Configuration Files and Settings

Claude Code uses multiple configuration files to manage settings, permissions, hooks, and integrations. Understanding these files helps you customize and optimize your Claude Code setup.

Configuration Hierarchy

Claude Code reads configuration from multiple locations with a specific precedence:

~/.claude/settings.json           (User-level settings)
.claude/settings.json             (Project-level settings)
.claude/settings.local.json       (Local developer overrides)

Settings cascade and merge, with later files overriding earlier ones.

Directory Structure

User Directory

Global configuration directory:

~/.claude/
├── settings.json              # User-level settings
├── .claude.json               # Authentication config
├── agents/                    # Global agents
│   ├── customer-support.md
│   └── security-auditor.md
├── commands/                  # Global commands
│   ├── check-file.md
│   └── generate-tests.md
├── conversations/             # Conversation history
│   ├── conv-123.json
│   └── conv-456.json
└── statsig/                   # Usage statistics

Project Directory

Project-specific configuration:

.claude/
├── CLAUDE.md                  # Project context and guidelines
├── settings.json              # Project settings
├── settings.local.json        # Local overrides (gitignored)
├── agents/                    # Project agents
│   ├── frontend-developer.md
│   └── backend-developer.md
├── commands/                  # Project commands
│   ├── setup-testing.md
│   └── deploy-staging.md
└── scripts/                   # Helper scripts
    ├── context-monitor.py
    └── token-counter.py

.mcp.json                      # MCP server configurations

settings.json

User Settings

Location: ~/.claude/settings.json User-level settings apply globally across all projects. Example:

{
  "model": "claude-sonnet-4-20250514",
  "telemetryEnabled": false,
  "cleanupPeriodDays": 30,
  "permissions": {
    "allow": [
      {
        "type": "exec",
        "pattern": "npm"
      },
      {
        "type": "exec",
        "pattern": "git"
      }
    ],
    "deny": [
      {
        "type": "read",
        "pattern": "**/.env*"
      },
      {
        "type": "read",
        "pattern": "**/secrets/**"
      }
    ]
  },
  "hooks": {
    "PreToolUse": [
      {
        "command": "echo 'Pre-tool use hook'",
        "description": "Log before tool usage"
      }
    ],
    "PostToolUse": [
      {
        "command": "echo 'Post-tool use hook'",
        "description": "Log after tool usage"
      }
    ]
  },
  "env": {
    "NODE_ENV": "development"
  }
}

Project Settings

Location: .claude/settings.json Project-specific settings for team sharing (committed to git). Example:

{
  "model": "claude-sonnet-4-20250514",
  "permissions": {
    "allow": [
      {
        "type": "exec",
        "pattern": "npm run *"
      },
      {
        "type": "exec",
        "pattern": "yarn *"
      }
    ],
    "additionalDirectories": [
      "~/projects/shared-library"
    ]
  },
  "hooks": {
    "PreToolUse": [
      {
        "command": "npm run lint",
        "description": "Run linter before file modifications"
      }
    ]
  },
  "enableAllProjectMcpServers": true,
  "enabledMcpjsonServers": [
    "github",
    "web-fetch"
  ]
}

Local Settings

Location: .claude/settings.local.json Developer-specific overrides (gitignored, never committed). Example:

{
  "model": "claude-haiku-4-20250514",
  "telemetryEnabled": false,
  "permissions": {
    "additionalDirectories": [
      "~/my-personal-scripts"
    ]
  },
  "env": {
    "DEBUG": "true"
  }
}

settings.json Fields

Model Selection

string

Claude model to use for conversations

Options:

claude-sonnet-4-20250514 - Balanced performance
claude-opus-4-20250514 - Maximum capability
claude-haiku-4-20250514 - Fast responses

Example:

{
  "model": "claude-sonnet-4-20250514"
}

Permissions

object

Control what Claude Code can access and execute

Structure:

{
  "permissions": {
    "allow": [
      {
        "type": "exec|read|write",
        "pattern": "glob-pattern"
      }
    ],
    "deny": [
      {
        "type": "exec|read|write",
        "pattern": "glob-pattern"
      }
    ],
    "additionalDirectories": [
      "/path/to/directory"
    ]
  }
}

