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+# GitHub Copilot Instructions for np Repository
+
+## Repository Overview
+
+This repository provides Nix flake templates for setting up Research Development Environments (RDE). The primary template is located in `templates/rde/` and is designed for data science and research projects supporting R, Python, and Julia.
+
+## Project Structure
+
+- `flake.nix` - Root flake defining available templates
+- `templates/rde/` - Main RDE template with Neovim-based development environment
+  - `flake.nix` - Template flake configuration with language support and tooling
+  - `flake.lock` - Locked dependencies for reproducibility
+  - `.envrc` - direnv configuration for automatic environment loading
+- `.github/workflows/` - CI/CD workflows for testing and updates
+  - `check.yml` - Tests RDE template on Ubuntu
+  - `check_macos.yml` - Tests RDE template on macOS
+  - `update.yml` - Automated daily dependency updates
+
+## Key Technologies
+
+- **Nix Flakes**: Reproducible development environments
+- **nixCats**: Custom Neovim configuration framework
+- **direnv**: Automatic environment loading
+- **Cachix**: Binary cache for faster builds (using `rde`, `rstats-on-nix`, and `nix-community` caches)
+
+## Language Support
+
+The RDE template supports multiple languages, controlled via `config.enabledLanguages` in `templates/rde/flake.nix`:
+
+- **R**: R wrapper, Quarto, air-formatter, language server, and custom R packages via overlays
+- **Python**: Python 3, basedpyright LSP, UV package manager
+- **Julia**: Julia REPL with Pluto.jl support
+
+## Development Commands
+
+The template provides project-specific commands (prefix with package name, default is `p`):
+
+- `p` - Launch Neovim
+- `p-g` - Launch Neovide GUI
+- `p-initProject` - Initialize project structure (data/, src/, docs/)
+- `p-updateDeps` - Update all dependencies (flake inputs, R packages, Python packages)
+- `p-r` - Launch R console
+- `p-py` / `p-ipy` - Launch Python/IPython REPL
+- `p-marimo` - Launch Marimo notebook
+- `p-jl` - Launch Julia REPL
+- `p-pluto` - Launch Pluto.jl notebook
+- `p-devenv` - Devenv integration (when enabled)
+
+## Nix Flake Conventions
+
+### Configuration Structure
+
+The RDE template uses a centralized `config` object at the top of `flake.nix`:
+
+```nix
+config = rec {
+  defaultPackageName = "p";
+  enabledLanguages = { julia = false; python = false; r = true; };
+  enabledPackages = { gitPlugins = enabledLanguages.r; devenv = false; };
+  theme = { colorscheme = "kanagawa"; background = "dark"; };
+};
+```
+
+### Overlays Pattern
+
+The template uses multiple overlays to extend nixpkgs:
+
+- `rOverlay` - Adds R packages via rix/rstats-on-nix
+- `pythonOverlay` - Configures Python packages
+- `rixOverlay` - Integrates R package snapshots from rstats-on-nix
+- `projectScriptsOverlay` - Custom shell scripts for project management
+- `extraPkgOverlay` - Additional theme and plugin configuration
+
+### Package Categories
+
+nixCats uses categories to organize functionality:
+
+- `lspsAndRuntimeDeps` - Language servers and runtime dependencies
+- `startupPlugins` - Neovim plugins loaded at startup
+- `optionalPlugins` - Plugins loaded on demand
+- `environmentVariables` - Language-specific environment setup
+- `extraWrapperArgs` - Additional wrapper arguments (e.g., unset PYTHONPATH for Python)
+
+## Testing & CI/CD
+
+### Local Testing
+
+```bash
+# Build the RDE template
+nix build ./templates/rde
+
+# Check the RDE template
+nix flake check ./templates/rde
+
+# Enter development shell
+nix develop ./templates/rde
+```
+
+### CI Workflows
+
+- **check.yml**: Runs on pushes to `templates/rde/flake.lock`, builds and checks the template on Ubuntu
+- **check_macos.yml**: Tests on macOS when `update_rde` branch is pushed
+- **update.yml**: Daily cron job that updates dependencies via `p-updateDeps` and creates PRs
+
+## Dependency Management
+
+### R Packages
+
+R packages are managed through rstats-on-nix pinned snapshots. The date is specified in the `rixpkgs.url` input:
+
+```nix
+rixpkgs.url = "github:rstats-on-nix/nixpkgs/2025-12-15";
+```
+
+Custom R packages can be added in `rOverlay` or via `r-packages.nix` file.
+
+### Python Packages
+
+Python packages use UV for management with nixpkgs Python as the interpreter:
+
+- Environment variables force UV to use nix Python: `UV_PYTHON_DOWNLOADS = "never"` and `UV_PYTHON = pkgs.python.interpreter`
+- PYTHONPATH is explicitly unset via `extraWrapperArgs`
+
+### Flake Inputs
+
+Dependencies are tracked in `flake.lock`. Key inputs include:
+
+- `nixpkgs` - NixOS 25.11
+- `rixpkgs` - R package snapshots from rstats-on-nix
+- `nixCats` - Custom Neovim configuration framework
+- `fran` - Extra R packages overlay
+- Plugin inputs for R.nvim ecosystem
+
+## Coding Style & Conventions
+
+1. **Nix Code**:
+   - Use `rec` for recursive attribute sets when needed
+   - Prefer `let...in` for local bindings
+   - Use `lib.optional` and `lib.optionalString` for conditional inclusion
+   - Keep configuration at the top of the file for easy customization
+
+2. **Shell Scripts** (in overlays):
+   - Always use `set -euo pipefail` for safety
+   - Provide user-friendly output with emojis and clear messages
+   - Check for existing files/directories before creating
+
+3. **Workflows**:
+   - Use `workflow_dispatch` for manual triggering
+   - Configure concurrency to cancel in-progress runs
+   - Use Cachix for binary caching with multiple caches
+
+## Common Patterns
+
+### Adding a New Language
+
+1. Add to `config.enabledLanguages`
+2. Create overlay for language-specific packages
+3. Add to `categoryDefinitions.lspsAndRuntimeDeps`
+4. Add command aliases in `packageDefinitions.hosts`
+5. Update `shellHook` with available commands
+
+### Adding Custom Scripts
+
+Add to `projectScriptsOverlay`:
+
+```nix
+myScript = prev.writeShellScriptBin "myScript" ''
+  #!/usr/bin/env bash
+  set -euo pipefail
+  # script content
+'';
+```
+
+### Plugin Integration
+
+For git-based plugins:
+1. Add flake input with `flake = false`
+2. Reference in nixCats inputs
+3. Add to `startupPlugins` or `optionalPlugins` categories
+
+## Important Notes
+
+- The template creates a `.gitignore` that excludes data files by default
+- R packages are installed to project-local `.Rlibs/` directory
+- Python UV is configured to never download Python, always using nixpkgs version
+- The template supports multiple platforms: x86_64-linux, aarch64-linux, aarch64-darwin
+- Neovim is wrapped with language-specific environment variables and PATH additions
+
+## File Generation
+
+When asked to initialize projects or generate common files, follow the patterns in:
+- `initProjectScript` for project structure
+- `.gitignore` template for what to exclude
+- `README.md` template for documentation structure