Complete Code Repository
Full repository structure, installation instructions, and series navigation
Complete Code Repository
All code from Episodes 1-5 is available in the companion GitHub repository. This section provides the complete repository structure, installation instructions, and navigation to all episodes in the series.
Repository Structure
The following directory tree shows the complete organization of all code, configuration files, and documentation from this 5-episode series:
research-orchestration/
├── README.md # Setup instructions
├── package.json # Node dependencies
├── requirements.txt # Python dependencies
├── .env.example # Environment variable template
│
├── claude-code-config/
│ ├── agents/
│ │ ├── literature-review.md # Literature review agent
│ │ ├── citation-manager.md # Citation management agent
│ │ └── pdf-analyzer.md # PDF analysis agent
│ ├── commands/
│ │ ├── search-papers.md # /search-papers command
│ │ ├── analyze-pdf.md # /analyze-pdf command
│ │ └── generate-bibliography.md # /generate-bibliography command
│ └── claude_desktop_config.json # MCP server configuration
│
├── mcp-servers/
│ ├── auth-server/ # From Episode 3
│ │ ├── server.ts
│ │ ├── package.json
│ │ └── README.md
│ ├── pdf-server/ # From Episode 4
│ │ ├── server.py
│ │ ├── requirements.txt
│ │ └── README.md
│ ├── citation-server/ # NEW: Citation database
│ │ ├── server.ts
│ │ ├── database.sqlite
│ │ ├── schema.sql
│ │ ├── package.json
│ │ └── README.md
│ └── playwright-automation/ # NEW: Browser automation MCP
│ ├── server.ts
│ ├── package.json
│ └── README.md
│
├── scripts/
│ ├── daily-routine.ts # Daily research check
│ ├── project-deep-dive.ts # Project-based workflow
│ ├── literature-review.ts # Complete lit review workflow
│ ├── incremental-update.ts # Daily incremental updates
│ ├── citation-network.ts # Citation network analysis
│ └── utils/
│ ├── citation-formatter.ts # Universal citation formatting
│ ├── file-organizer.ts # PDF organization utilities
│ └── database-helpers.ts # Database interaction helpers
│
├── integrations/
│ ├── obsidian-sync.ts # Obsidian vault integration
│ ├── notion-sync.ts # Notion database integration
│ └── zotero-export.ts # Zotero export utility
│
├── examples/
│ ├── step-by-step-review/ # Episode 5 example walkthrough
│ │ ├── step1-generate-queries.ts
│ │ ├── step2-multi-search.ts
│ │ ├── step3-deduplicate.ts
│ │ ├── step4-download.ts
│ │ ├── step5-extract.ts
│ │ ├── step6-analyze.ts
│ │ ├── step7-synthesize.ts
│ │ └── step8-generate-review.ts
│ └── domain-specific/
│ ├── cs-research.ts # Computer science workflow
│ ├── humanities-research.ts # Humanities workflow
│ └── biomedical-research.ts # Biomedical workflow
│
└── docs/
├── SETUP.md # Complete setup guide
├── TROUBLESHOOTING.md # Common issues and fixes
├── CUSTOMIZATION.md # How to adapt to your domain
└── API-REFERENCE.md # API documentation for MCP serversInstallation Instructions
Follow these steps to set up the complete research automation system on your local machine:
Clone Repository
Clone the repository to your local machine:
git clone https://github.com/your-org/research-orchestration.git
cd research-orchestrationInstall Dependencies
Install both Node.js and Python dependencies:
npm install
pip install -r requirements.txtConfigure Environment
Create environment configuration file:
cp .env.example .env
# Edit .env with your API keys and pathsOpen .env in your text editor and add:
- Anthropic API key
- Absolute paths to research directories
- Database connection strings (if applicable)
Setup MCP Servers
Build and configure all MCP servers:
# Auth server (Episode 3)
cd mcp-servers/auth-server && npm install && npm run build
# PDF server (Episode 4)
cd ../pdf-server && pip install -r requirements.txt
# Citation server (Episode 5)
cd ../citation-server && npm install && npm run build && npm run init-db
# Playwright automation (Episode 5)
cd ../playwright-automation && npm install && npm run buildConfigure Claude Code
Copy MCP configuration to Claude Code:
cp claude-code-config/claude_desktop_config.json ~/.config/claude/config.json
# Edit config.json to update absolute pathsOpen config.json and update all absolute paths to match your system:
- MCP server executable paths
- Research directory paths
- Database file paths
Run Example
Test the installation with the daily routine example:
npm run example:daily-routineExpected output: Console logs showing paper searches, PDF downloads, and citation extraction.
All code from Episodes 1-5 is MIT licensed and available for adaptation to your research needs. For questions or contributions, open a discussion in the GitHub repository. Your research revolution starts with this codebase.
Series Navigation
Navigate to all episodes in the AI-Powered Research Automation series:
Episode 1: The Manifesto
Time as the ultimate research currency
Episode 2: The Foundation
Understanding the AI research stack
Episode 3: Auth Bypass
Authentication and browser automation
Episode 4: PDF Intelligence
PDF extraction and citation management
Episode 5: Complete Workflow
Orchestrating your AI research system (You are here)
Your research revolution starts now. What will you automate first?