knot

knot

knot is a high-performance codebase indexer that extracts structural and semantic information from source code, enabling AI agents to understand, analyze, and navigate large code repositories. Currently supports Java, Kotlin (v0.7.4+), TypeScript, JavaScript/Node.js, HTML, and CSS/SCSS with full cross-language linking, with planned support for Rust and C/C++.

The indexer automatically builds:

• Vector Search Database (Qdrant) — semantic understanding via embeddings
• Graph Database (Neo4j) — architectural relationships via call graphs

This dual-database approach powers both:

• MCP (Model Context Protocol) Server — Exposes three tools to any LLM client (Claude, Gemini, ChatGPT, Cursor, etc.)
• CLI Tool (v0.8.0+) — Standalone knot command for terminal and scripting environments

✨ Key Features

🔍 Code Intelligence Tools

• search_hybrid_context: Semantic + structural search. Find code by meaning, class name, method signature, docstrings, or comments. Returns full context including dependencies.
• find_callers: Reverse dependency lookup. Identify dead code, perform impact analysis, or understand the full call chain of any function/method.
• explore_file: File anatomy inspection. Quickly see all classes, interfaces, methods, and functions in a file with signatures and documentation.

🏗️ Multi-Language Support

• Java: Full AST extraction with package awareness
• Kotlin (v0.7.4+): Complete support for Kotlin codebases with classes, interfaces, objects, companion objects, functions, methods, and properties. Fully compatible with tree-sitter-kotlin-ng grammar.
• TypeScript/TSX/CTS: Complete support for modern JavaScript/TypeScript codebases, including CommonJS TypeScript files
• JavaScript/Node.js (v0.7.4+): Vanilla JS, Node.js, and module systems (.js, .mjs, .cjs, .jsx)
• Hybrid Web Ecosystem (v0.6.5): Cross-language linking between JavaScript, HTML, and CSS for full-stack SPA analysis
• HTML (v0.6.3+): Custom elements (Web Components, Angular), id and class attribute indexing for cross-language CSS search
• JSX/TSX Attributes (v0.6.3+): Extracts id and className from React components for unified HTML/CSS discovery
• CSS/SCSS (v0.6.4+): Stylesheet indexing with class/ID selector extraction and variable tracking (CSS/SCSS variables, mixins, functions)
• Rust (Planned v0.8.x): Struct, trait, and macro analysis
• C/C++ (Planned v0.9.x): Pointer relationships and macro analysis

📚 Rich Comment Extraction

• Captures docstrings (JavaDoc, JSDoc) preceding declarations
• Extracts inline comments within method/function bodies
• Respects nesting boundaries (class comments don't capture method comments)
• Intelligently aggregates comment blocks

📊 Dual-Database Architecture

• Qdrant: Vector search for semantic code understanding
• Neo4j: Graph relationships for structural navigation

🚀 High Performance

• Parallel Streaming Pipeline: Overlaps CPU-bound embedding with I/O-bound ingestion via MPSC channels (v0.5.0+)
• Incremental Indexing: Uses SHA-256 hashes to skip unchanged files
• Real-time Watch Mode: Automatically re-indexes changed files in seconds via --watch
• CPU Parallelism: AST extraction via Rayon
• Scalable: Configurable batch processing and constant memory footprint (~2GB) regardless of repository size

🛠️ Installation

Prerequisites

Option A: Pre-compiled Binaries (macOS & Modern Linux)

Go to the Releases page and download the native executable for your platform.

Install via Shell Script (macOS & Linux):

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/raultov/knot/releases/latest/download/knot-installer.sh | sh && curl -sO https://raw.githubusercontent.com/raultov/knot/master/.knot-agent.md

This one-liner installs the knot binary and downloads the .knot-agent.md skill file to your current directory for use with AI agents and LLM-based code analysis tools.

