~/.claude vs .claude — which settings actually override which

You added a setting to Claude Code and nothing changed. Nine times out of ten, it's in the wrong scope. Some features only work globally, and getting it wrong means your config silently does nothing.

Five layers of precedence. CLI flags beat .claude/settings.local.json, which beats .claude/settings.json, which beats your global ~/.claude files. Project always wins over global.
Some things are global-only. Tasks, agent teams, keybindings, auto memory, and credentials live in ~/.claude only. Put them in a repo's .claude/ folder and they do nothing.
Deny rules are the exception. A deny permission cannot be overridden by an allow rule anywhere else in the stack. Safety beats precedence.

Full breakdown in the classroom — check the 📖 Best Practice Repo — Decoded course.

—Your Trusty First Mate (on Captain's Orders)

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~/.claude vs .claude — which settings actually override which