10. Reference

📌 Section 10 TL;DR (1 minute)

What’s inside: Complete command reference, troubleshooting guides, and daily checklists.

I need to…	Go to
Look up a command	10.1 Commands Table
Find keyboard shortcut	10.2 Keyboard Shortcuts
Configure settings	10.3 Configuration Reference
Fix an error	10.4 Troubleshooting
Quick daily reference	10.5 Cheatsheet
Set up workflow	10.6 Daily Workflow
Copy ready-to-use templates	examples/ directory — Commands, hooks, agents

Most Common Lookups:

Context full? → 10.4.1 Context Issues
MCP not working? → 10.4.4 MCP Troubleshooting
Need clean reinstall? → 10.4.3 Full Reinstall

Usage tip: Bookmark this section — you’ll reference it often.

Purpose: Quick lookup for all Claude Code information

10.1 Commands Table

Built-in Commands

Command	Action	Category
`/help`	Show all available commands	Navigation
`/clear`	Clear conversation history	Session
`/compact`	Summarize and compress context	Context
`/status`	Show session info (context, cost)	Info
`/usage`	Check rate limits and token allocation	Info
`/stats`	View usage statistics with activity graphs	Info
`/output-style`	Deprecated (Oct 2025) — use `/config` → “Preferred output style” instead (Default / Explanatory / Learning)	Display
`/feedback`	Report bugs or send feedback to Anthropic	Support
`/chrome`	Check Chrome connection, manage permissions	Mode
`/config`	View and modify global settings	Config
`/copy`	Copy last response to clipboard — interactive picker to select specific code blocks, or “Always copy full response” option (v2.1.59+)	Session
`/debug`	Systematic troubleshooting and error investigation	Debug
`/doctor`	Run diagnostics and troubleshooting checks	Debug
`/execute`	Exit Plan Mode	Mode
`/exit`	Exit Claude Code	Session
`/fast`	Toggle fast mode (Opus 4.6, 2.5x faster, 6x price)	Mode
`/hooks`	Interactive hook configuration	Config
`/init`	Generate starter CLAUDE.md based on project structure — ⚠️ output is LLM-generated; review and prune before committing (ETH Zürich research shows auto-generated context files reduce agent task success by ~3% and add 20%+ inference cost)	Config
`/login`	Log in to Claude account	Auth
`/logout`	Log out and re-authenticate	Auth
`/loop [interval] [prompt]`	Run a prompt or slash command on a recurring interval (e.g. `/loop 5m check the deploy`) — v2.1.71+	Automation
`/mcp`	Manage Model Context Protocol servers	Config
`/memory`	View and edit auto-memory (context Claude automatically saved across sessions via MEMORY.md) — v2.1.59+	Config
`/mobile`	Show App Store and Google Play download links	Info
`/model`	Change model (with left/right arrows for effort slider)	Mode
`/permissions`	Configure permission allowlists	Config
`/plan`	Enter Plan Mode	Mode
`/plugin`	Browse and install Claude Code plugins	Config
`/remote-control` (`/rc`)	Start remote control session (Pro/Max only)	Mode
`/rename`	Give current session a descriptive name	Session
`/resume`	Resume a previous session (from within a session)	Session
`/rewind`	Open rewind menu to undo recent changes	Edit
`/sandbox`	Enable OS-level isolation	Config
`Ctrl+D`	Exit Claude Code	Session

Quick Actions

Action	Shortcut
Run shell command	`!command`
Reference file	`@filename`
Cancel operation	`Ctrl+C`
Search history	`Ctrl+R`
Dismiss suggestion	`Esc`

10.2 Keyboard Shortcuts

Session Control

Shortcut	Action
`Enter`	Send message
`Shift+Enter`	New line in message
`Ctrl+C`	Cancel current operation
`Ctrl+D`	Exit Claude Code
`Ctrl+R`	Search command history
`Ctrl+L`	Clear screen (keeps context)
`Ctrl+B`	Run command in background
`Esc`	Stop Claude mid-action (context preserved)
`Esc×2` (double-tap)	Open rewind menu (same as `/rewind`)

Shortcut	Action
`Ctrl+A`	Jump to beginning of line
`Ctrl+E`	Jump to end of line
`Ctrl+W`	Delete previous word
`Ctrl+G`	Open plan in external text editor for editing
`Tab`	Autocomplete file paths
`↑` / `↓`	Navigate command history

Mode & Model Toggles

Shortcut	Action
`Alt+T` (`Option+T` on macOS)	Toggle thinking mode on/off
`Ctrl+O`	View thinking blocks

Voice Input

Shortcut	Action
`Space` (hold)	Push-to-talk — hold to speak, release to send (default binding)

Rebinding: The voice:pushToTalk binding is configurable in ~/.claude/keybindings.json (v2.1.71+). Add a custom binding if Space conflicts with your workflow:

{
  "voice:pushToTalk": "ctrl+space"
}

Toggle voice on/off with /voice. The push-to-talk binding only activates when voice mode is active.

