Update project configuration and clean up artifacts

- Update README with corrected documentation references
- Update package.json dependencies and scripts
- Remove obsolete certificate directory placeholder

Author: mvalancy

README.md

@@ -260,10 +260,17 @@ Anyone can propose ideas and assign personal priority. The community validates t
 - 🎯 **[Project Philosophy](./docs/philosophy.md)** - Core beliefs and design principles  
 - 🚀 **[Getting Started Guide](./docs/guides/getting-started.md)** - Step-by-step setup and first steps
 - 🏗️ **[Architecture Overview](./docs/guides/architecture-overview.md)** - System design and technical decisions
-- 🧪 **[Testing Guide](./tests/README.md)** - **E2E testing with robust authentication system**
-- 🤖 **[AI Agents Integration](./docs/guides/ai-agents-integration.md)** - Multi-agent AI system with tamagotchi-style companions
+
+### User Guides & Features
+- 📊 **[Graph Creation Workflow](./docs/features/graph-creation.md)** - Complete guide to creating and managing graphs
+- 🛡️ **[Admin System Guide](./docs/features/admin-system.md)** - Comprehensive admin panel documentation
 - 👥 **[User Flows](./docs/guides/user-flows.md)** - How teams actually use GraphDone
-- 🔌 **[API Documentation](./docs/api/graphql.md)** - GraphQL schema and integration guide
+- 🤖 **[AI Agents Integration](./docs/guides/ai-agents-integration.md)** - Multi-agent AI system with tamagotchi-style companions
+
+### Technical Reference
+- 🔌 **[API Documentation](./docs/api/graphql.md)** - Complete GraphQL schema and integration guide
+- 🧪 **[Testing Guide](./tests/README.md)** - E2E testing with robust authentication system
+- 🎯 **[Admin & Graph E2E Testing](./docs/testing/e2e-admin-graph-creation.md)** - Comprehensive testing for admin and graph creation
 - 🚀 **[Deployment Guide](./docs/deployment/README.md)** - Self-hosted and cloud deployment options
 - 🏷️ **[Version Management](./docs/version-management.md)** - How to update versions across the monorepo
 

certs/.gitkeep

@@ -21,6 +21,9 @@
     "test:e2e:ui": "playwright test --ui",
     "test:e2e:debug": "playwright test --debug",
     "test:all": "npm run test:unit && npm run test:e2e",
+    "test:comprehensive": "node run-all-tests.js",
+    "test:https": "node ssl-certificate-analysis.js && node mobile-https-compatibility-test.js",
+    "test:report": "open test-results/reports/index.html",
     "lint": "turbo run lint",
     "typecheck": "turbo run typecheck",
     "clean": "turbo run clean && rm -rf node_modules",