CodeGraph Installation & Setup Guide

December 18, 2025 · View on GitHub

This guide covers the complete installation process for CodeGraph, from building the binary to configuring the MCP server for use with Claude Code.

Table of Contents

  1. Prerequisites
  2. Building CodeGraph
  3. Setting Up SurrealDB
  4. Creating the Database Schema
  5. Configuration
  6. Indexing Your Codebase
  7. Running the MCP Server
  8. Daemon Mode
  9. Using Agentic Tools

Supported CLI Commands

  • start / stop / status — manage the MCP server transports (stdio/http)
  • index — index a project (supports --force, language filters, watch mode)
  • estimate — estimate indexing time/cost without persisting
  • config — init/show/set/get/validate configuration; agent-status/db-check live here
  • dbcheck — quick Surreal connectivity/schema canary
  • daemon — (feature-gated) file-watch daemon control

Legacy helper commands (code, test, perf, stats, clean, init) are no longer part of the CLI.

Prerequisites

Before installing CodeGraph, ensure you have:

  • macOS (the installer scripts target macOS; Linux users can adapt the commands)
  • Rust toolchain - Install from rustup.rs
  • Homebrew - Install from brew.sh
  • Ollama (recommended) - Install from ollama.com for local LLM/embedding support

Building CodeGraph

Use the full-features installation script to build CodeGraph with all capabilities:

cd /path/to/codegraph-rust
./install-codegraph-full-features.sh

This script:

  • Installs SurrealDB CLI via Homebrew if not present
  • Builds CodeGraph with all features enabled (daemon, AI-enhanced, all providers, LATS)
  • Installs the binary to ~/.cargo/bin/codegraph

What Gets Enabled

The full-features build includes:

  • All embedding providers (Ollama, LM Studio, Jina AI, OpenAI, ONNX)
  • All LLM providers (Anthropic, OpenAI, xAI Grok, Ollama, LM Studio)
  • Daemon mode (file watching & auto re-indexing)
  • HTTP server with SSE streaming
  • AutoAgents framework with LATS (Language Agent Tree Search)

Manual Build (Alternative)

If you prefer to build manually:

cargo install --path crates/codegraph-mcp-server --bin codegraph \
  --all-features --features autoagents-lats --force

Setting Up SurrealDB

CodeGraph requires SurrealDB for graph storage and vector search. You have two options:

# Install SurrealDB CLI
brew install surrealdb/tap/surreal

# Start SurrealDB with persistent storage
surreal start \
  --bind 0.0.0.0:3004 \
  --user root \
  --pass root \
  file://$HOME/.codegraph/surreal.db

For in-memory storage (data lost on restart):

surreal start --bind 0.0.0.0:3004 --user root --pass root memory

Option 2: Surreal Cloud (Free Tier Available)

  1. Sign up at surrealdb.com/cloud
  2. Create a free 1GB instance
  3. Note your connection URL, namespace, and credentials

Option 3: Surrealist IDE

Surrealist provides a graphical IDE for SurrealDB that makes database management easy:

  • Visual query editor with syntax highlighting
  • Schema visualization
  • Data browser and editor
  • Easy connection management

Download from surrealdb.com/surrealist or use the web version.

Creating the Database Schema

After starting SurrealDB, apply the CodeGraph schema:

Using the Apply Script

cd /path/to/codegraph-rust/schema

# Apply to local database (defaults: localhost:3004, root/root)
./apply-schema.sh

# Apply with custom settings
./apply-schema.sh \
  --endpoint ws://localhost:3004 \
  --namespace ouroboros \
  --database codegraph \
  --username root \
  --password root

Using SurrealDB CLI Directly

surreal sql \
  --endpoint ws://localhost:3004 \
  --namespace ouroboros \
  --database codegraph \
  --username root \
  --password root \
  < schema/codegraph.surql

Using Surrealist IDE

  1. Open Surrealist and connect to your database
  2. Navigate to the Query tab
  3. Open schema/codegraph.surql
  4. Execute the schema

Verify Schema Installation

surreal sql \
  --endpoint ws://localhost:3004 \
  --namespace ouroboros \
  --database codegraph \
  --username root \
  --password root \
  --command "INFO FOR DB;"

You should see tables like nodes, edges, chunks, symbol_embeddings, and functions like fn::semantic_search_chunks_with_context.

Configuration

CodeGraph uses a hierarchical configuration system. Settings can be specified via:

  1. Global config file (~/.codegraph/config.toml)
  2. Project-level config file (.codegraph/config.toml in project root)
  3. Environment variables (with CODEGRAPH_ prefix)
  4. .env file in project root

For detailed configuration examples (Ollama/LM Studio/Jina embeddings and OpenAI/xAI/Anthropic/OpenAI-compatible LLMs), see docs/AI_PROVIDERS.md.

Global Configuration (~/.codegraph/config.toml)

Create the directory and config file:

mkdir -p ~/.codegraph
cp config/example.toml ~/.codegraph/config.toml

Edit ~/.codegraph/config.toml:

# Embedding Configuration
[embedding]
provider = "ollama"                    # ollama | lmstudio | jina | openai
model = "qwen3-embedding:0.6b"         # Model name for your provider
dimension = 1024                       # 384, 768, 1024, 1536, 2048, 2560, 3072, 4096
batch_size = 32
normalize_embeddings = true
cache_enabled = true
ollama_url = "http://localhost:11434"
# lmstudio_url = "http://localhost:1234"  # For LM Studio

# LLM Configuration (for agentic tools)
[llm]
provider = "ollama"                    # ollama | anthropic | openai | xai | lmstudio
model = "qwen3:4b"                     # Model for reasoning
context_window = 32000                 # Affects tier selection for prompts
max_retries = 3

# Reranking (Optional - improves search quality)
[rerank]
provider = "jina"                      # jina | ollama
model = "jina-reranker-v3"
top_n = 10
candidates = 256

# Database Configuration
[database]
backend = "surrealdb"

[database.surrealdb]
connection = "ws://localhost:3004"
namespace = "ouroboros"
database = "codegraph"
# username = "root"
# password is best set via env: CODEGRAPH__DATABASE__SURREALDB__PASSWORD
strict_mode = false
auto_migrate = true

# Server Configuration
[server]
host = "0.0.0.0"
port = 3003

# Performance Tuning
[performance]
batch_size = 64                        # Embedding batch size
workers = 4                            # Rayon thread count
max_concurrent = 4                     # Concurrent embedding requests
max_texts_per_request = 256

# Daemon Configuration (for --watch mode)
[daemon]
auto_start_with_mcp = true             # Auto-start when MCP server starts
debounce_ms = 30
batch_timeout_ms = 200
exclude_patterns = ["**/node_modules/**", "**/target/**", "**/.git/**"]

# Monitoring
[monitoring]
enabled = true
metrics_enabled = true
trace_enabled = false
metrics_interval_secs = 60

# Security
[security]
require_auth = false
rate_limit_per_minute = 1200

Project-Level Configuration

Create .codegraph/config.toml in your project root for project-specific overrides:

# Project-specific settings override global config
[embedding]
model = "jina-embeddings-v4"           # Different model for this project
dimension = 2048

[llm]
provider = "anthropic"
model = "claude-sonnet-4"

Environment Variables

Environment variables override config files. Use the CODEGRAPH_ prefix:

# Embedding
export CODEGRAPH_EMBEDDING_PROVIDER=ollama
export CODEGRAPH_EMBEDDING_MODEL=qwen3-embedding:0.6b
export CODEGRAPH_EMBEDDING_DIMENSION=1024
export CODEGRAPH_MAX_CHUNK_TOKENS=32000