Shortcut	Action
`Shift+Down`	Cycle through active teammates (in-process mode)
`Ctrl+T`	Toggle task list visibility
`Enter`	View selected teammate’s session
`Escape`	Interrupt current turn, return to prompt

Useful Flag Combinations

Flags	Purpose	Example
`-c -p "msg"`	Resume session + single prompt	`claude -c -p "run tests"`
`-r <id> -p`	Resume specific session + prompt	`claude -r abc123 -p "check status"`
`-p -p`	Non-interactive automation	`claude -p -p "lint fix" < errors.txt`

Note: Combine resume flags with -p for scripting and CI/CD workflows.

10.3 Configuration Reference

CLAUDE.md Locations

Location	Scope	Committed
`~/.claude/CLAUDE.md`	All projects (global)	N/A
`/project/CLAUDE.md`	This project (shared)	✅ Yes
`/project/CLAUDE.local.md`	This project (local overrides)	❌ No (.gitignored)
`/project/.claude/CLAUDE.md`	Personal project config	❌ No
Parent/child directories	Auto-loaded in monorepos	Depends on location

Settings Files

File	Purpose	Committed
`settings.json`	Hook configuration	✅ Yes
`settings.local.json`	Permission overrides	❌ No

Permission Patterns

Pattern	Matches
`Bash(git *)`	Any git command
`Bash(npm test)`	Exactly npm test
`Edit`	All file edits
`Write`	All file writes
`WebSearch`	Web search
`mcp__serena__*`	All Serena tools
`Read(file_path:.env)`	Block reading any `.env*` file path
`Edit(file_path:*.pem)`	Block editing `.pem` certificates
`Bash(command:rm -rf)`	Block destructive bash commands

CLI Flags Reference

Complete reference for all Claude Code command-line flags, subcommands, and startup environment variables.

Session & Context

Flag	Short	Description
`--continue`	`-c`	Continue the most recent conversation in the current directory
`--resume <ID>`	`-r`	Resume a specific session by UUID or name, or show interactive picker
`--from-pr <NUMBER\|URL>`		Resume sessions linked to a specific GitHub PR
`--fork-session`		Create a new session ID when resuming (use with `--resume` or `--continue`)
`--session-id <UUID>`		Use a specific session UUID
`--no-session-persistence`		Disable session persistence (print mode only)
`--remote`		Create a new web session on claude.ai
`--teleport`		Resume a web session in your local terminal

Model & Configuration

Flag	Short	Description
`--model <NAME>`		Set model with alias (`sonnet`, `opus`, `haiku`) or full model ID
`--fallback-model <NAME>`		Auto-fallback model when default is overloaded (print mode only)
`--betas <LIST>`		Beta headers to include in API requests (API key users only)

Output & Format

Flag	Short	Description
`--print`	`-p`	Print response and exit without interactive mode (headless/SDK mode)
`--output-format <FORMAT>`		Output format: `text`, `json`, `stream-json`
`--input-format <FORMAT>`		Input format: `text`, `stream-json`
`--json-schema <SCHEMA>`		Get validated JSON matching schema (print mode only)
`--include-partial-messages`		Include partial streaming events (requires `--print` and `stream-json`)
`--verbose`		Enable verbose logging with full turn-by-turn output

Permissions & Security

Flag	Short	Description
`--dangerously-skip-permissions`		Skip ALL permission prompts — use with extreme caution
`--allow-dangerously-skip-permissions`		Enable permission bypassing as an option without activating it
`--permission-mode <MODE>`		Begin in specified mode: `default`, `plan`, `acceptEdits`, `bypassPermissions`
`--allowedTools <TOOLS>`		Tools that execute without prompting (permission rule syntax)
`--disallowedTools <TOOLS>`		Tools removed from model context entirely
`--tools <TOOLS>`		Restrict which built-in tools Claude can use (use `""` to disable all)
`--permission-prompt-tool <TOOL>`		MCP tool to handle permission prompts in non-interactive mode

