Refactor emacs configuration and clean up lab-tool project

- Reorganized emacs configuration with profiles in modules/development/emacs.nix
- Updated machine configurations to use new emacs module structure
- Cleaned up lab-tool project by removing archive, research, testing, and utils directories
- Streamlined lab-tool to focus on core deployment functionality with deploy-rs
- Added DEVELOPMENT.md documentation for lab-tool

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

packages/lab-tool/DEVELOPMENT.md

@@ -0,0 +1,148 @@
+# Lab Tool Development Guide
+
+## Build Commands
+
+### Build the Lab Tool Package
+```bash
+# Build the lab tool from project root
+nix build .#packages.x86_64-linux.lab
+
+# The binary will be available at ./result/bin/lab
+```
+
+### Quick Development Build
+```bash
+# From the lab-tool directory
+cd packages/lab-tool
+nix build .#lab-tool  # if available, otherwise use full path above
+```
+
+## Testing Commands
+
+### Test Lab Tool Functionality
+```bash
+# Test help command
+./result/bin/lab help
+
+# Test machine listing
+./result/bin/lab machines
+
+# Test status check
+./result/bin/lab status
+
+# Test dry-run deployment
+./result/bin/lab deploy little-rascal --dry-run
+
+# Test actual deployment
+./result/bin/lab deploy little-rascal
+```
+
+### Test System Integration
+```bash
+# Deploy configuration using nixos-rebuild (requires sudo access)
+sudo nixos-rebuild switch --flake .#little-rascal --show-trace
+
+# Or using lab tool (recommended)
+lab deploy little-rascal
+```
+
+## Development Workflow
+
+### 1. Make Changes
+Edit source files in:
+- `main.scm` - CLI interface
+- `lab/deployment.scm` - Deployment logic
+- `lab/machines.scm` - Machine management
+- `utils/*.scm` - Utility functions
+
+### 2. Build and Test
+```bash
+# Rebuild after changes
+nix build .#packages.x86_64-linux.lab
+
+# Test basic functionality
+./result/bin/lab help
+./result/bin/lab machines
+
+# Test deployment (dry-run first)
+./result/bin/lab deploy little-rascal --dry-run
+```
+
+### 3. Debug Issues
+```bash
+# Enable Guile debugging
+export GUILE_AUTO_COMPILE=0
+
+# Run with verbose output
+./result/bin/lab deploy little-rascal --dry-run
+
+# Check deploy-rs command directly
+deploy --help
+```
+
+## Common Development Tasks
+
+### Update Deploy-rs Command Format
+Edit `lab/deployment.scm` in the `build-deploy-command` function:
+```scheme
+;; Example: Add new flags
+(when new-option
+  (set! flags (cons "--new-flag=value" flags)))
+```
+
+### Add New Machine
+Add to the machine list in `lab/machines.scm` or config files.
+
+### Debug Deployment Issues
+1. Check the generated command with dry-run
+2. Test deploy-rs directly: `deploy '.#little-rascal' --dry-activate`
+3. Check flake structure: `nix flake show`
+
+### Module Structure
+- `main.scm` - Entry point and CLI parsing
+- `lab/core.scm` - Core lab functionality
+- `lab/deployment.scm` - Deploy-rs integration
+- `lab/machines.scm` - Machine management
+- `lab/monitoring.scm` - Health checks and monitoring
+- `lab/auto-update.scm` - Automatic update system
+- `utils/logging.scm` - Logging system with colors
+- `utils/config.scm` - Configuration management
+- `utils/ssh.scm` - SSH utilities
+- `utils/json.scm` - JSON handling
+
+## Troubleshooting
+
+### Build Failures
+```bash
+# Check flake structure
+nix flake show
+
+# Verify Guile syntax
+guile --no-auto-compile -c "(load \"main.scm\")"
+```
+
+### Runtime Errors
+```bash
+# Check module exports
+guile -c "(use-modules (lab deployment)) (display 'loaded)"
+
+# Test individual functions
+guile -c "(use-modules (lab deployment)) (deploy-machine \"little-rascal\" \"default\" '((dry-run . #t)))"
+```
+
+### Deploy-rs Issues
+```bash
+# Test deploy-rs directly
+deploy '.#little-rascal' --dry-activate
+
+# Check machine connectivity
+ssh sma@little-rascal 'echo "connected"'
+```
+
+## Best Practices
+
+1. **Always test with dry-run first**
+2. **Use the lab tool instead of direct nixos-rebuild when possible**
+3. **Check flake status before deployment** (`nix flake check`)
+4. **Keep commits atomic** - one feature/fix per commit
+5. **Update this file when adding new commands or workflows**