User Guide

You've scanned a repo and wired an editor. This guide explains how the pieces fit together - and how to get the most out of each.

The flow is simple. You scan a repo to build the evidence database and refresh the CodeGraph index. Your editor launches the MCP server, which reads that database. As you work, the server's tools, resources, and prompts answer "why does this code exist?" from history.

Start with the concepts, then dig into whichever piece you need.

• Concepts

  ---

  Evidence vs rationale, and how WhyGraph splits work with CodeGraph.

  Concepts

• Scanning your repo

  ---

  The scan phases, every flag, and the keep-fresh git hooks.

  Scanning

• Wiring your editor

  ---

  Per-agent setup for Claude Code, Cursor, VS Code, and Codex.

  Editors

• Using WhyGraph (MCP)

  ---

  How an agent calls the tools, resources, and prompts mid-task.

  MCP usage