System Prompt

Flag	Short	Description
`--system-prompt <TEXT>`		Replace entire system prompt with custom text
`--system-prompt-file <PATH>`		Load system prompt from file, replacing default (print mode only)
`--append-system-prompt <TEXT>`		Append custom text to default system prompt
`--append-system-prompt-file <PATH>`		Append file contents to default prompt (print mode only)

Agent & Subagent

Flag	Short	Description
`--agent <NAME>`		Specify an agent for the current session
`--agents <JSON>`		Define custom subagents dynamically via JSON
`--teammate-mode <MODE>`		Set agent team display: `auto`, `in-process`, `tmux`

MCP & Plugins

Flag	Short	Description
`--mcp-config <PATH\|JSON>`		Load MCP servers from JSON file or inline JSON string
`--strict-mcp-config`		Only use MCP servers from `--mcp-config`, ignore all others
`--plugin-dir <PATH>`		Load plugins from directory for this session only (repeatable)

Directory & Workspace

Flag	Short	Description
`--add-dir <PATH>`		Add additional working directories for Claude to access
`--worktree`	`-w`	Start Claude in an isolated git worktree (branched from HEAD)

Budget & Limits

Flag	Short	Description
`--max-budget-usd <AMOUNT>`		Maximum dollar amount for API calls before stopping (print mode only)
`--max-turns <NUMBER>`		Limit number of agentic turns (print mode only)

Integration

Flag	Short	Description
`--chrome`		Enable Chrome browser integration for web automation
`--no-chrome`		Disable Chrome browser integration for this session
`--ide`		Automatically connect to IDE on startup if exactly one valid IDE is available

Initialization & Maintenance

Flag	Short	Description
`--init`		Run initialization hooks and start interactive mode
`--init-only`		Run initialization hooks and exit without starting a session
`--maintenance`		Run maintenance hooks and exit

Debug & Diagnostics

Flag	Short	Description
`--debug <CATEGORIES>`		Enable debug mode with optional category filtering (e.g., `"api,hooks"`)

Settings Override

Flag	Short	Description
`--settings <PATH\|JSON>`		Path to settings JSON file or inline JSON string to load
`--setting-sources <LIST>`		Comma-separated sources to load: `user`, `project`, `local`
`--disable-slash-commands`		Disable all skills and slash commands for this session

Version & Help

Flag	Short	Description
`--version`	`-v`	Output the current version number
`--help`	`-h`	Show help information

Subcommands

Top-level commands run as claude <subcommand>:

Subcommand	Description
`claude "query"`	Start REPL with an initial prompt
`claude agents`	List configured agents
`claude auth login / logout / status`	Manage Claude Code authentication
`claude doctor`	Run diagnostics from the command line
`claude install`	Install or switch Claude Code native builds
`claude mcp add / remove / list / get / enable`	Configure MCP servers
`claude plugin`	Manage Claude Code plugins
`claude remote-control`	Manage remote control sessions
`claude setup-token`	Create a long-lived token for subscription usage
`claude update` / `claude upgrade`	Update to the latest version

Startup Environment Variables

Set these in your shell before launching Claude Code (these cannot be configured via settings.json):

Variable	Description
`CLAUDE_CODE_EXPERIMENTAL_AGENT_TEAMS=1`	Enable experimental agent teams
`CLAUDE_CODE_TMPDIR`	Override temp directory for internal files
`CLAUDE_CODE_ADDITIONAL_DIRECTORIES_CLAUDE_MD=1`	Enable additional directory CLAUDE.md loading
`DISABLE_AUTOUPDATER=1`	Disable automatic updates
`CLAUDE_CODE_EFFORT_LEVEL`	Control thinking depth for extended thinking models
`USE_BUILTIN_RIPGREP=0`	Use system ripgrep instead of built-in (useful on Alpine Linux)
`CLAUDE_CODE_SIMPLE`	Enable simple mode (Bash + Edit tools only, no agents/hooks/MCP)
`CLAUDE_BASH_NO_LOGIN=1`	Skip login shell invocation for BashTool

For variables configurable via the "env" key in settings.json (including MAX_THINKING_TOKENS, CLAUDE_CODE_SHELL, CLAUDE_CODE_ENABLE_TASKS, ANTHROPIC_API_KEY, ANTHROPIC_BASE_URL, and more), see section 10.3 Configuration Reference.