# LLM
export CODEGRAPH_LLM_PROVIDER=anthropic
export CODEGRAPH_LLM_MODEL=claude-sonnet-4

# Database
export CODEGRAPH_SURREALDB_URL=ws://localhost:3004
export CODEGRAPH_SURREALDB_NAMESPACE=ouroboros
export CODEGRAPH_SURREALDB_DATABASE=codegraph
export CODEGRAPH_SURREALDB_USERNAME=root
export CODEGRAPH_SURREALDB_PASSWORD=root

# API Keys (for cloud providers)
export ANTHROPIC_API_KEY=sk-ant-...
export OPENAI_API_KEY=sk-...
export JINA_API_KEY=jina_...
export XAI_API_KEY=xai-...

# Agent Architecture
export CODEGRAPH_AGENT_ARCHITECTURE=react    # react | lats

# Debugging
export CODEGRAPH_DEBUG=1                     # Enable debug logging

Using .env File

Create a .env file in your project root:

# Copy the example
cp .env.example .env

# Edit with your settings

Indexing Your Codebase

Before using the MCP server, you must index your codebase to create the graph and embeddings.

Basic Indexing

# Index current directory recursively
codegraph index . -r

# Index with specific languages
codegraph index . -r -l rust,typescript,python

# Index a specific path
codegraph index /path/to/codebase -r -l rust

Indexing Options

codegraph index <PATH> [OPTIONS]

Options:
  -r, --recursive           Recursively index subdirectories
  -l, --languages <LANGS>   Comma-separated list of languages to index
                            (rust, python, typescript, javascript, go, java,
                             cpp, c, swift, kotlin, csharp, ruby, php, dart)
  --exclude <PATTERN>       Glob patterns to exclude (can be repeated)
  --force                   Force re-index of all files
  --project-id <ID>         Custom project identifier

Examples

# Index a Rust project
codegraph index /path/to/rust-project -r -l rust

# Index a full-stack project with multiple languages
codegraph index . -r -l rust,typescript,python --exclude "**/node_modules/**" --exclude "**/target/**"

# Force complete re-index
codegraph index . -r -l rust --force

Verify Indexing

Check that data was indexed:

surreal sql \
  --endpoint ws://localhost:3004 \
  --namespace ouroboros \
  --database codegraph \
  --username root \
  --password root \
  --command "SELECT count() FROM nodes GROUP ALL; SELECT count() FROM chunks GROUP ALL;"

Running the MCP Server

With Claude Code

Add CodeGraph to your Claude Code MCP configuration. In your ~/.claude/claude_desktop_config.json or MCP settings:

{
  "mcpServers": {
    "codegraph": {
      "command": "/full/path/to/codegraph",
      "args": ["start", "stdio", "--watch"]
    }
  }
}

Important: Use the full absolute path to the binary. Find it with:

which codegraph
# Usually: /Users/<username>/.cargo/bin/codegraph

# Start MCP server with file watching
/full/path/to/codegraph start stdio --watch

# Without file watching
/full/path/to/codegraph start stdio

# Watch a specific directory
/full/path/to/codegraph start stdio --watch --watch-path /path/to/project

HTTP Mode (For Web Clients)

# Start HTTP server with SSE streaming
codegraph start http --host 127.0.0.1 --port 3000

# Test the endpoint
curl http://127.0.0.1:3000/health

The --watch Flag

When you include --watch, the MCP server automatically:

  • Monitors your project for file changes
  • Re-indexes modified files in the background
  • Keeps search results up-to-date

Without --watch, you must manually re-run codegraph index after making changes.

