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Claude Code Settings

Claude Code stores its config at ~/.claude/, but that directory also accumulates runtime data (history, cache, session state, etc.). We version-control only the portable configuration by selectively symlinking from the dotfiles repo:

~/dotfiles/.claude/              ← source of truth (git-tracked)
  ├── settings.json               ← preferences: model, plugins
  ├── settings.local.json         ← permissions: allow/deny lists, hooks
  ├── agents/                     ← custom agent definitions
  ├── commands/                   ← slash commands (/commit, /memory-*, etc.)
  └── skills/                     ← custom skills (audit, supply-chain-audit, etc.)

~/.claude/                        ← runtime directory
  ├── settings.json           → symlink to dotfiles
  ├── settings.local.json     → symlink to dotfiles
  ├── agents/                 → symlink to dotfiles
  ├── commands/               → symlink to dotfiles
  ├── skills/                 → symlink to dotfiles
  └── history.jsonl, cache/, projects/, ...  (local, not tracked)

setup.sh handles this via link_into_dir, which symlinks individual items without clobbering the runtime data that Claude Code writes alongside them.

Per-project overrides

Claude Code merges settings from multiple levels. Each project can have its own .claude/settings.local.json for context-specific permissions:

  • .config/.claude/settings.local.json — allows git add, ln, etc. for dotfile management
  • .config/nvim/.claude/settings.local.json — allows nvim-related operations

Permission philosophy

The global settings.local.json allowlists three categories:

  1. File tools (Edit, Read, Write, Glob, Grep) — always allowed
  2. Safe bash (git read ops, ls, find, mkdir, build tools like cargo/dune/uv/npm) — always allowed
  3. Git write ops (git add, git commit, git merge, etc.) — allowed, but git add -A is blocked by both deny rule and a PreToolUse hook

Still prompts (by design): git push, rm, curl/wget, brew install, sudo, and anything else not explicitly allowlisted.

Workflow for adding new permissions

When Claude prompts you for a command you want to always allow:

  1. Select "Always allow" in the prompt, OR
  2. Add the pattern to ~/dotfiles/.claude/settings.local.json and commit

Use Bash(command_prefix:*) syntax for allow rules (:* matches any suffix). Use Bash(*pattern*) glob syntax for deny rules.