Permission Types:

exec - Command execution
read - File reading
write - File writing

Pattern Examples:

{
  "permissions": {
    "allow": [
      { "type": "exec", "pattern": "npm" },
      { "type": "exec", "pattern": "git *" },
      { "type": "read", "pattern": "**/*.js" },
      { "type": "write", "pattern": "src/**" }
    ],
    "deny": [
      { "type": "read", "pattern": "**/.env*" },
      { "type": "read", "pattern": "**/secrets/**" },
      { "type": "exec", "pattern": "rm -rf" }
    ]
  }
}

Hooks

object

Automation hooks triggered at specific lifecycle events

Hook Types:

PreToolUse - Before tool execution
PostToolUse - After tool execution
Stop - On session stop
Notification - For notifications

Example:

{
  "hooks": {
    "PreToolUse": [
      {
        "command": "npm run lint",
        "description": "Lint before changes"
      },
      {
        "command": "npm test",
        "description": "Run tests"
      }
    ],
    "PostToolUse": [
      {
        "command": "git add .",
        "description": "Stage changes"
      }
    ],
    "Stop": [
      {
        "command": "echo 'Session ended'",
        "description": "Log session end"
      }
    ]
  }
}

Environment Variables

object

Environment variables available to Claude Code

Example:

{
  "env": {
    "NODE_ENV": "development",
    "DEBUG": "true",
    "API_URL": "http://localhost:3000"
  }
}

Warning: Never put sensitive keys in project settings (use .claude/settings.local.json instead).

Telemetry

boolean

Enable or disable usage telemetry

Default: true Example:

{
  "telemetryEnabled": false
}

Cleanup Period

number

Number of days to retain conversation history

Default: 30 Options:

7 - One week
30 - One month (default)
90 - Three months
365 - One year
-1 - Never delete

Example:

{
  "cleanupPeriodDays": 7
}

MCP Configuration

boolean

Auto-approve all MCP servers from .mcp.json

Default: false Example:

{
  "enableAllProjectMcpServers": true,
  "enabledMcpjsonServers": [
    "github",
    "web-fetch",
    "filesystem"
  ],
  "disabledMcpjsonServers": [
    "memory"
  ]
}

Statusline

object

Configure statusline display

Example:

{
  "statusline": {
    "command": "python3",
    "args": [".claude/scripts/context-monitor.py"],
    "refreshInterval": 5000
  }
}

.mcp.json

MCP (Model Context Protocol) server configurations. Location: Project root (.mcp.json) Structure:

{
  "mcpServers": {
    "server-name": {
      "command": "executable",
      "args": ["arg1", "arg2"],
      "env": {
        "VAR_NAME": "value"
      }
    }
  }
}

Complete Example

{
  "mcpServers": {
    "fetch": {
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-fetch"]
    },
    "filesystem": {
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-filesystem", "."],
      "env": {
        "ALLOWED_DIRECTORIES": "."
      }
    },
    "github": {
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-github"],
      "env": {
        "GITHUB_TOKEN": "${GITHUB_TOKEN}"
      }
    },
    "memory": {
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-memory"]
    }
  }
}

Server Configuration Fields

string

required

Executable command to start the server

array

Command-line arguments (optional)

object

Environment variables for the server (optional)

.claude.json

Authentication configuration. Location: ~/.claude.json Structure:

{
  "oauthAccount": {
    "accountUuid": "uuid-here",
    "emailAddress": "user@example.com",
    "refreshToken": "encrypted-token"
  },
  "apiKey": "sk-ant-xxx"
}

Warning: Contains sensitive authentication data. Never commit to git.

CLAUDE.md

Project context and guidelines. Location: .claude/CLAUDE.md Purpose:

Project overview
Coding standards
Architecture notes
Development guidelines
Important context for Claude

Example:

# Project Name

Brief project description.

## Architecture

Key architectural decisions and patterns.

