Permissions Audit

Review and reorganize Claude Code permission settings so global settings are the source of truth, project-local files stay minimal, and read vs write operations have clear separation.

When to Use

• Reviewing what tools and commands are pre-allowed
• Cleaning up accumulated ad-hoc permission entries
• After adding a new MCP server and deciding which operations to pre-allow
• Ensuring global vs project-local settings are properly split
• Periodic hygiene check on permission sprawl

Phase 1: Discover All Settings Files

Scan for every settings file that contributes to the effective permission set.

Locations to check:

• ~/.claude/settings.json — global settings (source of truth)
• <project>/.claude/settings.json — project shared settings (committed)
• <project>/.claude/settings.local.json — project local settings (gitignored)
• ~/.claude/.claude/settings.local.json — home directory project local
• Any dotfiles-managed copy (e.g. home/.claude/settings.json in a dotfiles repo)

Read all of them in parallel. If a file doesn't exist, note it and move on.

Phase 2: Audit

For each permission entry across all files, assess:

1. Redundancy — Is this entry already covered by a broader rule elsewhere?
   • Example: Bash(gws calendar events:*) is redundant when Bash(gws:*) exists globally
2. Misplacement — Is this general-purpose but stuck in a project-local file?
   • Example: Bash(python3:*) in project local when it's useful everywhere
3. Inconsistent granularity — Are similar tools allowed at different specificity levels?
   • Example: Global has gh pr list, gh pr view individually, but project local has gh:*
4. Missing read/write distinction — Are read-only and write operations mixed together?
5. Stale entries — One-time approvals that accumulated (e.g., a specific git command with hardcoded paths)

Present findings as a table with issues and proposed resolution for each.

Phase 3: Propose Reorganization

Design the new layout following these principles:

Global settings (source of truth)

Organize permissions into labeled sections by grouping related entries together. Do NOT use JSON comments (// or /* */) — settings.json must be valid JSON. Instead, rely on the ordering of entries to convey grouping. Within the allow array, cluster related permissions together in this order:

Section order (group entries in this sequence, no separators needed):

filesystem reads            — cat, tree, grep, wc, file reads
<lang> inspection           — go doc, cargo check, linters (no side effects)
GitHub CLI reads            — gh pr list/view/diff, gh issue list (no mutations)
external tool reads         — calendar, slack CLI, other read CLIs
web reads                   — WebSearch, WebFetch with domain allowlist
MCP <service> reads         — list, get, describe, search operations
build / test / install      — go build, cargo test, pnpm install (local side effects)
skills                      — Skill(superpowers:*), etc.

Project-local settings (minimal overrides)

Only keep entries that are genuinely project-specific:

• Broader tool access needed for a specific workflow (e.g., Bash(gh:*) for a repo that creates PRs frequently)
• Project-specific MCP tools not used elsewhere
• Temporary elevated access during active development

Clarifying questions

Before applying, ask the user about edge cases. Common questions:

• Scope of CLI tools: Should gh:* (all subcommands) go global, or keep read-only globally with broader access per-project?
• MCP write operations: Which write operations (send message, create issue) should stay prompted vs pre-allowed?
• Environment separation: Should dev and prod data sources have the same read access, or should prod be more restrictive?
• Dotfiles sync: Does the user maintain a dotfiles copy that needs updating?

Adapt questions to what's actually ambiguous — don't ask about things that are obvious from context.

Phase 4: Apply Changes

Once the user confirms the plan:

1. Write the updated global settings file
2. Write the trimmed project-local settings file
3. Update any dotfiles copies to stay in sync
4. Clear out entries from other local files that were absorbed into global

Phase 5: Summary

Present a before/after comparison:

File	Before	After
Global	N flat entries	M entries in K sections
Project local	X entries	Y entries (project-specific only)

List what moved where, and what still requires prompting (write operations not pre-allowed).