Merj - AI-Powered Git Merge Conflict Resolver

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

What is Merj?

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

Detects merge conflicts automatically after git pull
Analyzes both sides of the conflict using CodeRabbit
Understands your codebase using RAG (Retrieval-Augmented Generation)
Resolves conflicts intelligently using Claude AI
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.

Visit https://console.anthropic.com
Sign up or log in
Go to API Keys section
Click Create Key
Copy the key (starts with sk-ant-api03-)
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.

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

Pricing: ~$0.001 per 1000 tokens

3. GitHub Personal Access Token - REQUIRED

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

4. CodeRabbit Account -

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

Visit https://coderabbit.ai
Sign up for free account
Install CLI (see Step 3 above)
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:

Detection Phase
- Git pull executes and conflicts are identified
- Conflicted files are listed
Analysis Phase (for each conflict)
- CodeRabbit reviews changes on both branches
- RAG pipeline extracts relevant code context
- Context is saved to rag_output/
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
Review Phase
- You're shown the AI's resolution
- Options: Accept, Reject, or View details
- Accepted resolutions are staged in git
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

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

Name		Name	Last commit message	Last commit date
Latest commit History 34 Commits
bin		bin
flask_backend		flask_backend
lib		lib
my_chroma_db		my_chroma_db
rag_output		rag_output
rag_pipeline		rag_pipeline
scripts		scripts
.gitignore		.gitignore
README.md		README.md
package-lock.json		package-lock.json
package.json		package.json
requirements.txt		requirements.txt

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Merj - AI-Powered Git Merge Conflict Resolver

Table of Contents

What is Merj?

Quick Start

Complete Setup Guide

Prerequisites

Step 1: Clone and Install Node.js Components

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

Step 3: Install CodeRabbit CLI

Step 4: Configure All API Keys

Step 5: Authenticate GitHub

Step 6: Start the Flask Backend (for RAG)

Getting API Keys

1. Anthropic (Claude AI) - REQUIRED

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

3. GitHub Personal Access Token - REQUIRED

4. CodeRabbit Account -

Running Merj

Basic Workflow

What Happens During Conflict Resolution

Example Session

Advanced Commands

How It Works

Troubleshooting

Installation Issues

API Key Issues

Runtime Issues

Performance Issues

Testing Your Setup

1. Dry Run Test (No API Keys Needed)

2. Full Integration Test

3. Create a Test Conflict

Cost Estimates

Common Workflows

Working with Feature Branches

CI/CD Integration

Project Structure

Support

License

Authors

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