Reorganize repository structure for cleaner top-level directory

- Move development scripts to tools/ folder
  - setup.sh, run.sh, test.sh, build.sh, deploy.sh, document.sh
- Move Docker configuration to deployment/ folder
  - Dockerfile, docker-compose.yml, docker-compose.dev.yml
- Update all script references throughout documentation
- Update Docker paths in setup and run scripts
- Maintain git history with git mv for moved files

Top level now contains only essential files:
- README.md, LICENSE, package.json (core project files)
- CLAUDE.md, tsconfig.json, turbo.json (configuration)
- packages/, docs/, scripts/ (main directories)

Author: Matthew Valancy

CLAUDE.md

@@ -44,8 +44,8 @@ The project has a fully implemented monorepo structure with these commands:
 
 ```bash
 # Quick setup (recommended)
-./setup.sh                    # Complete environment setup
-./run.sh                      # Start all development servers
+./tools/setup.sh                    # Complete environment setup
+./tools/run.sh                      # Start all development servers
 
 # Manual setup
 npm install                   # Install dependencies
@@ -65,7 +65,7 @@ npm run db:migrate            # Run Prisma migrations
 npm run db:seed               # Seed database with test data
 
 # Docker development
-docker-compose -f docker-compose.dev.yml up  # With hot reload
+docker-compose -f deployment/docker-compose.dev.yml up  # With hot reload
 docker-compose up             # Production-like environment
 ```
 
@@ -103,21 +103,21 @@ When implementing features:
 
 ```bash
 # Initial setup
-./setup.sh                    # Set up development environment
-./run.sh                      # Start development servers
-./test.sh                     # Run test suite with linting and type checking
-./build.sh                    # Build all packages
-./deploy.sh                   # Deploy to staging/production
-./document.sh                 # Generate and deploy documentation
+./tools/setup.sh                    # Set up development environment
+./tools/run.sh                      # Start development servers
+./tools/test.sh                     # Run test suite with linting and type checking
+./tools/build.sh                    # Build all packages
+./tools/deploy.sh                   # Deploy to staging/production
+./tools/document.sh                 # Generate and deploy documentation
 
 # Docker development
-./run.sh --docker-dev         # Start with Docker (development)
-./run.sh --docker             # Start with Docker (production)
+./tools/run.sh --docker-dev         # Start with Docker (development)
+./tools/run.sh --docker             # Start with Docker (production)
 
 # Package-specific testing
-./test.sh --package core      # Test specific package
-./test.sh --coverage          # Run with coverage report
-./test.sh --watch             # Run in watch mode
+./tools/test.sh --package core      # Test specific package
+./tools/test.sh --coverage          # Run with coverage report
+./tools/test.sh --watch             # Run in watch mode
 
 # Turbo commands (alternative)
 npm run dev                   # Start all development servers
@@ -151,8 +151,8 @@ npm run typecheck             # Type check all packages
 
 🎯 **Ready for Development:**
 All foundation pieces are in place. To continue development:
-1. Run `./setup.sh` to initialize the development environment
-2. Use `./run.sh` to start development servers
+1. Run `./tools/setup.sh` to initialize the development environment
+2. Use `./tools/run.sh` to start development servers
 3. Access the working application at http://localhost:3000
 4. Use GraphQL Playground at http://localhost:4000/graphql
 5. Begin implementing specific features using the established patterns

README.md

@@ -49,8 +49,8 @@ GraphDone is built on the belief that:
 ```bash
 git clone https://github.com/your-org/graphdone.git
 cd graphdone
-./setup.sh
-./run.sh
+./tools/setup.sh
+./tools/run.sh
 ```
 
 Visit http://localhost:3000 to see the working application!
@@ -96,7 +96,7 @@ GraphDone is built for and by teams who think differently. We welcome contributi
 - Performance for large graphs
 
 **Get Started:**
-1. Run `./setup.sh && ./run.sh` to see the system working
+1. Run `./tools/setup.sh && ./tools/run.sh` to see the system working
 2. Read our [philosophy](./docs/philosophy.md) and [architecture](./docs/guides/architecture-overview.md)
 3. Pick an area that excites you and matches your skills
 4. Join discussions in GitHub Issues and pull requests

Dockerfile deployment/DockerfileDockerfile renamed to deployment/Dockerfile

@@ -34,22 +34,22 @@ Welcome to the GraphDone documentation! This directory contains comprehensive gu
 
 1. **Setup Development Environment**
    ```bash
-   ./setup.sh
+   ./tools/setup.sh
    ```
 
 2. **Start Development Servers**
    ```bash
-   ./run.sh
+   ./tools/run.sh
    ```
 
 3. **Run Tests**
    ```bash
-   ./test.sh
+   ./tools/test.sh
    ```
 
 4. **Build for Production**
    ```bash
-   ./build.sh --production
+   ./tools/build.sh --production
    ```
 
 ## 📖 Key Concepts

docker-compose.dev.yml deployment/docker-compose.dev.ymldocker-compose.dev.yml renamed to deployment/docker-compose.dev.yml

@@ -8,17 +8,17 @@ This guide covers various deployment options for GraphDone, from local developme
 
 ### Development (Local)
 ```bash
-./run.sh
+./tools/run.sh
 ```
 
 ### Development (Docker)
 ```bash
-./run.sh --docker-dev
+./tools/run.sh --docker-dev
 ```
 
 ### Production (Docker)
 ```bash
-./run.sh --docker
+./tools/run.sh --docker
 ```
 
 ## Environment Variables

docker-compose.yml deployment/docker-compose.ymldocker-compose.yml renamed to deployment/docker-compose.yml

@@ -275,7 +275,7 @@ graphdone/
 │   └── deployment/        # Deployment guides
 ├── scripts/               # Development and deployment scripts
 ├── .github/workflows/     # CI/CD pipelines
-└── docker-compose.yml    # Development environment
+└── deployment/           # Docker and deployment files
 ```
 