## Code Standards

- Follow ESLint rules
- Write tests for new features
- Update documentation

## Important Files

- `src/index.js` - Main entry point
- `config/` - Configuration files

## Commands

- `npm test` - Run tests
- `npm run build` - Build for production

Gitignore Recommendations

Add to .gitignore:

# Claude Code local settings
.claude/settings.local.json

# Claude authentication (never commit!)
.claude.json

# Conversation history (optional, team preference)
.claude/conversations/

# Scripts cache
.claude/scripts/*.pyc

Commit to git:

.claude/CLAUDE.md
.claude/settings.json
.claude/agents/
.claude/commands/
.mcp.json

Configuration Presets

Install pre-configured settings:

Security-Focused

cct --setting security/read-only-mode
cct --setting permissions/deny-sensitive-files
cct --setting security/strict-permissions

Performance-Optimized

cct --setting model/use-haiku
cct --setting retention/retention-7-days
cct --setting telemetry/disable-telemetry

Development-Friendly

cct --setting permissions/allow-npm-commands
cct --setting model/use-sonnet
cct --setting retention/retention-30-days

Best Practices

1. Separate Concerns

User settings: Personal preferences, global permissions
Project settings: Team standards, project permissions
Local settings: Developer-specific overrides, API keys

2. Security

Never commit API keys or secrets
Use environment variables for sensitive data
Add .claude/settings.local.json to .gitignore
Review permissions regularly

3. Team Collaboration

Commit .claude/settings.json for team consistency
Document required settings in README
Use environment variables for deployment-specific config
Share MCP configurations in .mcp.json

4. Performance

Set appropriate cleanupPeriodDays for conversation retention
Use Haiku model for simple tasks
Limit additionalDirectories to necessary paths
Monitor conversation history size

5. Documentation

Keep CLAUDE.md up to date with project changes
Document custom agents and commands
Explain hook purposes
Note required environment variables

Troubleshooting

Settings Not Applied

Check file locations:

ls -la ~/.claude/settings.json
ls -la .claude/settings.json
ls -la .claude/settings.local.json

Verify JSON syntax:

jsonlint ~/.claude/settings.json
jsonlint .claude/settings.json

Check permissions:

chmod 644 .claude/settings.json

Hooks Not Running

Verify hook configuration:

cat .claude/settings.json | jq '.hooks'

Test command manually:

npm run lint  # Test if command works

Check command availability:

which npm
which git

MCP Servers Not Working

Verify .mcp.json:

cat .mcp.json | jq '.mcpServers'

Test server manually:

npx -y @modelcontextprotocol/server-fetch

Check server permissions:

# In .claude/settings.json
{
  "enabledMcpjsonServers": ["server-name"]
}

Next Steps

CLI Flags Reference - All CLI flags
Environment Variables - Environment configuration
Install Components - Component installation
Health Check - Verify configuration

​Configuration Files and Settings

​Configuration Hierarchy

​Directory Structure

​User Directory

​Project Directory

​settings.json

​User Settings

​Project Settings

​Local Settings

​settings.json Fields

​Model Selection

​Permissions

​Hooks

​Environment Variables

​Telemetry

​Cleanup Period

​MCP Configuration

​Statusline

​.mcp.json

​Complete Example

​Server Configuration Fields

​.claude.json

​CLAUDE.md

​Gitignore Recommendations

​Configuration Presets

​Security-Focused

​Performance-Optimized

​Development-Friendly

​Best Practices

​1. Separate Concerns

​2. Security

​3. Team Collaboration

​4. Performance

​5. Documentation

​Troubleshooting

​Settings Not Applied

​Hooks Not Running

​MCP Servers Not Working

​Next Steps

Configuration Files and Settings

Configuration Hierarchy

Directory Structure

User Directory

Project Directory

settings.json

User Settings

Project Settings

Local Settings

settings.json Fields

Model Selection

Permissions

Hooks

Environment Variables

Telemetry

Cleanup Period

MCP Configuration

Statusline

.mcp.json

Complete Example

Server Configuration Fields

.claude.json

CLAUDE.md

Gitignore Recommendations

Configuration Presets

Security-Focused

Performance-Optimized

Development-Friendly

Best Practices

1. Separate Concerns

2. Security

3. Team Collaboration

4. Performance

5. Documentation

Troubleshooting

Settings Not Applied

Hooks Not Running

MCP Servers Not Working

Next Steps