Common Combinations:

# CI/CD mode - non-interactive with auto-accept
claude -p "fix linting errors" --dangerously-skip-permissions

# JSON output for scripting
claude -p "analyze code quality" --output-format json

# Economic analysis with Haiku
claude -p "review this file" --model haiku

# Allow access to a directory outside CWD
claude --add-dir ./src/components

# Plan mode for safety
claude --permission-mode plan

# Multi-directory project
claude --add-dir ../shared-lib ../utils ../config

# Limit agentic turns in automation
claude -p "refactor this module" --max-turns 10

# Resume specific session non-interactively
claude -r abc123 -p "summarize progress"

Safety Guidelines:

Flag	Risk Level	Use When
`--dangerously-skip-permissions`	High	Only in CI/CD, never on production
`--allowedTools`	Safe	Restricting tool access
`--disallowedTools`	Safe	Blocking specific tools
`--permission-mode plan`	Safe	Read-only exploration
`--debug`	Medium	Troubleshooting (verbose logs)

10.4 Troubleshooting

Interactive Troubleshooting: Use the /diagnose command for guided, interactive problem-solving. It auto-scans your environment and provides targeted solutions. See examples/commands/diagnose.md.

Quick Diagnostic Guide

Use this symptom-based guide for rapid issue identification and resolution:

Symptom	Likely Cause	Quick Fix	Prevention
”Context too long” error	Session accumulated too much context	`/compact` first, then `/clear` if needed	Compact regularly at 70%
Slow/delayed responses	High context usage (>75%)	Check `/status`, run `/compact`	Monitor context with `/status`
”Rate limit exceeded”	API throttling from frequent requests	Wait 2 minutes, use `--model haiku` for simple tasks, or use cc-copilot-bridge for flat-rate access	Batch operations, use `/compact`, consider Copilot Pro
Claude forgets instructions	Context overflow, CLAUDE.md lost	Create checkpoint, `/clear`, reload CLAUDE.md	Keep CLAUDE.md concise (<500 lines)
MCP server not connecting	Server crashed or config error	`claude mcp list`, check paths, restart server	Test servers after config changes
Permission prompts every time	Tool not in `allowedTools`	Add pattern to `settings.json` allowedTools	Use wildcards: `Bash(git *)`
Changes not taking effect	Cached configuration	Restart Claude Code session	Use `/exit` before config changes
Session won’t resume	Corrupted session file	Start fresh with `/clear`	Exit cleanly with `/exit` or `Ctrl+D`

Quick Diagnosis Flow:

Check context: /status → If >70%, run /compact
Check connectivity: Try simple command → If fails, check network
Check configuration: claude mcp list → Verify MCP servers
Check permissions: Review error message → Add to allowedTools if needed
Still failing: /doctor → Run diagnostics and verify system health

Common Issues Reference

Symptom	Cause	Solution
”Context too long”	Used 100% context	`/clear` or `/compact`
Slow responses	High context usage	`/compact`
”Permission denied”	Security settings	Check `settings.local.json`
Hook not running	Registration error	Check `settings.json` matcher
MCP tool not found	Server not running	Check `mcp.json` config
Agent not found	File naming	Check `.claude/agents/`
Command not found	Path error	Check `.claude/commands/`

Context Recovery

Context Level	Recommended Action
0-50%	Continue normally
50-75%	Be more specific in queries
75-90%	Use `/compact`
90%+	Use `/clear`

Common Errors

“Tool execution failed”

Check tool permissions in settings.local.json
Verify command syntax
Check for missing dependencies

“Agent not available”

Verify agent file exists in .claude/agents/
Check YAML frontmatter syntax
Restart Claude Code session

“Hook blocked operation”

Check hook exit code (2 = blocked)
Review hook error message
Adjust hook rules if needed

MCP Server Issues

Common MCP Errors and Solutions

Error 1: Tool Name Validation Failed

API Error 400: "tools.11.custom.name: String should match pattern '^[a-zA-Z0-9_-]{1,64}'"

Cause: MCP server name contains invalid characters.

Solution:

Server names must only contain: letters, numbers, underscores, hyphens
Maximum 64 characters
No special characters or spaces

Example:

# ❌ Wrong
claude mcp add my-server@v1 -- npx server

# ✅ Correct
claude mcp add my-server-v1 -- npx server

Error 2: MCP Server Not Found

MCP server 'my-server' not found

Cause: Server not properly registered or wrong scope.