Linux Requirements:

• Minimum glibc version: 2.38+
• Compatible distributions:
  • Ubuntu 24.04 LTS or later
  • Debian 13 (Trixie) or later
  • Fedora 39+ / RHEL 10+
  • Arch Linux (rolling release)

For older Linux distributions or Windows, use Docker (see Option B) or build from source (see Option C).

Option B: Docker (Universal Compatibility)

Docker images provide universal compatibility for any Linux distribution (including older versions with glibc < 2.38) and Windows.

Build the image locally:

docker build -t knot:latest . --network=host

Run the indexer:

# Use --network host to connect to databases running on your host machine
docker run --rm \
  -v /path/to/your/repo:/workspace \
  -e KNOT_REPO_PATH=/workspace \
  -e KNOT_NEO4J_PASSWORD=your-password \
  --network host \
  knot:latest \
  knot-indexer

Run the CLI tool:

docker run --rm \
  -v /path/to/your/repo:/workspace \
  -e KNOT_REPO_PATH=/workspace \
  -e KNOT_NEO4J_PASSWORD=your-password \
  --network host \
  knot:latest \
  knot search "user login flow"

Run the MCP server:

docker run --rm \
  -e KNOT_REPO_PATH=/workspace \
  -e KNOT_NEO4J_PASSWORD=your-password \
  --network host \
  knot:latest \
  knot-mcp

Note: The Dockerfile uses a multi-stage build (builder stage with Rust, runtime stage with Debian Trixie) to ensure a minimal, high-performance image. Use --network host to allow the container to access Qdrant and Neo4j running on your host machine.

Option C: Install via Cargo

cargo install --git https://github.com/raultov/knot

Option D: Build from Source

1. Start infrastructure with Docker:

docker compose up -d

2. Clone and build:

git clone https://github.com/raultov/knot
cd knot
cargo build --release

3. Configure:

cp .env.example .env
$EDITOR .env  # Set KNOT_REPO_PATH and Neo4j credentials

4. Index a codebase:

./target/release/knot-indexer

5. Query via CLI:

./target/release/knot search "your query"

6. Start the MCP server:

./target/release/knot-mcp

📖 Usage

Using the CLI (v0.8.0+)

The knot CLI provides the same capabilities as the MCP server via command-line commands, making it ideal for:

• Terminal-only environments
• Bash scripting and automation
• CI/CD pipelines
• Direct integration with other tools

Three main commands:

knot search — Semantic Code Search

knot search "user authentication" --max-results 10 --repo my-app

Find code entities by meaning, class names, docstrings, or comments.

knot callers — Reverse Dependency Lookup

knot callers "LoginService" --repo my-app

Find all code that references a specific entity (dead code detection, impact analysis, call chains).

knot explore — File Structure Inspection

knot explore "src/services/auth.ts" --repo my-app

List all classes, methods, functions in a file with signatures and documentation.

For detailed CLI usage guide, see .knot-agent.md — a machine-readable skill that teaches LLMs how to use knot CLI for autonomous code analysis.

Indexing a Codebase

Incremental Indexing (Default, v0.4.3+)

# First run: indexes all files
knot-indexer --repo-path /path/to/your/repo --neo4j-password secret

# Subsequent runs: only re-indexes changed files (fast!)
knot-indexer --repo-path /path/to/your/repo --neo4j-password secret

# NEW: Real-time Watch mode (v0.5.2+)
knot-indexer --watch --repo-path /path/to/your/repo --neo4j-password secret

How it works:

• Tracks file content via SHA-256 hashes in .knot/index_state.json
• Automatically detects: modified, added, and deleted files
• Only re-parses and re-embeds changed files
• Preserves graph relationships to unchanged files
• Processes entities in memory-efficient 512-entity chunks

Performance:

• Initial index (3800 files): ~60 minutes on standard hardware
• Incremental update (3 files changed): ~5-10 seconds
• Memory usage: Constant ~2GB regardless of repository size

Full Re-Index (Clean Mode)

# Force complete re-index (deletes all existing data)
knot-indexer --clean --repo-path /path/to/your/repo --neo4j-password secret

Use --clean when:

• You want to rebuild the entire index from scratch
• You've changed Tree-sitter queries or embedding models
• Troubleshooting indexing issues

Running E2E Integration Tests

To ensure indexer stability, run the E2E integration test suite:

# Run all language E2E tests (Java, TS, JS, HTML, CSS, Kotlin)
./tests/run_e2e.sh

# Run only Kotlin E2E tests
./tests/run_kotlin_e2e.sh

See tests/KOTLIN_E2E_TESTS.md for detailed coverage and troubleshooting.