Daemon Mode

For more control over file watching, use the standalone daemon:

Starting the Daemon

# Start watching a project (runs in background)
codegraph daemon start /path/to/project

# Start in foreground (for debugging)
codegraph daemon start /path/to/project --foreground

# Filter by languages
codegraph daemon start /path/to/project --languages rust,typescript

# Exclude patterns
codegraph daemon start /path/to/project \
  --exclude "**/node_modules/**" \
  --exclude "**/target/**"

Managing the Daemon

# Check daemon status
codegraph daemon status /path/to/project
codegraph daemon status /path/to/project --json

# Stop the daemon
codegraph daemon stop /path/to/project

Daemon vs --watch

Feature--watch flagdaemon command
Runs with MCP serverYesIndependent
Background processNo (inline)Yes
Multiple projectsNoYes
Fine-grained controlLimitedFull
Status monitoringNoYes

Use --watch for simple single-project setups with Claude Code. Use daemon for complex multi-project environments or when you need independent control.

Using Agentic Tools

CodeGraph provides 8 agentic MCP tools that use multi-step reasoning to analyze your codebase:

Available Tools

ToolPurposeWhen to Use
agentic_code_searchSemantic code search with AI insightsFinding code patterns, exploring unfamiliar codebases
agentic_dependency_analysisAnalyze dependencies and impactBefore refactoring, understanding coupling
agentic_call_chain_analysisTrace execution pathsDebugging, understanding data flow
agentic_architecture_analysisAssess system architectureArchitecture reviews, onboarding
agentic_api_surface_analysisAnalyze public interfacesAPI design reviews, breaking change detection
agentic_context_builderGather comprehensive contextBefore implementing new features
agentic_semantic_questionAnswer complex codebase questionsDeep understanding questions
agentic_complexity_analysisIdentifies high-risk code hotspots for refactoringarchitectural flaws and complexities

Example Queries

In Claude Code, simply ask questions - the agentic tools will be used automatically:

Code Search:

"Find all places where authentication is handled in this codebase"

Dependency Analysis:

"What would be affected if I change the UserService class?"

Call Chain Analysis:

"Trace the execution path from HTTP request to database query in the payment flow"

Architecture Analysis:

"Give me an overview of this project's architecture and main components"

API Surface:

"What public APIs does the auth module expose?"

Context Building:

"I need to add rate limiting to the API. Gather all relevant context."

Agent Architecture Selection

CodeGraph supports two reasoning architectures:

ReAct (Default) - Fast, single-pass reasoning:

export CODEGRAPH_AGENT_ARCHITECTURE=react

LATS - Deeper, tree-search reasoning (slower but more thorough):

export CODEGRAPH_AGENT_ARCHITECTURE=lats

Tier-Aware Prompting

The agent automatically adjusts its behavior based on the context window of the LLM you configured for CodeGraph (set .env CODEGRAPH_CONTEXT_WINDOW=ctx):

TierContext WindowBehavior
Small< 50K tokensTerse prompts, 5 max steps
Medium50K-150KBalanced prompts, 10 max steps
Large150K-500KDetailed prompts, 15 max steps
Massive> 500KExploratory prompts, 20 max steps

This means you can use smaller local models for quick queries and larger cloud models for comprehensive analysis.

Debugging Agent Behavior

Enable debug logging to see agent reasoning:

export CODEGRAPH_DEBUG=1

View debug logs:

python tools/view_debug_logs.py --follow

Troubleshooting

Common Issues

"Cannot connect to SurrealDB"

  • Ensure SurrealDB is running: surreal start ...
  • Check the connection URL matches your config
  • Verify namespace and database exist

"No embeddings found"

  • Ensure you've indexed the project: codegraph index . -r -l <languages>
  • Check your embedding provider is running (Ollama, LM Studio, etc.)

"GraphFunctions not initialized"

  • Apply the schema: ./schema/apply-schema.sh
  • Verify functions exist: INFO FOR DB;

MCP server not appearing in Claude Code

  • Use the full absolute path to the binary
  • Check Claude Code's MCP logs for errors
  • Verify the binary is executable: chmod +x /path/to/codegraph

Getting Help

  • Check logs with CODEGRAPH_DEBUG=1
  • View the README for additional configuration options
  • Check codegraph --help for CLI documentation