Refactor template: extract scripts, overlays, and hosts into separate modules

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

templates/rde/README.md

@@ -0,0 +1,65 @@
+# Research Development Environment (RDE) Template
+
+This is a Nix flake template for setting up research development environments with support for R, Python, and Julia.
+
+## Structure
+
+The template is organized into several directories for better maintainability:
+
+```
+templates/rde/
+├── flake.nix              # Main flake configuration (290 lines)
+├── overlays/              # Nix overlays for packages
+│   ├── r.nix             # R packages configuration
+│   ├── python.nix        # Python packages configuration
+│   ├── rix.nix           # rstats-on-nix integration
+│   ├── theme.nix         # Neovim theme configuration
+│   └── project-scripts.nix # Project initialization scripts
+├── hosts/                 # Host/command configurations
+│   ├── default.nix       # Merges all host configs
+│   ├── python.nix        # Python commands (marimo, ipy, etc.)
+│   ├── julia.nix         # Julia commands (jl, pluto, etc.)
+│   ├── r.nix             # R commands
+│   └── utils.nix         # Utility commands (initProject, etc.)
+└── scripts/               # Shell scripts
+    ├── initPython.sh     # Initialize Python project
+    ├── initProject.sh    # Initialize project structure
+    ├── updateDeps.sh     # Update all dependencies
+    └── activateDevenv.sh # Activate devenv shell
+```
+
+## Benefits of This Structure
+
+1. **Modularity**: Each component is in its own file, making it easier to understand and modify
+2. **Maintainability**: Changes to one language or feature don't affect others
+3. **Readability**: Main flake.nix is now ~290 lines instead of 688
+4. **Reusability**: Individual modules can be easily reused or replaced
+5. **Testability**: Smaller files are easier to test and debug
+
+## Configuration
+
+Edit the `config` section in `flake.nix` to customize:
+
+- `defaultPackageName`: Name of your project/package
+- `enabledLanguages`: Enable/disable R, Python, Julia support
+- `enabledPackages`: Enable additional features like devenv
+- `theme`: Configure Neovim color scheme
+
+## Extending
+
+To add new functionality:
+
+- **New packages**: Add overlays in `overlays/`
+- **New commands**: Add host configs in `hosts/`
+- **New scripts**: Add shell scripts in `scripts/`
+- **New languages**: Create new host and overlay files
+
+## Usage
+
+Use this template with:
+
+```bash
+nix flake init -t github:dwinkler1/np#rde
+```
+
+Then run `direnv allow` or enter the dev shell with `nix develop`.