Solution:

Check scope settings (local/user/project)
Terminal window
```
claude mcp list  # Verify server is listed
```
Ensure you’re in the correct directory for local scope
Restart Claude Code session

Re-add server if needed:

claude mcp add my-server -s user -- npx @my/server

Error 3: Windows Path Issues

Error: Cannot find module 'C:UsersusernameDocuments'

Cause: Backslashes in Windows paths not properly escaped.

Solution:

# ❌ Wrong
claude mcp add fs -- npx -y @modelcontextprotocol/server-filesystem C:\Users\username\Documents

# ✅ Correct - Use forward slashes
claude mcp add fs -- npx -y @modelcontextprotocol/server-filesystem C:/Users/username/Documents

# ✅ Correct - Escape backslashes
claude mcp add fs -- npx -y @modelcontextprotocol/server-filesystem "C:\\Users\\username\\Documents"

MCP Debugging Techniques

Enable Debug Mode:

# Debug all MCP connections
claude --mcp-debug

# View MCP status inside Claude Code
/mcp

View Log Files:

# macOS
tail -f ~/Library/Logs/Claude/mcp*.log

# Linux
tail -f ~/.local/share/claude/logs/mcp*.log

# Windows (PowerShell)
Get-Content "$env:APPDATA\Claude\logs\mcp*.log" -Wait -Tail 50

Manual Server Test:

# Test if server works standalone
npx -y @modelcontextprotocol/server-filesystem ~/Documents

# Expected: Server should start and output JSON-RPC messages
# If it crashes immediately, check server logs

Quick Diagnostic Commands:

# List all configured servers
claude mcp list

# Test specific server
claude --mcp-debug -p "List available tools"

# Remove and re-add server
claude mcp remove my-server
claude mcp add my-server -s user -- npx @my/server

Connection Failed: Common Causes

Error	Cause	Solution
`ECONNREFUSED`	Server not running	Check `mcp.json` command is correct
`Timeout after 30s`	Slow initialization	Increase timeout or check server logs
`Module not found`	Missing dependencies	Run `npm install` in server directory
`Permission denied`	File access	Check file permissions on server executable
`ENOENT`	Server binary not found	Verify npx/npm is in PATH
`Invalid JSON`	Server output malformed	Check server version compatibility

Serena MCP specific issues:

# Index not found
serena list-memories
# If empty, re-index:
# In your project, ask Claude: "Index this project with Serena"

# Session not persisting
# Check mcp.json has correct data directory:
{
  "mcpServers": {
    "serena": {
      "command": "npx",
      "args": ["-y", "@serenaai/serena-mcp"],
      "env": {
        "SERENA_DATA_DIR": "/absolute/path/to/.serena"
      }
    }
  }
}

Context7 MCP issues:

# Documentation not found
# Ensure you're searching for official libraries:
# ✅ "React useState documentation"
# ❌ "my-custom-lib documentation" (not in Context7)

# Slow lookups
# Context7 fetches from official docs - network dependent
# Check your internet connection

Sequential Thinking MCP issues:

# "Sequential not responding"
# Sequential uses significant compute - expect 10-30s responses
# Not an error, just be patient

# Quality seems off
# Sequential works best with specific, well-defined problems
# ✅ "Debug why user authentication fails on mobile"
# ❌ "Make the app better"

Permission Issues

Pattern matching problems:

// ❌ Wrong - too specific
{
  "allowedTools": ["Bash(npm test)"]
}
// This ONLY allows exactly "npm test"

// ✅ Right - use wildcards
{
  "allowedTools": ["Bash(npm *)"]
}
// This allows any npm command

Common permission patterns:

{
  "allowedTools": [
    "Bash(git *)",           // All git commands
    "Bash(npm *)",           // All npm commands
    "Bash(pytest *)",        // All pytest commands
    "Edit",                  // All file edits
    "Write",                 // All file writes
    "Read",                  // All file reads
    "mcp__serena__*",        // All Serena tools
    "mcp__context7__*",      // All Context7 tools
    "Task"                   // Allow agent delegation
  ]
}

Timeout Issues

Claude stops responding mid-task:

Possible causes:

Network interruption - Check your internet connection
API rate limit - Wait 1-2 minutes and retry
Context exhausted - Use /compact or /clear
Long-running operation - Some MCP operations take 30s+

Workaround for long operations:

# Instead of:
"Analyze all 500 files in the codebase"

# Break into chunks:
"Analyze files in /src/components/ first"
"Now analyze /src/utils/"
"Finally analyze /src/services/"

Installation Issues

Windows-specific problems:

# npm global install fails
# Run PowerShell as Administrator
npm install -g @anthropic-ai/claude-code

# PATH not updated
# Manually add to PATH:
$env:Path += ";$env:APPDATA\npm"

# Permission errors
# Check antivirus isn't blocking Node.js

macOS-specific problems:

# "Command not found" after install
# Check shell config loaded:
source ~/.zshrc  # or ~/.bashrc

# Permission denied on /usr/local
# Don't use sudo with npm
# Fix permissions:
sudo chown -R $(whoami) /usr/local

# curl install blocked
# Check firewall/VPN settings

Linux-specific problems:

# npm not found
# Install Node.js first:
curl -fsSL https://deb.nodesource.com/setup_lts.x | sudo -E bash -
sudo apt-get install -y nodejs

# Global install permission issues
# Configure npm to use home directory:
mkdir ~/.npm-global
npm config set prefix '~/.npm-global'
echo 'export PATH=~/.npm-global/bin:$PATH' >> ~/.bashrc
source ~/.bashrc

One-Shot Health Check Scripts

Diagnostic scripts for instant troubleshooting. Get them from:

Windows: examples/scripts/check-claude.ps1
macOS/Linux: examples/scripts/check-claude.sh
Bridge health: python examples/scripts/bridge.py --health (LM Studio connectivity)

Full Clean Reinstall Procedures

⚠️ Nuclear option for corrupted installations. Use when all else fails.

Get the scripts from:

Windows: examples/scripts/clean-reinstall-claude.ps1
macOS/Linux: examples/scripts/clean-reinstall-claude.sh

When to use clean reinstall:

Mysterious errors that persist after normal troubleshooting
Corrupted configuration files
Breaking changes after Claude Code updates
Migration to new machine (export/import workflow)

What gets deleted:

✓ Claude Code binary and npm packages
✓ Downloaded models and cache
✓ Local session data
⚠️ Config file (optional - backed up by default)

What survives:

✓ Project-level .claude/ folders
✓ Project CLAUDE.md files
✓ Custom agents, skills, commands, hooks (in projects)
✓ MCP server configurations (in mcp.json)

10.5 Cheatsheet

One-Page Quick Reference

╔══════════════════════════════════════════════════════════╗
║                 CLAUDE CODE CHEATSHEET                   ║
╠══════════════════════════════════════════════════════════╣
║                                                          ║
║  ESSENTIAL COMMANDS                                      ║
║  ─────────────────                                       ║
║  /help      Show commands     /clear    Fresh start      ║
║  /status    Session info      /compact  Save context     ║
║  /plan      Safe mode         /rewind   Undo changes     ║
║  /exit      Quit              Ctrl+C    Cancel           ║
║                                                          ║
║  QUICK ACTIONS                                           ║
║  ─────────────                                           ║
║  !command   Run shell         @file     Reference file   ║
║  Ctrl+R     Search            ↑/↓       History          ║
║                                                          ║
║  CONTEXT MANAGEMENT                                      ║
║  ──────────────────                                      ║
║  🟢 0-50%   Work freely                                  ║
║  🟡 50-75%  Be selective                                 ║
║  🔴 75-90%  /compact now                                 ║
║  ⚫ 90%+    /clear required                              ║
║                                                          ║
║  PERMISSION MODES                                        ║
║  ────────────────                                         ║
║  Default     Ask before changes                           ║
║  Auto-accept Execute without asking                       ║
║  Plan Mode   Read-only exploration                        ║
║                                                           ║
║  CONFIGURATION                                            ║
║  ─────────────                                            ║
║  ~/.claude/CLAUDE.md         Global settings              ║
║  /project/CLAUDE.md          Project settings             ║
║  .claude/settings.json       Hooks config                 ║
║  .claude/settings.local.json Permission overrides         ║
║                                                           ║
║  .claude/ FOLDER                                          ║
║  ───────────────                                          ║
║  agents/    Custom agents     commands/  Slash commands   ║
║  hooks/     Event scripts     rules/     Auto-load rules  ║
║  skills/    Knowledge modules                             ║
║                                                           ║
║  THINKING MODE (Opus 4.5/4.6: adaptive depth in 4.6)      ║
║  ─────────────────────────────────────────                ║
║  Alt+T          Toggle on/off   Current session           ║
║  /config        Global setting  Persists across sessions  ║
║  Note: "ultrathink" keywords are now cosmetic only        ║
║                                                           ║
║  MCP SERVERS                                              ║
║  ───────────                                              ║
║  Serena       Semantic code analysis                      ║
║  Context7     Library documentation                       ║
║  Sequential   Structured reasoning                        ║
║  Postgres     Database queries                            ║
║  Playwright   Browser automation                          ║
║                                                           ║
║  HOOKS (events)                                           ║
║  ──────────────                                           ║
║  PreToolUse       Before tool (security)                  ║
║  PostToolUse      After tool (format, log)                ║
║  UserPromptSubmit On message (enrich context)             ║
║                                                           ║
║  WORKFLOW                                                 ║
║  ────────                                                 ║
║  Describe → Analyze → Review → Accept/Reject → Verify     ║
║                                                           ║
║  BEST PRACTICE: Always read the diff before accepting!    ║
║                                                           ║
╚══════════════════════════════════════════════════════════╝

