├── Title: Chapter Title
├── Max pages: X
├── Sources: [relevant excerpts only]
├── Research: [relevant research data]
├── Outline: [section structure]
└── Style: [formatting requirements]

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Phase 6: Review & Build

Objective

Quality assurance and PDF generation.

Review Process

Build Process

# Full compilation
./scripts/compile.sh

# Output
Compiling document...
Running pdflatex (1/3)...
Running biber...
Running pdflatex (2/3)...
Running pdflatex (3/3)...

✅ Compilation successful!
Output: latex/main.pdf

Error Handling

> Check latex/main.log for errors and fix them.
  Common issues:
  - Undefined citations: add to bibliography.bib
  - Duplicate labels: rename with chapter prefix
  - Overfull hbox: adjust figure/table width

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Complete Timeline

Phase	Activities	Parallelism
1. Collection	Gather sources	-
2. Analysis	Read sources	3+ agents
3. Research	External tools	User sequential
4. Planning	Create structure	Orchestrator
5. Writing	Generate chapters	5+ agents
6. Review	QA and build	2+ agents