Mastering Claude Code: 12 Advanced Features & Best Practices for AI‑Powered Development

As a heavy user of Claude Code, I run it daily on personal projects and at work, often with the --dangerously-skip-permissions flag to quickly turn ideas into code. In our team, AI‑IDE tooling consumes billions of tokens each month.

CLI agents like Claude Code, Gemini CLI, Cursor, and Codex CLI are now mature, and I evaluate them based on whether the final pull request can be merged, not on UI polish.

Over the past months I have systematically explored every feature of Claude Code, from the basic CLAUDE.md file and custom slash commands to sub‑agents, hooks, and the SDK.

CLAUDE.md

The CLAUDE.md file at the repository root is the most important document—it acts as the agent’s "constitution" and explains how the repo operates.

Record only the tools and APIs that at least ~30% of engineers will use; other tools go in product‑specific Markdown files.

Set a token budget for each internal tool; if a tool cannot be described concisely, it does not belong in CLAUDE.md.

Writing Advice & Common Anti‑Patterns

Start with guardrails, not long manuals. Use CLAUDE.md to address common errors.

Avoid embedding long documents directly with @; instead, tell the agent when and why to read a specific file.

Never give only a negative constraint like --foo-bar; always provide an alternative.

Treat CLAUDE.md as a pressure‑test mechanism—keep it short to force simplification of code and tools.

Example simplified snippet:

# Monorepo
## Python
- Always ...
- Test with <command>
... 10 more ...
## <Internal CLI Tool>
... 10 bullets, focused on the 80% of use cases ...
- <usage example>
- Always ...
- Never <x>, prefer <Y>
For <complex usage> or <error> see path/to/<tool>_docs.md

Synchronize CLAUDE.md with AGENTS.md for compatibility with other AI IDEs.

Compact, Context & Clear

Run /context to see how your 200k‑token window is used; a new session costs ~20k tokens, leaving ~180k for changes.

Typical workflow includes: /compact (avoid – it compresses opaquely and can break). /clear + /catchup to restart simply.

Document‑then‑clear for large tasks: write a plan to a .md file, then /clear and resume.

Custom Slash Commands

Use slash commands as lightweight shortcuts, not as replacements for richer tooling. /catchup: let Claude read all changed files in the current Git branch. /pr: clean code, stage changes, and prepare a pull request.

Maintaining many custom commands is an anti‑pattern; natural language should suffice for most tasks.

Custom Sub‑Agents

Sub‑agents can offload context but introduce two problems: context gating and forced human‑defined workflows. Instead, embed key context in CLAUDE.md and let the main agent decide when to delegate via Task(...).

Hooks

Hooks complement CLAUDE.md recommendations. We use two types:

Pre‑commit blocking hooks that check a token‑generated file and prevent commits until tests pass.

Non‑blocking feedback hooks that provide lightweight post‑action signals.

Avoid blocking during the write phase; let the agent finish its plan before validation.

Planning Mode

For any large feature change, use the built‑in planning mode to align with Claude on implementation steps and checkpoints before execution.

Skills

Skills formalize the "scripted" agent model, offering a more robust abstraction than traditional MCP APIs.

MCP (Model Context Protocol)

MCP should act as a minimal, secure gateway providing only high‑level tools such as download_raw_data, take_sensitive_gated_action, and execute_code_in_environment_with_state.

Claude Code SDK

The SDK enables batch scripting, internal chat tools, and rapid prototyping, often replacing LangChain or CrewAI for our projects.

Claude Code GHA

Running Claude Code as a GitHub Action turns a personal CLI tool into an auditable, enterprise‑grade component that can automatically open PRs from Slack, Jira, or CloudWatch alerts.

$ query-claude-gha-logs --since 5d | claude -p "look for stuck Claude runs, fix them, and open a PR"

settings.json

Key configuration options include HTTPS_PROXY/HTTP_PROXY for debugging, MCP_TOOL_TIMEOUT/BASH_MAX_TIMEOUT_MS for long‑running commands, ANTHROPIC_API_KEY for enterprise usage, and a permissions list for audit.

Conclusion: Treat CLAUDE.md as a high‑level guardrail, use planning mode for complex changes, leverage the SDK and GHA for scalability, and fine‑tune settings.json for advanced customization.