Project Structure

Complete directory structure and file descriptions for the documentation template.

Overview

project/
├── latex/                      # LaTeX document files
│   ├── main.tex               # Main document (includes, packages)
│   ├── bibliography.bib       # BibTeX references
│   └── chapters/              # Chapter files
│       ├── 01-introduction.tex
│       ├── 02-background.tex
│       └── ...
├── sources/                    # Input source documents
│   ├── thesis.pdf
│   └── report.docx
├── research-prompts/           # External research
│   ├── notebooklm.md          # NotebookLM prompt
│   ├── perplexity.md          # Perplexity prompt
│   ├── scopus.md              # Scopus AI prompts
│   └── results/               # Research output
│       ├── notebooklm.md
│       ├── perplexity.md
│       └── scopus.md
├── plan/                       # Document planning
│   ├── DOCUMENT_PLAN.md       # Overall structure
│   └── CHAPTER_ASSIGNMENTS.md # Per-chapter requirements
├── agents/                     # Agent configurations
│   ├── AGENT_GUIDELINES.md    # Writing rules
│   ├── chapter-writer.md      # Chapter writing prompt
│   ├── researcher.md          # Research prompt
│   └── reviewer.md            # Review prompt
├── scripts/                    # Automation scripts
│   ├── compile.sh             # LaTeX → PDF
│   ├── clean.sh               # Remove build files
│   ├── check-citations.sh     # Verify citations
│   ├── word-count.sh          # Count words
│   └── verify-setup.sh        # Check installation
├── .claude/                    # Claude Code config
│   ├── settings.json          # Model settings
│   └── CLAUDE.md              # Project context
├── .opencode/                  # OpenCode config
│   ├── config.yaml            # Provider settings
│   ├── .env.example           # API key template
│   └── prompts/               # Custom prompts
└── .gitignore                  # Git ignore rules

Directory Details

latex/

LaTeX document and all related files.

File	Purpose
main.tex	Main document with preamble, includes
bibliography.bib	BibTeX citation database
chapters/*.tex	Individual chapter files

Naming Convention:

chapters/
├── 01-introduction.tex
├── 02-background.tex
├── 03-methodology.tex
└── XX-name.tex

sources/

Input documents for analysis.

Supported Formats:

• PDF (.pdf) - Primary format
• Word (.docx) - Documents
• Text (.txt, .md) - Notes

Size Considerations

Large PDFs may need to be split for efficient processing.

research-prompts/

External research prompts and results.

research-prompts/
├── notebooklm.md      # Template prompt
├── perplexity.md      # Template prompt
├── scopus.md          # Template prompts
├── QUICK_REFERENCE.md # Cheat sheet
└── results/           # Output (gitignored)
    ├── notebooklm.md
    ├── perplexity.md
    └── scopus.md

plan/

Document planning files.

File	Content
DOCUMENT_PLAN.md	Overall structure, page budgets
CHAPTER_ASSIGNMENTS.md	Per-chapter requirements

agents/

Agent prompt templates.

File	Agent Type
AGENT_GUIDELINES.md	General writing rules
chapter-writer.md	Chapter generation
researcher.md	Source analysis
reviewer.md	Quality review

scripts/

Automation shell scripts.

Script	Function
compile.sh	Full LaTeX build
clean.sh	Remove build artifacts
check-citations.sh	Find missing citations
word-count.sh	Document statistics
verify-setup.sh	Installation check

.claude/

Claude Code configuration.

.claude/
├── settings.json    # Model preferences
└── CLAUDE.md        # Project context file

CLAUDE.md provides project context:

# Project Overview
This is a documentation project...

## Key Files
- latex/main.tex
- agents/AGENT_GUIDELINES.md

## Style Guidelines
- Academic prose
- Proper citations

.opencode/

OpenCode multi-provider configuration.

.opencode/
├── config.yaml      # Provider settings
├── .env.example     # API key template
├── .env             # API keys (gitignored!)
└── prompts/         # Custom prompts

File Conventions

Chapter Naming

XX-descriptive-name.tex

Examples:
01-introduction.tex
02-background.tex
03-attack-vectors.tex

Label Format

% Chapters
\label{ch:introduction}
\label{ch:background}

% Sections (chapter-prefixed)
\label{sec:ch01-motivation}
\label{sec:ch02-related-work}

% Figures
\label{fig:ch03-architecture}

% Tables
\label{tab:ch04-comparison}

BibTeX Keys

authorYYYY       # smith2024
orgYYYYtopic     # owasp2024llm

Creating New Projects

# Copy template
cp -r template/ my-new-document/
cd my-new-document/

# Initialize git
git init

# Configure project
# Edit .claude/CLAUDE.md
# Edit plan/DOCUMENT_PLAN.md

# Start work
claude