Using the MCP Server

The MCP server exposes three tools to any compatible AI client:

Tool 1: search_hybrid_context

Find code by meaning or keywords

Query: "How is user authentication implemented?"
Result: All auth-related code, signatures, docstrings, and dependencies

Capabilities:

• Semantic search by functionality
• Class/method/function name lookup
• Docstring and inline comment search
• Architectural pattern discovery
• Full dependency context

Tool 2: find_callers

Find who calls a specific function

Query: "Find callers of getCurrentTimeInSeconds"
Result: All code that invokes this function + file locations

Advanced: Search by Signature (NEW in v0.7.4)

# Find by full signature (Java)
echo '{"method":"tools/call","params":{"name":"find_callers","arguments":{"entity_name":"registerUser(String"}}}' | knot-mcp

# Find by parameter type (Kotlin)
echo '{"method":"tools/call","params":{"name":"find_callers","arguments":{"entity_name":"findById(Int"}}}' | knot-mcp

# Find by type annotation (TypeScript)
echo '{"method":"tools/call","params":{"name":"find_callers","arguments":{"entity_name":"(EventData"}}}' | knot-mcp

Use Cases:

• Dead Code Detection: Zero callers = unused code
• Impact Analysis: "What breaks if I modify this?"
• Refactoring Safety: Find all references before removing

Tool 3: explore_file

Understand file structure

Query: "What's in BrowserService.ts?"
Result: All classes, methods, and functions with signatures and docs

Use Cases:

• Quick file navigation
• Module structure overview
• Finding all methods in a class without reading line-by-line

🔗 MCP Client Configuration

Supported Clients

knot works with any MCP-compatible AI client:

• ✅ Claude Desktop (Anthropic)
• ✅ Gemini CLI (Google)
• ✅ ChatGPT CLI / GPT (OpenAI)
• ✅ Cursor (AI IDE)
• ✅ Any standard MCP client

Configuration Examples

Claude Desktop

Add to claude_desktop_config.json:

{
  "mcpServers": {
    "knot": {
      "command": "/absolute/path/to/knot/target/release/knot-mcp",
      "env": {
        "KNOT_REPO_PATH": "/path/to/indexed/repo",
        "KNOT_QDRANT_URL": "http://localhost:6334",
        "KNOT_NEO4J_URI": "bolt://localhost:7687",
        "KNOT_NEO4J_USER": "neo4j",
        "KNOT_NEO4J_PASSWORD": "your-password"
      }
    }
  }
}

Gemini CLI

{
  "mcpServers": {
    "knot": {
      "command": "/absolute/path/to/knot/target/release/knot-mcp",
      "env": {
        "KNOT_REPO_PATH": "/path/to/indexed/repo",
        "KNOT_QDRANT_URL": "http://localhost:6334",
        "KNOT_NEO4J_URI": "bolt://localhost:7687",
        "KNOT_NEO4J_USER": "neo4j",
        "KNOT_NEO4J_PASSWORD": "your-password"
      }
    }
  }
}

ChatGPT / GPT CLI

Similar JSON configuration in your client's MCP configuration file.

⚙️ Configuration Reference

All options can be set via environment variables (.env) or CLI flags. Environment variables take precedence.

🎨 Custom Tree-sitter Queries

The built-in extraction queries (queries/java.scm, queries/typescript.scm) can be overridden without recompiling:

KNOT_CUSTOM_QUERIES_PATH=/path/to/my/queries ./target/release/knot-indexer

Place java.scm and/or typescript.scm in your custom directory. Missing files fall back to built-in defaults.