10.6 Daily Workflow & Checklists

Daily Workflow Pattern

┌─────────────────────────────────────────────────────────────┐
│                    DAILY WORKFLOW                           │
├─────────────────────────────────────────────────────────────┤
│                                                             │
│  MORNING (Setup)                                            │
│  ───────────────                                            │
│  □ Git pull latest changes                                  │
│  □ Review context with /status                              │
│  □ Load project memory (/sc:load if using Serena)           │
│  □ Review yesterday's progress                              │
│                                                             │
│  WORK SESSION                                               │
│  ────────────                                               │
│  □ Define task clearly before starting                      │
│  □ Use TodoWrite for multi-step work                        │
│  □ Commit after each completed task                         │
│  □ /compact when context >70%                               │
│  □ Take breaks every 90 minutes                             │
│                                                             │
│  END OF DAY                                                 │
│  ──────────                                                 │
│  □ Commit all work in progress                              │
│  □ Save session (/sc:save)                                  │
│  □ Note blockers or next steps                              │
│  □ Push to remote                                           │
│                                                             │
└─────────────────────────────────────────────────────────────┘

Prompt Quality Checklist

Use this before sending complex requests:

□ WHAT: Clear deliverable described?
□ WHERE: File paths/locations specified?
□ HOW: Constraints/approach mentioned?
□ WHY: Context for decision-making?
□ VERIFY: Success criteria defined?

Example applying checklist:

❌ Vague: "Add user authentication"

✅ Complete:
"Add JWT authentication to the /api/login endpoint.
- WHERE: src/api/auth/login.ts
- HOW: Use jsonwebtoken library (already in deps),
       bcrypt for password comparison
- CONSTRAINTS: Token expires in 24h, include userId and role
- VERIFY: Test with wrong password, expired token, invalid token"

Appendix: Templates Collection

💡 Production-Ready Examples: For complete, battle-tested templates including advanced commands (/pr, /release-notes, /sonarqube) and security hooks, see the examples/ directory. The templates below are minimal starting points.

A.1 Agent Template

---
name: your-agent-name
description: Use this agent when [specific trigger]
model: sonnet
tools: Read, Write, Edit, Bash, Grep, Glob
skills: []
---

# Agent Name

## Role Definition
You are an expert in [domain].

## Activation Triggers
Use this agent when:
- [Trigger 1]
- [Trigger 2]

## Methodology
1. [Step 1]
2. [Step 2]
3. [Step 3]

## Output Format
[Expected deliverables]

## Examples
[Concrete usage examples]

A.2 Skill Template

---
name: skill-name
description: Expert guidance for [domain]
allowed-tools: Read Grep Bash
argument-hint: "[--option] <required_arg>"   # if the skill accepts $ARGUMENTS
---

# Skill Name

## Expertise Areas
- [Area 1]
- [Area 2]

## Methodology
1. [Step 1]
2. [Step 2]

## Checklists
- [ ] [Check 1]
- [ ] [Check 2]

## Examples
[Good and bad patterns]

A.3 Command Template

---
description: Brief description of what this command does
argument-hint: "<first_arg> [second_arg] [--flag]"
---
# Command Name

## Purpose
[What this command does]

## Process
1. **Step 1**: [Instructions]
2. **Step 2**: [Instructions]

## Arguments
- $ARGUMENTS[0] (or $0): First argument - [How to handle]
- $ARGUMENTS[1] (or $1): Second argument - [How to handle]

## Output Format
[Expected output]

A.4 Hook Templates

PreToolUse (Security)

