Claude Code Auto-Run Configuration

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I’ll help you set up Claude Code and configure it for automatic operation. Let me search for the latest documentation on this.Based on my research, I’ll help you set up Claude Code and configure it for automatic operation. Here’s a comprehensive guide:

Installation and Setup

1. Install Claude Code

For macOS/Linux/WSL:

# Install via npm (recommended)
npm install -g @anthropics/claude

# Or using curl installer
curl -fsSL https://claude.ai/install.sh | bash

For Windows: Use WSL (Windows Subsystem for Linux) first, then follow the Linux installation steps.

2. Authentication

After installation, run:

claude

You’ll be prompted to authenticate. Choose one of:

  • Claude Console (default) - requires active billing at console.anthropic.com
  • Claude App with Pro/Max subscription
  • API Key directly

Configuring Automatic Permissions

Unfortunately, the “Yes, and don’t ask again for similar commands” feature has known bugs where Claude Code continues to ask for permissions even after being granted. Here are the best workarounds:

Method 1: Skip Permissions Flag (Most Effective)

Run Claude Code with the --dangerously-skip-permissions flag to bypass all permission prompts:

claude --dangerously-skip-permissions

To make this permanent, add an alias to your shell configuration:

For bash (~/.bashrc):

alias claude='claude --dangerously-skip-permissions'

For zsh (~/.zshrc):

alias claude='claude --dangerously-skip-permissions'

Method 2: Configure Settings File

Create or edit ~/.claude/settings.json:

{
  "permissions": {
    "allow": [
      "Bash(*)",
      "FileEdit(*)",
      "FileView(*)",
      "Git(*)"
    ]
  },
  "dangerouslySkipPermissions": true
}

Method 3: Project-Specific Configuration

For project-specific settings, create .claude/settings.local.json in your project directory:

{
  "permissions": {
    "allow": [
      "Bash(git:*)",
      "Bash(npm:*)",
      "Bash(yarn:*)",
      "FileEdit(*)",
      "FileView(*)"
    ]
  }
}

Additional Auto-Run Configuration

Enable Auto-Updates

Claude Code automatically updates itself by default. To disable if needed:

export DISABLE_AUTOUPDATER=true

Set Default Model

Configure your preferred model in settings:

{
  "env": {
    "ANTHROPIC_MODEL": "claude-opus-4-1-20250805"
  }
}

Create Custom Commands

Create custom commands in .claude/commands/ directory for automated workflows. Example:

.claude/commands/auto-commit.md:

Automatically commit all changes with a descriptive message:
1. Stage all changes
2. Generate commit message based on changes
3. Commit with generated message
4. Push to current branch

Tips for Smoother Operation

  1. Use Plan Mode: Press Shift+Tab twice to activate Plan Mode, which separates research and analysis from execution

  2. Queue Multiple Commands: You can queue up multiple instructions and Claude will execute them sequentially when appropriate

  3. Project Documentation: Run /init to create a CLAUDE.md file that helps Claude understand your project structure

  4. Hooks for Automation: Use /hooks to set up automatic actions:

    • PreToolUse: Before Claude executes any tool
    • PostToolUse: After successful tool completion

Important Notes

  • The permission system is designed with security as the top priority, which can make it overly aggressive. Complex commands with pipes or certain arguments may trigger permission requests even when broadly allowed

  • The --dangerously-skip-permissions flag is generally safe for personal projects but use caution in production environments

  • Permissions use pattern matching in settings files, but wildcard syntax can be tricky and may require exact command matching

The automatic permission issues are acknowledged bugs that the Anthropic team is aware of. Until fixed, the --dangerously-skip-permissions flag remains the most reliable solution for uninterrupted workflow.