Claude Code System Prompt: Master CLAUDE.md Configuration
Manas Takalpati
Founder, Blue Orchid
The system prompt is the single most important configuration in Claude Code. Get it right and Claude becomes a seamless extension of how you think about your codebase. Get it wrong and you fight the AI every step.
How System Prompts Work
Claude Code loads instructions from CLAUDE.md files in three layers:
- Global -
~/.claude/CLAUDE.md- Applied to every project - Project -
./CLAUDE.md- Specific to one codebase - Nested - Subdirectory CLAUDE.md files - Scoped to specific modules
Each layer stacks. Global sets baseline preferences. Project overrides for specific needs. Nested adds module-specific context.
The Global CLAUDE.md
Your personal defaults that follow you everywhere:
## Work Style
- Communication: Direct, no hype
- Git: Feature branches only
- Quality: Run lint/tests before marking complete
## Conventions
- TypeScript strict mode
- Prefer Server Components
- No default exports except pages
The Project CLAUDE.md
Codebase-specific rules:
# My SaaS App
## Stack
Next.js 14, TypeScript, Tailwind, Supabase
## Commands
npm run dev / npm run build / npm run test
## Architecture
App Router, Server Components by default, Zod validation
Most impactful sections: Commands (so Claude can run your project), architecture decisions (prevents wrong paradigms), and conventions (keeps output consistent).
Hooks
Hooks run scripts before or after Claude Code actions. Defined in .claude/settings.json:
{
"hooks": {
"PostToolUse": [{
"matcher": "Edit|Write",
"hook": "npx prettier --write $CLAUDE_FILE_PATH"
}]
}
}
Essential hooks: Auto-format on save, git diff on edit, lint on write.
Custom Slash Commands
Create .claude/commands/review.md to define reusable prompts triggered with /review.
Tips for Great System Prompts
- Be specific, not aspirational ("use early returns" not "write clean code")
- Include negative examples (what NOT to do)
- Update when your project evolves
- Keep under 100 lines
For the complete Claude Code workflow, see Claude Code Complete Guide.
Frequently Asked Questions
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