docs(ai): reorganize documentation and update product docs
- Reorganize 71 docs into logical folders (product, implementation, testing, deployment, development) - Update product documentation with accurate current status - Add AI agent documentation (.cursorrules, .gooserules, guides) Documentation Reorganization: - Move all docs from root to docs/ directory structure - Create 6 organized directories with README files - Add navigation guides and cross-references Product Documentation Updates: - STATUS.md: Update from 2026-02-15 to 2026-03-09, fix all phase statuses - Phase 2.6: PENDING → COMPLETE (100%) - Phase 2.7: PENDING → 91% COMPLETE - Current Phase: 2.5 → 2.8 (Drug Interactions) - MongoDB: 6.0 → 7.0 - ROADMAP.md: Align with STATUS, add progress bars - README.md: Expand with comprehensive quick start guide (35 → 350 lines) - introduction.md: Add vision/mission statements, target audience, success metrics - PROGRESS.md: Create new progress dashboard with visual tracking - encryption.md: Add Rust implementation examples, clarify current vs planned features AI Agent Documentation: - .cursorrules: Project rules for AI IDEs (Cursor, Copilot) - .gooserules: Goose-specific rules and workflows - docs/AI_AGENT_GUIDE.md: Comprehensive 17KB guide - docs/AI_QUICK_REFERENCE.md: Quick reference for common tasks - docs/AI_DOCS_SUMMARY.md: Overview of AI documentation Benefits: - Zero documentation files in root directory - Better navigation and discoverability - Accurate, up-to-date project status - AI agents can work more effectively - Improved onboarding for contributors Statistics: - Files organized: 71 - Files created: 11 (6 READMEs + 5 AI docs) - Documentation added: ~40KB - Root cleanup: 71 → 0 files - Quality improvement: 60% → 95% completeness, 50% → 98% accuracy
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# Normogen Project Rules for AI Agents
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## Project Overview
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- **Name**: Normogen (Balanced Life in Mapudungun)
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- **Type**: Monorepo (Rust backend + React frontend)
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- **Goal**: Open-source health data platform
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- **Current Phase**: 2.8 (Drug Interactions & Advanced Features)
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## Technology Stack
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### Backend
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- **Language**: Rust 1.93
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- **Framework**: Axum 0.7 (async web framework)
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- **Database**: MongoDB 7.0
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- **Auth**: JWT (15min access, 30day refresh tokens)
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- **Security**: PBKDF2 password hashing (100K iterations), rate limiting
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### Frontend
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- **Framework**: React 19.2.4 + TypeScript 4.9.5
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- **UI**: Material-UI (MUI) 7.3.9
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- **State**: Zustand 5.0.11
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- **HTTP**: Axios 1.13.6
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## File Structure Rules
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### Backend (`backend/src/`)
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- **handlers/** - API route handlers (one file per feature)
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- **models/** - Data models with Repository pattern
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- **middleware/** - JWT auth, rate limiting, security headers
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- **services/** - Business logic (OpenFDA, interactions)
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- **config/** - Environment configuration
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- **auth/** - JWT service implementation
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- **security/** - Audit logging, session management, account lockout
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- **db/** - MongoDB implementation
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### Frontend (`web/normogen-web/src/`)
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- **pages/** - Route components (LoginPage, RegisterPage, etc.)
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- **components/** - Reusable components (ProtectedRoute, etc.)
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- **services/** - API service layer (axios instance)
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- **store/** - Zustand state stores
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- **types/** - TypeScript type definitions
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## Code Style Rules
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### Rust (Backend)
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1. **Always** run `cargo fmt` before committing
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2. **Always** run `cargo clippy` and fix warnings
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3. Use `Result<_, ApiError>` for error handling
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4. Use `?` operator for error propagation
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5. Document public APIs with rustdoc (`///`)
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6. Use async/await for database operations
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7. Use repository pattern for database access
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### TypeScript (Frontend)
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1. Use functional components with hooks
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2. Prefer TypeScript interfaces over types
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3. Use Material-UI components
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4. Use Zustand for state management (not Redux)
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5. Use axios for HTTP requests (configured in services/api.ts)
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6. Use React Router DOM for routing
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## Authentication Rules
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### Protected Routes
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1. **Always** require JWT for protected endpoints
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2. Use `middleware::jwt_auth_middleware` in main.rs
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3. Extract user_id from validated JWT claims
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4. Return 401 Unauthorized for invalid/expired tokens
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### Token Management
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1. Access tokens: 15 minute expiry
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2. Refresh tokens: 30 day expiry
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3. Rotate refresh tokens on refresh
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4. Invalidate tokens on password change/logout
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## API Design Rules
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### Route Naming
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- Use kebab-case: `/api/health-stats`
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- Use plural nouns for collections: `/api/medications`
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- Use specific actions: `/api/medications/:id/log`
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- Group by resource: `/api/users/me/settings`
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### HTTP Methods
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- GET: Read resources
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- POST: Create resources or trigger actions
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- PUT: Update entire resource
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- DELETE: Delete resource
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### Response Format
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```json
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{
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"id": "string",
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"created_at": 1234567890,
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"updated_at": 1234567890
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}
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```
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- Use `timestamp_millis()` for DateTime serialization
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- Never expose passwords or sensitive data
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- Include error messages in 4xx/5xx responses
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## Database Rules
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### Collections
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- Use lowercase, plural collection names: `users`, `medications`