#!/bin/bash
INPUT=$(cat)
COMMAND=$(echo "$INPUT" | jq -r '.tool_input.command // ""')

# Block dangerous patterns
[[ "$COMMAND" =~ "dangerous-pattern" ]] && { echo "BLOCKED" >&2; exit 2; }

exit 0

PostToolUse (Formatting)

#!/bin/bash
INPUT=$(cat)
FILE_PATH=$(echo "$INPUT" | jq -r '.tool_input.file_path // ""')

# Auto-format
[[ "$FILE_PATH" =~ \.(ts|tsx)$ ]] && npx prettier --write "$FILE_PATH" 2>/dev/null

exit 0

UserPromptSubmit (Context)

#!/bin/bash
CONTEXT="[Custom context here]"
cat << EOF
{"hookSpecificOutput":{"additionalContext":"$CONTEXT"}}
EOF
exit 0

A.5 settings.json Template

{
  "hooks": {
    "PreToolUse": [
      {
        "matcher": "Bash",
        "hooks": [{"type": "command", "command": ".claude/hooks/security.sh", "timeout": 5000}]
      }
    ],
    "PostToolUse": [
      {
        "matcher": "Edit|Write",
        "hooks": [{"type": "command", "command": ".claude/hooks/format.sh"}]
      }
    ],
    "UserPromptSubmit": [
      {
        "matcher": "",
        "hooks": [{"type": "command", "command": ".claude/hooks/context.sh"}]
      }
    ]
  }
}

A.6 settings.local.json Template

{
  "permissions": {
    "allow": [
      "Bash(git *)",
      "Bash(npm test)",
      "Bash(pnpm *)",
      "Edit",
      "Write"
    ],
    "deny": [
      "Bash(rm -rf *)",
      "Bash(sudo *)"
    ],
    "ask": [
      "Bash(npm publish)",
      "Bash(git push --force)"
    ]
  }
}

A.7 CLAUDE.md Template

# Project Name

## Tech Stack
- [Technology 1]
- [Technology 2]

## Code Conventions
- [Convention 1]
- [Convention 2]

## Architecture
- [Pattern 1]
- [Pattern 2]

## Commands
- `npm run dev` - Start development
- `npm test` - Run tests

11. AI Ecosystem: Complementary Tools

Quick jump: Why Complementarity · Tool Matrix · Practical Workflows · Integration Patterns

Reading time: 10 minutes

Skill level: Intermediate

Goal: Chain Claude Code with the right AI tools for optimal workflows

TL;DR: Claude Code excels at contextual reasoning and multi-file implementation. Combine it with Perplexity (research), Gemini (images), Kimi (slides), and NotebookLM (synthesis) for a complete AI-powered development workflow.

10. Reference

📌 Section 10 TL;DR (1 minute)

Quick Navigation by Need:

Most Common Lookups:

10.1 Commands Table

Built-in Commands

Quick Actions

10.2 Keyboard Shortcuts

Session Control

Input & Navigation

Mode & Model Toggles

Voice Input

Agent Teams Navigation

Useful Flag Combinations

10.3 Configuration Reference

CLAUDE.md Locations

Settings Files

Permission Patterns

CLI Flags Reference

Session & Context

Model & Configuration

Output & Format

Permissions & Security

System Prompt

Agent & Subagent

MCP & Plugins

Directory & Workspace

Budget & Limits

Integration

Initialization & Maintenance

Debug & Diagnostics

Settings Override

Version & Help

Subcommands

Startup Environment Variables

10.4 Troubleshooting

Quick Diagnostic Guide

Common Issues Reference

Context Recovery

Common Errors

MCP Server Issues

Error 1: Tool Name Validation Failed

Error 2: MCP Server Not Found

Error 3: Windows Path Issues

MCP Debugging Techniques

Permission Issues

Timeout Issues

Installation Issues

One-Shot Health Check Scripts

Full Clean Reinstall Procedures

10.5 Cheatsheet

One-Page Quick Reference

10.6 Daily Workflow & Checklists

Daily Workflow Pattern

Prompt Quality Checklist

Appendix: Templates Collection

A.1 Agent Template

A.2 Skill Template

A.3 Command Template

A.4 Hook Templates

PreToolUse (Security)

PostToolUse (Formatting)

UserPromptSubmit (Context)

A.5 settings.json Template

A.6 settings.local.json Template

A.7 CLAUDE.md Template

11. AI Ecosystem: Complementary Tools