A complete guide to CLAUDE.md, custom commands, skills, agents, and permissions, and how to set them up properly.

Most Claude Code users treat the .claude folder like a black box. They know it exists. They've seen it appear in their project root. But they've never opened it, let alone understood what every file inside it does.
That's a missed opportunity.
The .claude folder is the control center for how Claude behaves in your project. It holds your instructions, your custom commands, your permission rules, and even Claude's memory across sessions. Once you understand what lives where and why, you can configure Claude Code to behave exactly the way your team needs it to.
This guide walks through the entire anatomy of the folder, from the files you'll use daily to the ones you'll set once and forget.

Two folders, not one

Before diving in, one thing worth knowing upfront: there are actually two .claude directories, not one.