🔄 Workflow Example

Step 1: Index a Java project

./target/release/knot-indexer --repo-path /home/user/my-java-app --neo4j-password secret

Step 2: Query via CLI (Instant search)

./target/release/knot search "authentication logic"
./target/release/knot callers "UserService.login"

Step 3: Start MCP server (For AI Agents)

./target/release/knot-mcp

Step 4: Use with Claude Desktop

• Claude will list the three tools in its Tools menu
• Ask: "Search for all authentication logic"
• Ask: "Find who calls the login method"
• Ask: "Explore the structure of UserService.java"

🤖 Auto-Configuring AI Agents

knot includes a universal .prompt file in its root directory that automatically configures modern AI coding agents (Cursor, Cline, opencode, Claude, etc.) to use the knot-mcp tools correctly.

The directive explicitly instructs AI agents to prioritize:

• search_hybrid_context — for semantic code discovery (instead of grep)
• find_callers — for reverse dependency analysis (instead of finding references manually)
• explore_file — for file structure inspection (instead of reading line-by-line)

This ensures that when you ask an AI agent to analyze, refactor, or understand your code, it leverages the full power of the vector and graph databases rather than falling back to context-blind regex searches. The .prompt file is universal and tool-agnostic, working with any LLM client that reads codebase directives.

🤝 Contributing

Contributions are welcome! Please ensure:

• All code passes cargo clippy
• Code is formatted with cargo fmt
• Changes are compatible with Rust 2024 edition

📜 License

This project is licensed under the MIT License. See LICENSE for details.

🚀 Roadmap

Current Release (v0.8.3 — Dry-Run Mode for Deployment Platforms) ✅

• ✅ Dry-Run Mode: MCP server can run in offline mode for quality checks on deployment platforms.
• ✅ Platform-Agnostic: Removed all platform-specific references; compatible with any deployment platform.
• ✅ Enhanced Reliability: Graceful handling of missing database connections for validation scenarios.

Previous Release (v0.8.2 — Quality & Doc Refactor) ✅

• ✅ MCP Quality: Enhanced tool descriptions for better agent discovery and usage safety.
• ✅ Token-Efficient Docs: Modularized agent skill guide into docs/agent-skills/ for on-demand loading.
• ✅ Rust Phase 1: Infrastructure prepared for Rust 2024 integration.

Earlier Release (v0.8.1 — CLI UX & Docker Integration) ✅

• ✅ Silenced CLI Logs: Default log level set to error for knot CLI (cleaner Markdown output).
• ✅ 100% E2E Dual-Testing: All 35 integration tests simultaneously verify both MCP and CLI.
• ✅ Docker CLI Support: Official Docker image now includes the knot binary.
• ✅ Agent Guidance: Enhanced .knot-agent.md with signature-based search warnings.

Phase 6 (v0.8.0 — CLI Interface & Unified Core) ✅

• ✅ CLI Tool: Standalone knot command with search, callers, and explore subcommands.
• ✅ Unified Architecture: Shared core logic (src/cli_tools/) used by both CLI and MCP.
• ✅ LLM Skill File: .knot-agent.md teaches AI agents how to use CLI for autonomous analysis.

Upcoming (v0.8.x+)

Phase 7: Rust Support

• Support .rs files
• Struct, trait, and impl tracking
• Macro invocation analysis

Upcoming (v0.9.x+)

Phase 8: C/C++ Support

• Support .c, .cpp, .h, .hpp files
• Pointer and memory relationship tracking
• Header inclusion graph analysis

Long-Term Vision

• Python support
• Go support
• C# support
• IDE plugins (VS Code, IntelliJ, Vim)
• Web UI for graph visualization
• Language Server Protocol (LSP) integration
• Automated Code Review tool (MCP-based)

💬 Questions?

For issues, feature requests, or discussions, please open a GitHub issue.