User Guide

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

The flow is simple. The portal scans a repo to build the evidence database and refresh the CodeGraph index. Your editor connects to the project's MCP endpoint on the portal, which reads that database. As you work, the endpoint'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, branch membership, and the keep-fresh git hooks.

  Scanning

• Wiring your editor

  ---

  The agents the portal connects: Claude Code, Cursor, VS Code, and Codex.

  Editors

• Using WhyGraph (MCP)

  ---

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

  MCP usage

• The Explorer

  ---

  The portal's web view of the graph, evidence, and rationale.

  Explorer

• The Chat assistant

  ---

  Ask questions in English; it calls WhyGraph's tools and charts the answers.

  Chat