Permissions And Safety

Permissions and Safety

Claude Code can read files, write files, run commands and browse the web. Understanding how it decides what to do — and how you control that — keeps you in charge of your own codebase.

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The Three Permission Tiers

Claude Code uses three modes for tool execution:

1. Auto-approve (runs without asking)

Actions in your “allowed” list in CLAUDE.md or in global settings. Typically: reading files, running tests, running the dev server.

2. Prompt-for-approval (asks before running)

Anything not on the auto-approve list. Claude Code shows you the command and waits for you to press Enter or deny it.

3. Never (blocked entirely)

Some actions can be blocked outright via settings: pushing to certain branches, deleting certain files, calling external APIs, etc.

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What Claude Code Can Do By Default

Out of the box, without any configuration:

Action	Default behavior
Read any file in the working directory	Auto (always)
Write/edit files in the working directory	Prompts first time, remembers choice
Run npm, node, python commands	Prompts for approval
Run git read commands (status, diff, log)	Auto
Run git commit, git push	Prompts for approval
Delete files	Prompts for approval
Make HTTP requests	Prompts for approval
Install packages	Prompts for approval

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Understanding the Prompt Dialog

When Claude Code needs approval to run a command, it shows:

Claude wants to run:
  npm install axios

Allow? [y/n/always/never]

Your options:

• y — allow this one time
• n — deny this one time
• always — add to auto-approve list for this session
• never — block this command for this session

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Global Safety Settings

You can set global permissions in ~/.claude/settings.json (created automatically):

{
  "permissions": {
    "allow": [
      "Bash(npm run dev)",
      "Bash(npm run build)",
      "Bash(npm test)",
      "Bash(git status)",
      "Bash(git diff*)",
      "Bash(git log*)"
    ],
    "deny": [
      "Bash(git push --force*)",
      "Bash(rm -rf*)"
    ]
  }
}

The allow and deny arrays use glob patterns. The asterisk matches anything.

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Project-Level Settings

For project-specific rules, use .claude/settings.json in your project root:

{
  "permissions": {
    "allow": [
      "Bash(npm run dev)",
      "Bash(npx drizzle-kit generate)"
    ],
    "deny": [
      "Bash(npx drizzle-kit push)"
    ]
  }
}

Project settings override global settings for commands that match both.

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The Hooks System

Hooks let you run shell commands automatically before or after Claude Code actions. This is covered in depth in Module 04, but here’s the concept:

{
  "hooks": {
    "PostToolUse": [
      {
        "matcher": "Write",
        "hooks": [
          { "type": "command", "command": "npm run lint -- --fix" }
        ]
      }
    ]
  }
}

This example automatically runs ESLint after every file write. Hooks are powerful for enforcing code quality without thinking about it.

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What Claude Code Cannot Do

Some things are architecturally impossible regardless of permissions:

• It cannot access files outside your working directory (without explicit --dangerously-skip-permissions flag, which you should never use)
• It cannot read your environment variables unless you explicitly pass them
• It cannot send arbitrary network requests from within the secure sandbox
• It cannot run as root or escalate privileges

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A Word on Trust

Claude Code is a tool that executes code on your machine. The same caution you’d apply to any automated script applies here:

• Don’t run claude as root or with sudo
• Keep your ANTHROPIC_API_KEY secret — it’s your billing credential
• Review unfamiliar commands before approving them
• Use the deny list for destructive operations on important projects

Claude Code will tell you what it’s doing before it does it. That transparency is your main safety mechanism — use it.

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Recovering from Mistakes

Claude Code makes mistakes sometimes. Here’s how to recover:

Claude edited a file incorrectly:

git diff   # see what changed
git checkout -- filename.js   # restore one file
git checkout -- .   # restore all changed files

Claude deleted a file:

git checkout -- deleted-file.js   # only works if the file was tracked by git

Claude installed a package you didn’t want:

npm uninstall package-name

Claude made multiple changes you want to undo:

git stash   # stash all uncommitted changes

This is another reason to use git from day one in every project: it’s your undo button for everything Claude Code does.

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Next module: Building Web Apps