The folders Claude Code reads, explained
Everything Loadout does starts with a folder on your disk. These explain what is in them, what is safe to delete and how to do it by hand, with no app involved.
- Where Claude Code skills are storedPersonal skills live in ~/.claude/skills, project skills in .claude/skills, plugin skills inside the plugin. All four levels, the Windows path, which wins.
- Where Codex CLI skills are storedFind Codex CLI skills in .agents/skills at user and repository scope, check older .codex/skills setups, and disable a skill without deleting its files.
- How to find the Claude Code skills you never useUse /skill-doctor to find Claude Code skills with no recorded usage, check missing history, and turn skills off before deciding what to delete.
- Claude Code skill usage counts: where they liveFind Claude Code skill usage with /skill-doctor, or inspect the skillUsage counters in ~/.claude.json. What recorded counts can and cannot tell you.
- What /checkup cleans up, and what it leaves behindThe /checkup command is an alias of /doctor. Review its setup findings, understand proposed skill and permission changes, and use /skill-doctor for usage.
- How to disable an MCP server in Claude CodeDisable an MCP server in Claude Code without deleting its configuration. Use the /mcp toggle, or choose which servers a single session loads.
- How to remove an MCP server from Claude Codeclaude mcp remove deletes the entry, but only in the scope and directory you run it from. What the command leaves behind, and how to check the server is gone.
- How to uninstall a Claude Code pluginThe /plugin uninstall command, the four places a plugin lives, why the files stay on disk, and the scope mistake that makes an uninstalled plugin come back.
- What is inside the ~/.claude folderWhat is taking the space in ~/.claude, what Claude Code already deletes for you after 30 days, what it never touches, and how to purge one project safely.