When CLAUDE.md rules are ignored, hooks never fire, or an MCP server shows no tools, the file usually didn't load, loaded from an unexpected location, or got overridden. This guide covers what the diagnostic entries (/context, /memory, /skills, /doctor, /mcp, and more) actually show, safe-mode bisection, and a table of six high-frequency error messages with fixes.
Claude Code reads settings from five levels — managed settings, CLI flags, project local, shared project, and user — where plain values are overridden by higher levels while list keys like permissions.allow merge across scopes. This guide covers each file's role, the allow/deny/ask rule syntax, and how to verify your settings with /status and claude doctor.
Global skills live in ~/.claude/skills/, but they go missing in new sessions or the Desktop App? The problem usually isn't a missing file — it's that the skill descriptions aren't being loaded into context. This post clarifies the CLI vs Desktop App differences, the role of settings.json, and the most reliable fix.