Refactor AGENTS.md files for improved project setup documentation

- Consolidated setup instructions into AGENTS.md for each component: extralit-server, extralit-frontend, and extralit SDK.
- Updated installation and development commands for clarity and consistency.
- Removed outdated CLAUDE.md files and streamlined content to focus on essential setup and usage information.
- Enhanced architecture notes and prerequisites for better guidance on project dependencies.

Author: JonnyTran

AGENTS.md

@@ -1,91 +1,70 @@
-# CLAUDE.md
+# AGENTS.md - Project Setup Instructions
 
-This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+## Component-Specific Setup
 
-## Architecture Overview
+Each component has its own AGENTS.md with setup details:
+- **extralit-server/AGENTS.md** - Backend server setup
+- **extralit-frontend/AGENTS.md** - Frontend UI setup
+- **extralit/AGENTS.md** - Python SDK setup
 
-Extralit is a multi-component system for scientific literature data extraction with human-in-the-loop workflows:
+## Prerequisites
 
-- **extralit-server/**: FastAPI backend server with PostgreSQL database, handles users, datasets, records, and API interactions
-- **extralit-frontend/**: Vue.js/Nuxt.js web UI for data visualization, annotation, and team collaboration
-- **extralit/**: Python SDK client library for programmatic interaction with the server
-- **Vector Database**: External Elasticsearch/OpenSearch for scalable vector similarity searches
+- Python 3.10+ (server) / 3.9+ (SDK)
+- Node.js 18+
+- Docker & Docker Compose (for full stack)
+- PDM (Python package manager)
 
-## Development Commands
+## Quick Setup
 
-### Server (extralit-server/)
 ```bash
-cd extralit-server/
-pdm run server-dev        # Start server with auto-reload + worker
-pdm run server           # Start server only
-pdm run worker           # Start background worker only
-pdm run migrate          # Run database migrations
-pdm run test             # Run tests
-pdm run test-cov         # Run tests with coverage
-pdm run lint             # Run ruff linting
+# Install PDM
+pip install pdm
+
+# Setup all components
+cd extralit-server && pdm install -G test
+cd ../extralit && pdm install -e ".[dev]"
+cd ../extralit-frontend && npm install
+
+# Run migrations
+cd extralit-server && pdm run migrate
+
+# Start services (requires Docker)
+docker-compose up -d
 ```
 
-### Frontend (extralit-frontend/)
+## Development Workflow
+
+### Running Services
 ```bash
-cd extralit-frontend/
-npm run dev              # Development server
-npm run build            # Production build
-npm run test             # Run Jest tests
-npm run test:watch       # Run tests in watch mode
-npm run test:coverage    # Run tests with coverage report
-npm run e2e              # Run Playwright e2e tests (interactive UI)
-npm run e2e:silent       # Run e2e tests in headless mode
-npm run e2e:report       # Show Playwright test report
-npm run lint             # ESLint check
-npm run lint:fix         # Fix ESLint issues
-npm run format           # Format with Prettier
-npm run format:check     # Check formatting without modifying files
-npm run generate-icons   # Generate icon components from SVG files
+cd extralit-server && pdm run server-dev  # Server + worker
+cd extralit-frontend && npm run dev        # Frontend
 ```
 
-### Client SDK (extralit/)
+### Testing
 ```bash
-cd extralit/
-pdm run test             # Run tests
-pdm run test-cov         # Run tests with coverage
-pdm run lint             # Run ruff linting
-pdm run all              # Format, lint, and test
+cd extralit-server && pdm run test         # Server tests
+cd extralit && pdm run test                # SDK tests
+cd extralit-frontend && npm run test       # Frontend tests
 ```
 
-## Key Development Notes
-
-### Frontend Architecture
-- Transitioning from Vuex to Pinia (v1/ directory contains new architecture)
-- Uses domain-driven design with entities, use cases, and dependency injection
-- Component structure: base (stateless) → features (page-specific) → global (reusable)
+### Code Quality
+```bash
+pdm run lint              # Python linting (ruff)
+npm run lint              # Frontend linting (ESLint)
+npm run format            # Frontend formatting (Prettier)
+```
 
-### Backend Structure
-- FastAPI with SQLAlchemy ORM and Alembic migrations
-- Background job processing with Redis Queue (rq)
-- OAuth2 authentication with JWT tokens
-- Webhook system for external integrations
-- Document processing with OCR capabilities
+## Architecture Notes
 
-### Database Management
-- Alembic handles all database schema changes
-- Use `pdm run revision` to create new migrations after model changes
-- Always run `pdm run migrate` before starting development
+- **extralit-server/**: FastAPI + PostgreSQL + Redis Queue
+- **extralit-frontend/**: Vue.js/Nuxt.js (Vuex → Pinia migration)
+- **extralit/**: Python SDK client
+- **Vector DB**: Elasticsearch/OpenSearch (separate service)
 
-### Testing
-- Backend: pytest with async support, factory-boy for fixtures
-- Frontend: Jest for unit tests, Playwright for e2e
-- Python packages require Python 3.9+ (extralit) or 3.10+ (extralit-server)
-- Node.js 18+ required for frontend
-
-### Container Environment
-- Docker Compose setup available for full stack development
-- Services: Elasticsearch, Redis, MinIO for file storage
-- See `.github/workflows/copilot-setup-steps.yml` for complete environment setup
-
-### Linting Configuration
-- Python: Ruff with shared configuration across packages
-- Frontend: ESLint + Prettier with TypeScript support
-- Pre-commit hooks for code formatting and linting
+### Key Patterns
+- Backend: SQLAlchemy ORM, Alembic migrations, async pytest
+- Frontend: Domain-driven design, dependency injection
+- Database: Always use Alembic for schema changes
 
 # Agent Instructions