Add inline comments and extract Lua config for better clarity

Co-authored-by: dwinkler1 <22460147+dwinkler1@users.noreply.github.com>

templates/rde/REFACTORING.md

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+# Template Refactoring Summary
+
+## Overview
+This document summarizes the refactoring improvements made to the RDE (Research Development Environment) template flake.
+
+## Changes Made
+
+### 1. File Structure Reorganization
+**Before**: Single 688-line `flake.nix` file
+**After**: Modular structure with 17 files across 5 directories
+
+```
+templates/rde/
+├── flake.nix (261 lines) - Main configuration
+├── README.md - User documentation
+├── REFACTORING.md - This file
+├── overlays/ (5 files)
+│   ├── r.nix - R package configuration
+│   ├── python.nix - Python package configuration
+│   ├── rix.nix - rstats-on-nix integration
+│   ├── theme.nix - Neovim theme setup
+│   └── project-scripts.nix - Script wrapper definitions
+├── hosts/ (5 files)
+│   ├── default.nix - Merges all host configs
+│   ├── python.nix - Python command definitions
+│   ├── julia.nix - Julia command definitions
+│   ├── r.nix - R command definitions
+│   └── utils.nix - Utility command definitions
+├── lib/ (2 files)
+│   ├── shell-hook.nix - Dev shell welcome message
+│   └── mini-notify-config.lua - Neovim notification config
+└── scripts/ (4 files)
+    ├── initPython.sh - Python project initialization
+    ├── initProject.sh - Project structure setup
+    ├── updateDeps.sh - Dependency update script
+    └── activateDevenv.sh - Devenv activation
+```
+
+### 2. Key Improvements
+
+#### Separation of Concerns
+- **Config**: Main configuration stays in flake.nix
+- **Overlays**: Package modifications isolated in overlays/
+- **Hosts**: Command definitions organized by language in hosts/
+- **Scripts**: Shell scripts extracted to scripts/ directory
+- **Helpers**: Utility functions in lib/
+
+#### Readability
+- Reduced main file from 688 to 261 lines (62% reduction)
+- Added strategic comments explaining key sections
+- Extracted long inline strings to separate files
+- Grouped related functionality together
+
+#### Maintainability
+- Language-specific changes isolated to dedicated files
+- Easy to add new languages (create new host/overlay files)
+- Easy to modify scripts without touching Nix code
+- Clear separation between different concerns
+
+#### Reusability
+- Individual overlays can be reused in other projects
+- Host definitions can be copied/modified independently
+- Scripts can be tested/modified separately
+- Modular design allows selective adoption
+
+### 3. Specific Extractions
+
+#### Shell Scripts (200+ lines → 4 files)
+- `initPython.sh`: Python project initialization logic
+- `initProject.sh`: Directory structure and git setup
+- `updateDeps.sh`: Dependency update automation
+- `activateDevenv.sh`: Devenv shell activation
+
+#### Overlays (100+ lines → 5 files)
+- `r.nix`: R package management with rix integration
+- `python.nix`: Python package configuration
+- `rix.nix`: rstats-on-nix package source
+- `theme.nix`: Neovim colorscheme handling
+- `project-scripts.nix`: Script wrapper generation
+
+#### Host Definitions (200+ lines → 5 files)
+- `python.nix`: marimo, ipy, py, initPython commands
+- `julia.nix`: jl, pluto, initJl commands
+- `r.nix`: R console command
+- `utils.nix`: initProject, updateDeps, devenv commands
+- `default.nix`: Merges all host configurations
+
+#### Helper Functions (40+ lines → 2 files)
+- `shell-hook.nix`: Dev shell welcome message generation
+- `mini-notify-config.lua`: Neovim notification filtering
+
+### 4. Added Documentation
+
+#### README.md
+- Overview of template purpose
+- Directory structure explanation
+- Benefits of modular design
+- Configuration instructions
+- Extension guidelines
+- Usage examples
+
+#### Inline Comments
+- Section headers in flake.nix
+- Explanation of key configuration blocks
+- Purpose of each import
+- Documentation of categories and settings
+
+### 5. Benefits Achieved
+
+1. **Maintainability**: 
+   - Changes to one language don't affect others
+   - Easy to locate and modify specific functionality
+   - Clear ownership of different components
+
+2. **Readability**:
+   - Main file is now scannable and understandable
+   - Related code grouped together
+   - Inline documentation guides users
+
+3. **Testability**:
+   - Scripts can be tested independently
+   - Overlays can be verified in isolation
+   - Smaller files are easier to debug
+
+4. **Extensibility**:
+   - Clear patterns for adding new languages
+   - Easy to add new commands
+   - Simple to customize per language
+
+5. **Learning**:
+   - New users can understand the template structure
+   - Examples in each file guide modifications
+   - Documentation explains purpose and usage
+
+## Migration Guide
+
+For users of the old template:
+1. The functionality remains identical
+2. Configuration in the main config section is the same
+3. All commands work exactly as before
+4. To customize, now edit the specific file in the appropriate directory
+
+## Future Improvements
+
+Possible future enhancements:
+- Add validation scripts for configuration
+- Create unit tests for individual modules
+- Add more language examples (Go, Rust, etc.)
+- Create a configuration wizard script
+- Add CI/CD integration examples