Merj - AI-Powered Git Merge Conflict Resolver

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Merj automatically detects and resolves Git merge conflicts using Claude AI, CodeRabbit code reviews, and intelligent code context from your repository.

Table of Contents

• What is Merj?
• Quick Start
• Complete Setup Guide
• Getting API Keys
• Running Merj
• How It Works
• Troubleshooting
• Testing Your Setup
• Cost Estimates

What is Merj?

Merj transforms the tedious process of resolving Git merge conflicts into an intelligent, semi-automated workflow:

1. Detects merge conflicts automatically after git pull
2. Analyzes both sides of the conflict using CodeRabbit
3. Understands your codebase using RAG (Retrieval-Augmented Generation)
4. Resolves conflicts intelligently using Claude AI
5. Presents solutions for your review and approval

Instead of manually editing conflict markers, you get AI-powered resolutions with explanations.

Quick Start

Get Merj running in 5 minutes:

# 1. Clone the repository
git clone https://github.com/Anay-jo/MergeConflictResolver.git
cd MergeConflictResolver

# 2. Run quick setup (Node.js dependencies only)
npm install && npm link

# 3. Set up GitHub authentication
merj auth

# 4. Set Claude AI key (required)
export ANTHROPIC_API_KEY="sk-ant-..."

# 5. Try it!
cd your-git-repo
merj pull

For full functionality with CodeRabbit and RAG, continue to Complete Setup Guide.

Complete Setup Guide

Prerequisites

• Node.js v18+ (Download)
• Python 3.8+ (Download)
• Git 2.0+
• GitHub Account with Personal Access Token
• API Keys for Claude AI and Voyage AI (see Getting API Keys)

Step 1: Clone and Install Node.js Components

# Clone the repository
git clone https://github.com/Anay-jo/MergeConflictResolver.git
cd MergeConflictResolver

# Install Node.js dependencies
npm install

# Make 'merj' command available globally
npm link

# Verify installation
merj --help

Step 2: Set Up Python Environment (for RAG Pipeline)

# Create Python virtual environment
python3 -m venv venv

# Activate virtual environment
# On macOS/Linux:
source venv/bin/activate
# On Windows:
# venv\Scripts\activate

# Install Python dependencies
pip install -r requirements.txt
pip install -r flask_backend/requirements.txt

Step 3: Install CodeRabbit CLI

# Install CodeRabbit CLI globally
curl -fsSL https://cli.coderabbit.ai/install.sh | sh

# Reload your shell configuration
source ~/.zshrc  # or ~/.bashrc for bash users

# Verify installation
coderabbit --version

# Log in to CodeRabbit (opens browser)
coderabbit auth login

Step 4: Configure All API Keys

Create a .env file in the project root (or set environment variables):

# Required API Keys
export ANTHROPIC_API_KEY="sk-ant-api03-xxxxx"  # Claude AI (Required)
export VOYAGE_API_KEY="pa-xxxxx"                # Embeddings (Required for RAG)

# Optional Configuration
export MAIN_REF="origin/main"                   # Your main branch
export MODEL="claude-3-5-sonnet-20241022"       # Claude model to use

Step 5: Authenticate GitHub

# Run authentication command
merj auth

# Enter your GitHub Personal Access Token when prompted
# The token will be stored securely in ~/.merjrc

Step 6: Start the Flask Backend (for RAG)

# In a separate terminal, activate Python environment
source venv/bin/activate

# Start Flask backend
cd flask_backend
python app.py

# You should see: "Running on http://127.0.0.1:5000"

Getting API Keys

1. Anthropic (Claude AI) - REQUIRED

Claude AI analyzes and resolves your merge conflicts.

1. Visit https://console.anthropic.com
2. Sign up or log in
3. Go to API Keys section
4. Click Create Key
5. Copy the key (starts with sk-ant-api03-)
6. Set it: export ANTHROPIC_API_KEY="your-key-here"

Pricing: ~$0.01-0.02 per conflict resolution

2. Voyage AI (Code Embeddings) - Required for RAG

Voyage AI creates semantic embeddings of your code for intelligent context retrieval.

1. Visit https://www.voyageai.com
2. Sign up for an account
3. Go to Dashboard → API Keys
4. Create a new key
5. Copy the key (starts with pa-)
6. Set it: export VOYAGE_API_KEY="your-key-here"

Pricing: ~$0.001 per 1000 tokens

3. GitHub Personal Access Token - REQUIRED

1. Visit https://github.com/settings/tokens
2. Click Generate new token (classic)
3. Name it (e.g., "Merj CLI")
4. Select scopes:
   • ✅ repo (Full control of private repositories)
   • ✅ read:org (Read org and team membership)
5. Click Generate token
6. Copy immediately (won't be shown again!)
7. Use with: merj auth

4. CodeRabbit Account -

CodeRabbit provides intelligent code review insights for both sides of the conflict.

1. Visit https://coderabbit.ai
2. Sign up for free account
3. Install CLI (see Step 3 above)
4. Authenticate: coderabbit auth login

Running Merj

Basic Workflow

# 1. Ensure Flask backend is running (in separate terminal)
cd flask_backend && python app.py

# 2. Navigate to your git repository
cd /path/to/your/repo

# 3. Pull changes (Merj will handle conflicts)
merj pull

# 4. Follow the prompts to review and accept/reject resolutions

What Happens During Conflict Resolution

When you run merj pull and conflicts are detected:

1. Detection Phase

   • Git pull executes and conflicts are identified
   • Conflicted files are listed

2. Analysis Phase (for each conflict)

   • CodeRabbit reviews changes on both branches
   • RAG pipeline extracts relevant code context
   • Context is saved to rag_output/

3. Resolution Phase

   • Claude AI receives:
     • The conflicted file with markers
     • CodeRabbit's analysis
     • Similar code patterns from your codebase
   • Claude generates a clean, merged version

4. Review Phase

   • You're shown the AI's resolution
   • Options: Accept, Reject, or View details
   • Accepted resolutions are staged in git

5. Completion

   • All accepted files are committed
   • Summary shows resolved/rejected counts

Example Session

$ merj pull

🔍 Checking authentication...
✅ Authenticated as: joshuachen

📦 Repository: merj/test-repo
🌿 Current branch: feature-branch
🎯 Remote: origin

Pulling from origin...

⚠️  Merge conflicts detected in 2 files:
  - src/auth.py
  - src/database.py

Starting AI-powered resolution...

[1/2] Resolving: src/auth.py
📊 CodeRabbit: Found 3 code quality issues
🧠 Claude AI: Analyzing conflict...
✨ Resolution ready!

The conflict is between:
- LOCAL: Added password hashing with bcrypt
- REMOTE: Added rate limiting for login attempts

Proposed resolution combines both features safely.

Accept this resolution? (Y/n): Y
✅ Resolution applied to src/auth.py

[2/2] Resolving: src/database.py
...

Summary:
✅ Resolved: 2 files
❌ Rejected: 0 files
⚠️  Failed: 0 files

Advanced Commands

# Force push changes
merj push --force

# Use a different Claude model
MODEL=claude-3-opus-20240229 merj pull

# Debug mode (verbose output)
DEBUG=true merj pull

# Skip CodeRabbit analysis
SKIP_CODERABBIT=true merj pull

How It Works

┌─────────────┐
│  merj pull  │
└─────┬───────┘
      ↓
┌─────────────────────────┐
│ Git Pull & Detect       │
│ Conflicts               │
└─────┬───────────────────┘
      ↓
┌─────────────────────────┐
│ CodeRabbit Analysis     │
│ (Review both branches)  │
└─────┬───────────────────┘
      ↓
┌─────────────────────────┐
│ RAG Pipeline            │
│ (Find similar code)     │
└─────┬───────────────────┘
      ↓
┌─────────────────────────┐
│ Claude AI               │
│ (Generate resolution)   │
└─────┬───────────────────┘
      ↓
┌─────────────────────────┐
│ User Review             │
│ (Accept/Reject)         │
└─────┬───────────────────┘
      ↓
┌─────────────────────────┐
│ Git Commit              │
│ (Stage accepted files)  │
└─────────────────────────┘

Troubleshooting

Installation Issues

"merj: command not found"

# Re-link the CLI
npm link

# Or use npx
npx merj pull

"Python module not found"

# Ensure virtual environment is activated
source venv/bin/activate  # macOS/Linux
# or
venv\Scripts\activate  # Windows

# Reinstall dependencies
pip install -r requirements.txt

"CodeRabbit: command not found"

# Reinstall CodeRabbit CLI
curl -fsSL https://cli.coderabbit.ai/install.sh | sh

# Restart terminal or reload shell
source ~/.zshrc  # or ~/.bashrc

API Key Issues

"Claude API error 401: Unauthorized"

• Check your Anthropic API key is correct
• Ensure it starts with sk-ant-api03-
• Verify at https://console.anthropic.com

"Voyage AI authentication failed"

• Verify your Voyage API key
• Should start with pa-
• Check key has access to voyage-code-3 model

"GitHub authentication failed"

• Regenerate token at GitHub Settings
• Ensure token has repo scope
• Run merj auth again

Runtime Issues

"Flask backend connection refused"

# Check if Flask is running
curl http://127.0.0.1:5000/api/health

# If not, start it:
cd flask_backend
python app.py

"No conflicts detected"

# Verify conflicts exist
git status

# Should show:
# both modified:   filename.py

"ChromaDB error"

# Clear ChromaDB cache
rm -rf rag_pipeline/demo_chroma_db/

# Restart Flask backend

"Resolution looks wrong"

• Check RAG context: cat rag_output/llm_context.txt
• Review CodeRabbit findings: cat rag_output/coderabbit_review.json
• Try different Claude model: MODEL=claude-3-opus-20240229

Performance Issues

• Slow resolution: Reduce RAG context chunks (default: 5)
• High API costs: Use smaller Claude model (sonnet vs opus)
• Memory issues: Process one conflict at a time

Testing Your Setup

1. Dry Run Test (No API Keys Needed)

Test your installation without making API calls:

./test_dry_run.sh

This validates:

• ✅ All files installed correctly
• ✅ Dependencies are present
• ✅ File permissions are correct

2. Full Integration Test

Test with real API calls using a mock conflict:

export ANTHROPIC_API_KEY="your-key"
./test_full_integration.sh

This tests:

• Complete conflict resolution flow
• API integrations
• User approval workflow

3. Create a Test Conflict

# Create test repository
mkdir test-merge && cd test-merge
git init

# Create initial file
echo "original content" > test.txt
git add test.txt
git commit -m "Initial commit"

# Create conflicting changes
git checkout -b feature
echo "feature change" > test.txt
git add test.txt
git commit -m "Feature change"

git checkout main
echo "main change" > test.txt
git add test.txt
git commit -m "Main change"

# Merge with conflicts
git merge feature  # Creates conflict

# Now use Merj
merj pull

Cost Estimates

Per conflict resolution:

• Claude AI: $0.01-0.02 (2 API calls)
• Voyage AI: <$0.001 (embeddings)
• CodeRabbit: Free tier available
• Total: ~$0.02 per conflict

Monthly estimates (100 conflicts):

• Light usage: ~$2
• Regular usage: ~$5-10
• Heavy usage: ~$20-30

Common Workflows

Working with Feature Branches

# Create feature branch
git checkout -b feature/new-feature

# Make changes and push
git add .
git commit -m "Add new feature"
merj push

# Later, pull with conflict resolution
git checkout main
git pull origin main
git checkout feature/new-feature
merj pull origin main  # Merj handles conflicts

CI/CD Integration

Add to your CI pipeline:

# .github/workflows/merge.yml
- name: Setup Merj
  run: |
    npm install -g merj
    merj auth

- name: Resolve conflicts
  env:
    ANTHROPIC_API_KEY: ${{ secrets.ANTHROPIC_API_KEY }}
  run: |
    merj pull --auto-accept

Project Structure

MergeConflictResolver/
├── bin/
│   ├── index.js                 # CLI entry point
│   ├── merj.js                  # Main commands
│   └── resolve_with_claude.js   # Claude AI integration
├── lib/
│   ├── auth.js                  # GitHub authentication
│   └── git.js                   # Git operations
├── rag_pipeline/
│   ├── chunker.py               # Code parser
│   ├── embedder.py              # Voyage AI integration
│   ├── chroma.py                # Vector database
│   └── local_remote_rag.py      # RAG retrieval
├── flask_backend/
│   └── app.py                   # REST API server
├── scripts/
│   └── review_two_sides_with_cr.py  # CodeRabbit integration
├── rag_output/                  # Generated context files
│   ├── llm_context.txt
│   └── coderabbit_review.json
└── package.json                 # Node dependencies

Support

• Issues: GitHub Issues
• Documentation: This README
• Updates: Watch the repository for new features

License

ISC License - See LICENSE file

Authors

Anay, Sam, Ayush, and Josh

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Ready to resolve conflicts intelligently? Follow the Quick Start to begin!