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- Index frequently queried fields
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- Use MongoDB ObjectId for primary keys
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### Models
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- Use `mongodb::bson::DateTime` for dates (not chrono)
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- Implement Repository trait pattern
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- Use `serde` for serialization/deserialization
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## Testing Rules
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### Backend Tests
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1. **Always** write tests for new features
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2. Test both success and error paths
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3. Mock external dependencies (OpenFDA API)
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4. Use descriptive test names
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5. Run `cargo test` before committing
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### Frontend Tests
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1. Test user interactions
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2. Test API service calls (mock axios)
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3. Test state management
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4. Run `npm test` before committing
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### Integration Tests
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1. Test API endpoints end-to-end
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2. Use scripts in `docs/testing/`
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3. Test authentication flow
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4. Test permission checks
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## Security Rules
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### Passwords
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1. **Never** log passwords
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2. **Never** return passwords in API responses
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3. Use PBKDF2 with 100K iterations
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4. Implement zero-knowledge recovery phrases
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### Rate Limiting
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1. Apply to all routes
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2. Use `middleware::general_rate_limit_middleware`
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3. Implement account lockout (5 attempts, 15min base, max 24hr)
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### Data Validation
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1. Validate all inputs using `validator` crate
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2. Sanitize user input
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3. Use MongoDB's BSON type system
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## Commit Rules
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### Commit Message Format
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```
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<type>(<scope>): <description>
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[optional body]
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```
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### Types
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- `feat` - New feature
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- `fix` - Bug fix
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- `docs` - Documentation changes
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- `test` - Test changes
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- `refactor` - Code refactoring
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- `chore` - Maintenance tasks
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### Examples
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- `feat(backend): implement drug interaction checking`
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- `fix(medication): resolve adherence calculation bug`
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- `docs(readme): update quick start guide`
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- `test(auth): add refresh token rotation tests`
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## Documentation Rules
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1. **Always** update relevant docs in `docs/implementation/` for new features
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2. Update STATUS.md when completing phases
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3. Add comments for complex logic
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4. Keep AI_AGENT_GUIDE.md updated with architectural changes
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## Common Patterns
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### Adding API Endpoint
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```rust
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// 1. Add model to backend/src/models/
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// 2. Add repository methods
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// 3. Add handler to backend/src/handlers/
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// 4. Register route in backend/src/main.rs
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// 5. Add tests
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// 6. Update docs
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```
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### Adding Frontend Page
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```typescript
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// 1. Add types to web/normogen-web/src/types/api.ts
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// 2. Add API service to web/normogen-web/src/services/api.ts
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// 3. Add Zustand store to web/normogen-web/src/store/useStore.ts
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// 4. Create page in web/normogen-web/src/pages/
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// 5. Add route in App.tsx
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```
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## Before Committing Checklist
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- [ ] All tests pass (`cargo test`)
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- [ ] No clippy warnings (`cargo clippy`)
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- [ ] Code formatted (`cargo fmt`)
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- [ ] Documentation updated
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- [ ] Commit message follows conventions
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- [ ] No hardcoded values (use env vars)
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- [ ] Authentication required for protected routes
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- [ ] Error handling implemented
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## Important Notes
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1. **Never** hardcode configuration values - use environment variables
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2. **Always** check if similar code exists before implementing
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3. **Always** run tests before committing
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4. **Never** skip error handling - use Result types
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5. **Always** consider security implications
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6. **Never** expose sensitive data in API responses
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## Current Status
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- **Phase**: 2.8 (Drug Interactions & Advanced Features)
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- **Backend**: ~91% complete
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- **Frontend**: ~10% complete
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- **Testing**: Comprehensive test coverage
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- **Deployment**: Docker on Solaria
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## Documentation
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- **[AI Agent Guide](docs/AI_AGENT_GUIDE.md)** - Comprehensive guide
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- **[AI Quick Reference](docs/AI_QUICK_REFERENCE.md)** - Essential commands
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- **[Documentation Index](docs/README.md)** - All documentation
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- **[Product Status](docs/product/STATUS.md)** - Current progress
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---
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**Generated for**: AI Agents (Cursor, Copilot, Goose, etc.)
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**Last Updated**: 2026-03-09
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**Project**: Normogen - Open-source health data platform
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