 ## Technology Stack & Implementation
@@ -480,7 +480,7 @@ GraphDone includes a comprehensive setup script that handles all prerequisites a
 # Clone and setup
 git clone https://github.com/your-org/graphdone.git
 cd graphdone
-./setup.sh
+./tools/setup.sh
 ```
 
 The setup script will:
@@ -495,27 +495,27 @@ The setup script will:
 
 ```mermaid
 graph LR
-    START[./setup.sh] --> DEV[./run.sh]
-    DEV --> TEST[./test.sh]
-    TEST --> BUILD[./build.sh]
-    BUILD --> DEPLOY[./deploy.sh]
+    START[./tools/setup.sh] --> DEV[./tools/run.sh]
+    DEV --> TEST[./tools/test.sh]
+    TEST --> BUILD[./tools/build.sh]
+    BUILD --> DEPLOY[./tools/deploy.sh]
     
     DEV -.-> CODE[Code Changes]
     CODE -.-> DEV
     
     subgraph "Available Commands"
-        RUN1[./run.sh --docker-dev]
-        RUN2[./test.sh --coverage]
-        RUN3[./test.sh --package core]
-        BUILD1[./build.sh --production]
+        RUN1[./tools/run.sh --docker-dev]
+        RUN2[./tools/test.sh --coverage]
+        RUN3[./tools/test.sh --package core]
+        BUILD1[./tools/build.sh --production]
     end
 ```
 
 ### Running the System
 
 Start all development servers:
 ```bash
-./run.sh
+./tools/run.sh
 ```
 
 This provides:
@@ -550,10 +550,10 @@ For containerized development:
 
 ```bash
 # Full Docker development environment
-./run.sh --docker-dev
+./tools/run.sh --docker-dev
 
 # Production-like environment
-./run.sh --docker
+./tools/run.sh --docker
 
 # Individual service testing
 docker-compose up -d postgres  # Database only
@@ -666,8 +666,8 @@ agent.subscribe('node.priorityChanged', async (node) => {
 # Get started in 30 seconds
 git clone https://github.com/your-org/graphdone.git
 cd graphdone
-./setup.sh
-./run.sh
+./tools/setup.sh
+./tools/run.sh
 ```
 
 Visit http://localhost:3000 to see the working application!
@@ -710,16 +710,16 @@ GraphDone is built for and by teams who think differently. We welcome contributi
 ### 🔧 **Development Workflow**
 ```bash
 # Set up development environment
-./setup.sh
+./tools/setup.sh
 
 # Make your changes
 git checkout -b feature/your-improvement
 
 # Test your changes
-./test.sh --coverage
+./tools/test.sh --coverage
 
 # Build and verify
-./build.sh
+./tools/build.sh
 
 # Submit your contribution
 git push origin feature/your-improvement

docs/README.md

@@ -23,7 +23,7 @@ git clone https://github.com/your-org/graphdone.git
 cd graphdone
 
 # Run setup script
-./setup.sh
+./tools/setup.sh
 ```
 
 The setup script will:
@@ -60,7 +60,7 @@ npm run build
 Start the development servers:
 
 ```bash
-./run.sh
+./tools/run.sh
 ```
 
 This will start: