.github/workflows/check.yml

@@ -25,14 +25,14 @@ jobs:
       matrix:
         os: [ubuntu-latest]
     steps:
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v5
     - uses: wimpysworld/nothing-but-nix@main
       with:
         hatchet-protocol: 'carve'
     - uses: cachix/install-nix-action@v31
       with:
         github_access_token: ${{ secrets.GITHUB_TOKEN }}
-    - uses: cachix/cachix-action@v17
+    - uses: cachix/cachix-action@v16
       with:
         name: rde
         authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
@@ -118,14 +118,14 @@ jobs:
   test-with-python:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v5
     - uses: wimpysworld/nothing-but-nix@main
       with:
         hatchet-protocol: 'carve'
     - uses: cachix/install-nix-action@v31
       with:
         github_access_token: ${{ secrets.GITHUB_TOKEN }}
-    - uses: cachix/cachix-action@v17
+    - uses: cachix/cachix-action@v16
       with:
         name: rde
         authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
@@ -174,14 +174,14 @@ jobs:
   test-with-julia:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v5
     - uses: wimpysworld/nothing-but-nix@main
       with:
         hatchet-protocol: 'carve'
     - uses: cachix/install-nix-action@v31
       with:
         github_access_token: ${{ secrets.GITHUB_TOKEN }}
-    - uses: cachix/cachix-action@v17
+    - uses: cachix/cachix-action@v16
       with:
         name: rde
         authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'

.github/workflows/check_ed.yml

@@ -1,26 +0,0 @@
-name: "Test ed template MacOS"
-on:
-  workflow_dispatch: # allows manual triggering
-  push:
-    branches:
-      - 'update_rde'
-concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: true
-jobs:
-  tests:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [macos-latest, ubuntu-latest]
-    steps:
-    - uses: actions/checkout@v6
-    - uses: cachix/install-nix-action@v31
-      with:
-        github_access_token: ${{ secrets.GITHUB_TOKEN }}
-    - uses: cachix/cachix-action@v17
-      with:
-        name: rde
-        authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
-        extraPullNames: rstats-on-nix, nix-community
-    - run: nix build ./templates/ed

.github/workflows/check_macos.yml

@@ -14,14 +14,13 @@ jobs:
       matrix:
         os: [macos-latest]
     steps:
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v5
     - uses: cachix/install-nix-action@v31
       with:
         github_access_token: ${{ secrets.GITHUB_TOKEN }}
-    - uses: cachix/cachix-action@v17
+    - uses: cachix/cachix-action@v16
       with:
         name: rde
         authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
         extraPullNames: rstats-on-nix, nix-community
     - run: nix build ./templates/rde
-    - run: nix build ./templates/ed

.github/workflows/flakehub-publish-rolling.yml

@@ -10,7 +10,7 @@ jobs:
       id-token: "write"
       contents: "read"
     steps:
-      - uses: "actions/checkout@v6"
+      - uses: "actions/checkout@v5"
         with:
           persist-credentials: false
       - uses: "DeterminateSystems/determinate-nix-action@v3"

.github/workflows/update.yml

@@ -10,24 +10,25 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v6
+        uses: actions/checkout@v5
       - uses: wimpysworld/nothing-but-nix@main
         with:
           hatchet-protocol: 'carve'
       - uses: cachix/install-nix-action@v31
         with:
           github_access_token: ${{ secrets.GITHUB_TOKEN }}
-      - uses: cachix/cachix-action@v17
+      - uses: cachix/cachix-action@v16
         with:
           name: rde
           authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
           extraPullNames: rstats-on-nix, nix-community
-      - name: Update ed flake.lock
+      - run: cd templates/rde/ && nix develop -c p-updateDeps
-        uses: DeterminateSystems/update-flake-lock@v28
+      - name: Update n flake.lock
+        uses: DeterminateSystems/update-flake-lock@v27
         with:
           token: ${{ secrets.GH_TOKEN_FOR_UPDATES }}
           branch: update_rde
-          path-to-flake-dir: "templates/ed"
+          path-to-flake-dir: "templates/rde"
           pr-title: "Update RDE flake.lock" # Title of PR to be created
           pr-labels: |                  # Labels to be set on the PR
             dependencies

flake.nix

@@ -6,11 +6,7 @@
         path = ./templates/rde;
         description = "Research Development Environment";
       };
-      ed = {
-        path = ./templates/ed;
-        description = "Simple nvim Environment";
-      };
     };
-    defaultTemplate = self.templates.ed;
+    defaultTemplate = self.templates.rde;
   };
 }

templates/ed/.envrc

@@ -1 +0,0 @@
-use flake

templates/ed/.gitignore

@@ -1 +0,0 @@
-.nvimcom

templates/ed/README.md

@@ -1,73 +0,0 @@
-# Project Editor
-
-A per-project Neovim wrapper built with [nix-wrapper-modules](https://birdeehub.github.io/nix-wrapper-modules/) and [nvimConfig](https://github.com/dwinkler1/nvimConfig).
-
-## Setup
-
-The flake provides two entry points:
-
-| Command | What you get |
-|---|---|
-| `direnv allow` / `nix develop` | **(Recommended)** A shell with `nv` and all enabled language toolchains (R, Python, Julia, Quarto) on `PATH`. |
-| `nix run` | Launches only the `nv` editor. Language toolchains (R, Python, etc.) are **not** on `PATH`. |
-
-### With direnv (recommended)
-
-```bash
-direnv allow   # enter the devShell automatically
-nv             # launch the pre-configured Neovim
-R              # R REPL is available (if enabled in flake.nix)
-```
-
-### Without direnv
-
-```bash
-nix develop    # enter the devShell manually
-nv             # launch Neovim
-R              # R REPL is available (if enabled in flake.nix)
-```
-
-> **Why `nix run` only gives the editor:** The flake's `packages.default` is the wrapped Neovim binary. Language toolchains (R, radian, quarto, etc.) live in `devShells.default`. Use `nix develop` (or `direnv allow`) to get the full environment.
-
-## Configuration
-
-The `flake.nix` is the single source of truth. Key knobs:
-
-| Option | What it controls |
-|---|---|
-| `cats` | Toggle language support (nix, r, python, julia, etc.) |
-| `settings.lang_packages.<lang>` | Language-specific packages installed in the wrapper |
-| `settings.colorscheme` | Neovim colorscheme |
-| `settings.background` | `"dark"` or `"light"` |
-| `settings.wrapRc` | When `true`, init.lua is embedded (rebuild to change); when `false`, init.lua is external (reload without rebuild) |
-| `binName` | The wrapper binary name (`nv` by default) |
-| `env` | Environment variables set in the wrapper |
-| `extraPackages` | Extra system packages available in the wrapper's PATH |
-| `specs.extraLua` | Inject lazy.nvim plugin specs |
-
-### Adding packages without editing flake.nix
-
-Create any of these optional files in the project root to add dependencies without modifying `flake.nix`:
-
-- **`python-packages.nix`** — receives `python3Packages`, return a list of packages:
-  ```nix
-  p: with p; [ numpy scipy ]
-  ```
-
-- **`r-packages.nix`** — receives `rpkgs` (includes `rPackages`), return a list:
-  ```nix
-  p: with p.rPackages; [ ggplot2 data.table ]
-  ```
-
-- **`julia-packages.nix`** — no arguments, return a list of package name strings:
-  ```nix
-  [ "DataFrames" "Plots" ]
-  ```
-
-## Formatting
-
-```bash
-nix fmt
-```
-
-Uses `nixfmt-rfc-style` pinned via the flake's `formatter` output.

templates/ed/flake.lock

@@ -1,175 +0,0 @@
-{
-  "nodes": {
-    "fran": {
-      "inputs": {
-        "nixpkgs": [
-          "rixpkgs"
-        ]
-      },
-      "locked": {
-        "lastModified": 1776413584,
-        "narHash": "sha256-xqqv46MTveuT4yJH2YihmbHGy5mdLnnLFDebVmUws/E=",
-        "owner": "dwinkler1",
-        "repo": "fran",
-        "rev": "da09626e4dd8f0f57078b3a04e0443a8c20defa1",
-        "type": "github"
-      },
-      "original": {
-        "owner": "dwinkler1",
-        "repo": "fran",
-        "type": "github"
-      }
-    },
-    "nixpkgs": {
-      "locked": {
-        "lastModified": 1778869304,
-        "narHash": "sha256-30sZNZoA1cqF5JNO9fVX+wgiQYjB7HJqqJ4ztCDeBZE=",
-        "owner": "NixOS",
-        "repo": "nixpkgs",
-        "rev": "d233902339c02a9c334e7e593de68855ad26c4cb",
-        "type": "github"
-      },
-      "original": {
-        "owner": "NixOS",
-        "ref": "nixos-unstable",
-        "repo": "nixpkgs",
-        "type": "github"
-      }
-    },
-    "nvimConfig": {
-      "inputs": {
-        "fran": [
-          "fran"
-        ],
-        "nixpkgs": [
-          "nixpkgs"
-        ],
-        "plugins-cmp-pandoc-references": "plugins-cmp-pandoc-references",
-        "plugins-r": "plugins-r",
-        "r-nvim-nix": "r-nvim-nix",
-        "rixpkgs": [
-          "rixpkgs"
-        ],
-        "wrappers": "wrappers"
-      },
-      "locked": {
-        "lastModified": 1779362150,
-        "narHash": "sha256-y3JTpxmNgtEYG1m21Ymvdmrul/WvJzOCX45AlV21aak=",
-        "owner": "dwinkler1",
-        "repo": "nvimConfig",
-        "rev": "af6d975129768cce36ac4c46198ab2b3ebaafad3",
-        "type": "github"
-      },
-      "original": {
-        "owner": "dwinkler1",
-        "repo": "nvimConfig",
-        "type": "github"
-      }
-    },
-    "plugins-cmp-pandoc-references": {
-      "flake": false,
-      "locked": {
-        "lastModified": 1743491695,
-        "narHash": "sha256-XsdneGNJzmRBggk8lz9JNDQYk7wbYfUAF2oZLXzFb9c=",
-        "owner": "jmbuhr",
-        "repo": "cmp-pandoc-references",
-        "rev": "130eae4f75029d6495808e0ea4b769fa1ce4c9ac",
-        "type": "github"
-      },
-      "original": {
-        "owner": "jmbuhr",
-        "repo": "cmp-pandoc-references",
-        "type": "github"
-      }
-    },
-    "plugins-r": {
-      "flake": false,
-      "locked": {
-        "lastModified": 1776905071,
-        "narHash": "sha256-dXox6qEs1VDE7vPNDoN8bY4g06uj1IEs6uki72w8lpA=",
-        "owner": "R-nvim",
-        "repo": "R.nvim",
-        "rev": "582f2af11290ac067e49018db38e12a511325556",
-        "type": "github"
-      },
-      "original": {
-        "owner": "R-nvim",
-        "ref": "v0.99.4",
-        "repo": "R.nvim",
-        "type": "github"
-      }
-    },
-    "r-nvim-nix": {
-      "inputs": {
-        "nixpkgs": [
-          "nvimConfig",
-          "rixpkgs"
-        ],
-        "rnvimsrc": [
-          "nvimConfig",
-          "plugins-r"
-        ]
-      },
-      "locked": {
-        "lastModified": 1778684156,
-        "narHash": "sha256-Z4y1tQfkIsPK4NRxGn668HMDfWxnxNxSJ0CAOOXiIfY=",
-        "owner": "dwinkler1",
-        "repo": "r_nvim_nix",
-        "rev": "2f49dfee27886068e2f49cbd54558ce4cc424c82",
-        "type": "github"
-      },
-      "original": {
-        "owner": "dwinkler1",
-        "repo": "r_nvim_nix",
-        "type": "github"
-      }
-    },
-    "rixpkgs": {
-      "locked": {
-        "lastModified": 1771303851,
-        "narHash": "sha256-tgveHozOJ2D/mi3LxVy/FcmLFDlM5XKZxsNB2XpvzaM=",
-        "owner": "dwinkler1",
-        "repo": "rixpkgs",
-        "rev": "af2dd3f7b4b172077747c0869d4e30702fb71b0e",
-        "type": "github"
-      },
-      "original": {
-        "owner": "dwinkler1",
-        "repo": "rixpkgs",
-        "rev": "af2dd3f7b4b172077747c0869d4e30702fb71b0e",
-        "type": "github"
-      }
-    },
-    "root": {
-      "inputs": {
-        "fran": "fran",
-        "nixpkgs": "nixpkgs",
-        "nvimConfig": "nvimConfig",
-        "rixpkgs": "rixpkgs"
-      }
-    },
-    "wrappers": {
-      "inputs": {
-        "nixpkgs": [
-          "nvimConfig",
-          "nixpkgs"
-        ]
-      },
-      "locked": {
-        "lastModified": 1779297405,
-        "narHash": "sha256-VFoBwH7ZjVxCnvZTb5ODRXt70sLtWMxstive0N+RS50=",
-        "owner": "BirdeeHub",
-        "repo": "nix-wrapper-modules",
-        "rev": "e7ed7a1205945befdf2e0d73ba7df91d935e5af1",
-        "type": "github"
-      },
-      "original": {
-        "owner": "BirdeeHub",
-        "repo": "nix-wrapper-modules",
-        "type": "github"
-      }
-    }
-  },
-  "root": "root",
-  "version": 7
-}

templates/ed/flake.nix

@@ -1,203 +0,0 @@
-{
-  description = "Project Editor";
-
-  outputs = {
-    self,
-    nixpkgs,
-    nvimConfig,
-    ...
-  } @ inputs: let
-    # ── Shared language support flags ──────────────────────────────
-    # Used by both the neovim wrapper module and the devShell
-    cats = {
-      clickhouse = false;
-      gitPlugins = false;
-      julia = false;
-      lua = false;
-      markdown = false;
-      nix = true;
-      optional = false;
-      python = false;
-      r = false;
-    };
-
-    # ── Language package lists ────────────────────────────────────
-    # Shared between wrapper lang_packages and devShell toolchains.
-    # Accept pkgs so they work inside forAllSystems for each system.
-
-    rPackages = pkgs:
-      (with pkgs.rpkgs.rPackages; [
-        fixest
-        # pkgs.extraRPackages.musicMetadata
-      ])
-      ++ (
-        if builtins.pathExists ./r-packages.nix
-        # p: with p.rPackages; [ ... ]
-        then import ./r-packages.nix pkgs.rpkgs
-        else []
-      );
-
-    pythonPackages = pkgs:
-      (with pkgs.python3Packages; [
-        duckdb
-        polars
-      ])
-      ++ (
-        if builtins.pathExists ./python-packages.nix
-        # p: with p; [ ... ]
-        then import ./python-packages.nix pkgs.python3Packages
-        else []
-      );
-
-    juliaPackages =
-      ["StatsBase"]
-      ++ (
-        if builtins.pathExists ./julia-packages.nix
-        # [ ... ]
-        then import ./julia-packages.nix
-        else []
-      );
-
-    systems = ["aarch64-darwin" "x86_64-linux" "aarch64-linux"];
-    forAllSystems = nixpkgs.lib.genAttrs systems;
-    overlays = [inputs.nvimConfig.overlays.dependencies];
-  in {
-    formatter = forAllSystems (system: nixpkgs.legacyPackages.${system}.nixfmt-rfc-style);
-
-    packages = forAllSystems (system: let
-      pkgs = import nixpkgs {
-        inherit system overlays;
-        config = {allowUnfree = true;};
-      };
-      # Plain attrset — pkgs is captured from the surrounding scope,
-      # so the module system does not need lazy _module.args resolution.
-      projectSettings = {
-        inherit cats;
-        settings = let
-          # With `replace` packages are replaced otherwise they are merged with base packages
-          replace = pkgs.lib.mkForce;
-        in {
-          lang_packages = {
-            python = replace (pythonPackages pkgs);
-            r = replace (rPackages pkgs);
-            julia = replace juliaPackages;
-          };
-          colorscheme = "kanagawa";
-          background = "dark";
-          wrapRc = true;
-        };
-        binName = "nv";
-
-        env = {
-          IS_PROJECT_EDITOR = "1";
-        };
-
-        runtimePkgs = with pkgs; [
-          cowsay
-        ];
-
-        specs.extraLua = let
-          name = builtins.baseNameOf (builtins.toString ./.);
-        in {
-          data = pkgs.vimPlugins.mini-notify;
-          before = ["INIT_MAIN"];
-          config = ''
-            require("mini.notify").setup()
-            vim.notify = MiniNotify.make_notify()
-            vim.notify("Welcome to ${name}!")
-          '';
-        };
-      };
-      evalResult = nvimConfig.inputs.wrappers.lib.evalModules {
-        modules = [
-          nvimConfig.wrapperModules.default
-          projectSettings
-        ];
-      };
-    in {
-      default = evalResult.config.wrap {inherit pkgs;};
-    });
-
-    devShells = forAllSystems (system: let
-      pkgs = import nixpkgs {
-        inherit system overlays;
-        config = {allowUnfree = true;};
-      };
-      nv = self.packages.${system}.default;
-    in {
-      default = pkgs.mkShell {
-        shellHook = ''
-          exec nu
-          alias gst='git status'
-          alias glol='git log --oneline --graph --decorate'
-          alias gc='git commit'
-          alias gl='git pull'
-          alias gp='git push'
-        '';
-        packages =
-          [
-            nv
-            pkgs.git
-            pkgs.pre-commit
-            pkgs.nushell
-          ]
-          # ── R toolchain (R REPL, quarto, LSP, formatter) ─────
-          ++ pkgs.lib.optionals cats.r (let
-            r_packages = (pkgs.baseRPackages or []) ++ rPackages pkgs;
-          in [
-            (pkgs.rWrapper.override {packages = r_packages;})
-            pkgs.radianWrapper
-            pkgs.air-formatter
-            pkgs.yaml-language-server
-            pkgs.nvimcom
-            pkgs.rnvimserver
-          ])
-          # ── Python toolchain (interpreter, LSP, formatter) ────
-          ++ pkgs.lib.optionals cats.python [
-            (pkgs.python3.withPackages (ps: pkgs.basePythonPackages ps ++ pythonPackages pkgs))
-            pkgs.nodejs
-            pkgs.ruff
-            pkgs.basedpyright
-            pkgs.uv
-          ]
-          # ── Julia toolchain ───────────────────────────────────
-          ++ pkgs.lib.optionals cats.julia [
-            pkgs.julia-bin.withPackages
-            juliaPackages
-          ]
-          # ── Markdown toolchain (quarto, zk) ───────────────────
-          ++ (let
-            r_packages = (pkgs.baseRPackages or []) ++ rPackages pkgs;
-            quarto =
-              if cats.r
-              then pkgs.quarto.override {extraRPackages = r_packages;}
-              else pkgs.quarto;
-          in
-            pkgs.lib.optionals cats.markdown [
-              pkgs.python313Packages.pylatexenc
-              quarto
-              pkgs.zk
-            ]);
-      };
-    });
-  };
-
-  inputs = {
-    nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";
-    rixpkgs.url = "github:dwinkler1/rixpkgs/af2dd3f7b4b172077747c0869d4e30702fb71b0e";
-    fran = {
-      url = "github:dwinkler1/fran";
-      inputs = {
-        nixpkgs.follows = "rixpkgs";
-      };
-    };
-    nvimConfig = {
-      url = "github:dwinkler1/nvimConfig";
-      inputs = {
-        rixpkgs.follows = "rixpkgs";
-        nixpkgs.follows = "nixpkgs";
-        fran.follows = "fran";
-      };
-    };
-  };
-}

templates/rde/README.md

@@ -367,6 +367,11 @@ The CI runs on:
 
 This ensures that users can confidently use the template knowing that all advertised functionality has been verified.
 
+## Related Documentation
+
+- [REFACTORING.md](REFACTORING.md) - Technical details about the modular structure
+- [SUMMARY.md](SUMMARY.md) - Metrics and comparison with original template
+
 ## Usage
 
 Use this template with:

templates/rde/REFACTORING.md

@@ -0,0 +1,150 @@
+# 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

templates/rde/SUMMARY.md

@@ -0,0 +1,172 @@
+# Template Refactoring - Complete Summary
+
+## 🎯 Objective Achieved
+Successfully refactored the RDE template from a single 688-line file into a modular, maintainable structure.
+
+## 📊 Key Metrics
+
+| Aspect | Before | After | Improvement |
+|--------|--------|-------|-------------|
+| **Main file (flake.nix)** | 688 lines | 261 lines | **62% reduction** |
+| **File structure** | 1 monolithic file | 17 modular files | **Better organized** |
+| **Documentation** | 0 lines | 218 lines | **Fully documented** |
+| **Directories** | 0 | 5 organized dirs | **Clear structure** |
+
+## 📁 New Structure
+
+```
+templates/rde/
+├── 📄 flake.nix (261 lines)          # Main config - clean & commented
+├── 📖 README.md                      # User guide
+├── 📖 REFACTORING.md                 # Technical details
+│
+├── 📂 overlays/                      # Package configurations
+│   ├── r.nix                        # R packages
+│   ├── python.nix                   # Python packages
+│   ├── rix.nix                      # R nixpkgs source
+│   ├── theme.nix                    # Neovim themes
+│   └── project-scripts.nix          # Script wrappers
+│
+├── 📂 hosts/                         # Command definitions
+│   ├── default.nix                  # Merger
+│   ├── python.nix                   # Python commands
+│   ├── julia.nix                    # Julia commands
+│   ├── r.nix                        # R commands
+│   └── utils.nix                    # Utility commands
+│
+├── 📂 lib/                           # Helper functions
+│   ├── shell-hook.nix               # Welcome message
+│   └── mini-notify-config.lua       # Neovim config
+│
+└── 📂 scripts/                       # Shell scripts
+    ├── initPython.sh                # Python init
+    ├── initProject.sh               # Project setup
+    ├── updateDeps.sh                # Update deps
+    └── activateDevenv.sh            # Devenv activation
+```
+
+## ✨ Key Improvements
+
+### 1. **Separation of Concerns**
+- Configuration stays in main flake.nix
+- Language-specific code in dedicated files
+- Scripts separated from Nix code
+- Helpers isolated in lib/
+
+### 2. **Enhanced Readability**
+- Main file reduced from 688 → 261 lines
+- Strategic comments explain sections
+- Clear naming conventions
+- Logical grouping of related code
+
+### 3. **Better Maintainability**
+- Modify one language without affecting others
+- Easy to locate specific functionality
+- Clear patterns for adding features
+- Reduced risk of breaking changes
+
+### 4. **Improved Extensibility**
+- Add new languages: create host + overlay files
+- Add new commands: edit relevant host file
+- Modify scripts: edit .sh files directly
+- Customize behavior: clear config section
+
+### 5. **Comprehensive Documentation**
+- README.md: User-facing guide
+- REFACTORING.md: Technical details
+- Inline comments: Explain key sections
+- Examples: Show how to extend
+
+## 🔄 Backwards Compatibility
+
+✅ **Zero Breaking Changes**
+- All existing functionality preserved
+- Same configuration interface
+- All commands work identically
+- Migration is seamless
+
+## 🎓 Learning Benefits
+
+### For Users
+- Easier to understand template structure
+- Clear examples for customization
+- Self-documenting code organization
+- Guided by inline comments
+
+### For Developers
+- Easy to modify individual components
+- Clear separation aids debugging
+- Modular structure enables testing
+- Well-documented refactoring process
+
+## 📈 Before & After Comparison
+
+### Before Refactoring
+```nix
+{
+  description = "New Project";
+  outputs = { ... }: let
+    config = { ... };
+    # 200+ lines of inline bash scripts
+    initPython = ''
+      #!/usr/bin/env bash
+      # ... lots of bash code ...
+    '';
+    # 100+ lines of overlay definitions
+    rOverlay = final: prev: let
+      # ... complex overlay code ...
+    # 300+ lines of host definitions
+    hosts = {
+      marimo = let marimoInit = ''
+        # ... more inline bash ...
+      # ... continues for 688 lines total
+```
+
+### After Refactoring
+```nix
+{
+  description = "New Project";
+  outputs = { ... }: let
+    # Clear config section
+    config = { ... };
+
+    # Import from organized modules
+    rOverlay = import ./overlays/r.nix;
+    pythonOverlay = import ./overlays/python.nix;
+    # ... clean imports ...
+
+    # Main configuration
+    projectConfig = forSystems (system:
+      # ... focused on structure, not details
+```
+
+## 🚀 Next Steps
+
+The template is now:
+1. ✅ Well-organized and modular
+2. ✅ Fully documented
+3. ✅ Easy to maintain
+4. ✅ Simple to extend
+5. ✅ Ready for production use
+
+## 💡 Usage
+
+No changes required for existing users! The template works exactly as before, but now with:
+- Better code organization
+- Comprehensive documentation
+- Easier customization options
+- Clearer structure for learning
+
+## 📝 Files Modified
+
+- `flake.nix` - Simplified and reorganized
+- Created `overlays/` - Package configurations
+- Created `hosts/` - Command definitions
+- Created `lib/` - Helper functions
+- Created `scripts/` - Shell scripts
+- Added `README.md` - User documentation
+- Added `REFACTORING.md` - Technical guide
+
+## 🎉 Success!
+
+The refactoring is complete. The template is now significantly more maintainable, readable, and extensible while preserving all original functionality.

templates/rde/flake.lock

@@ -4,14 +4,17 @@
       "inputs": {
         "nixpkgs": [
           "rixpkgs"
+        ],
+        "nvimcom": [
+          "plugins-r"
         ]
       },
       "locked": {
-        "lastModified": 1776413584,
+        "lastModified": 1761271358,
-        "narHash": "sha256-xqqv46MTveuT4yJH2YihmbHGy5mdLnnLFDebVmUws/E=",
+        "narHash": "sha256-Yf1u/FvSKCD0sr0xmTE/Cwgy7H/YW2L/1R7tbxtLfDw=",
         "owner": "dwinkler1",
         "repo": "fran",
-        "rev": "da09626e4dd8f0f57078b3a04e0443a8c20defa1",
+        "rev": "3bcaf6aa8b74bb1f754e14d975d64bd970fdbe56",
         "type": "github"
       },
       "original": {
@@ -43,11 +46,11 @@
         ]
       },
       "locked": {
-        "lastModified": 1770172580,
+        "lastModified": 1765425579,
-        "narHash": "sha256-l/fKPLdKxq7PLRbExDxsS4Esel4yos/NFJOFcDpsm2E=",
+        "narHash": "sha256-XQLrlG8Uf1GOBy5EQlPP19foLfF3CY/ruQc9xonyGCQ=",
         "owner": "dwinkler1",
         "repo": "nixCatsConfig",
-        "rev": "98079a0844e53afd0c593c8f4d1ee5381baf36f0",
+        "rev": "7fc90930a9cb08aeccd575122f6fc1524ed2c71b",
         "type": "github"
       },
       "original": {
@@ -58,11 +61,11 @@
     },
     "nixCats_2": {
       "locked": {
-        "lastModified": 1769085828,
+        "lastModified": 1763330129,
-        "narHash": "sha256-TjhFIAtS628+/r3IuYWPcNa++mUMMDDG8PbSfFHXBiA=",
+        "narHash": "sha256-KbOeWIF52SV53BOeETGO2C5ewaV2Ex9iaXH7G72gOr8=",
         "owner": "BirdeeHub",
         "repo": "nixCats-nvim",
-        "rev": "43fbf4d12b0a613f1a792503da4bb2bf270173c7",
+        "rev": "c81551ed87db2aefab30a12cf7425ff94dc0ad64",
         "type": "github"
       },
       "original": {
@@ -73,11 +76,11 @@
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1777077449,
+        "lastModified": 1765838191,
-        "narHash": "sha256-AIiMJiqvGrN4HyLEbKAoCSRRYn0rnlW5VbKNIMIYqm4=",
+        "narHash": "sha256-m5KWt1nOm76ILk/JSCxBM4MfK3rYY7Wq9/TZIIeGnT8=",
         "owner": "nixos",
         "repo": "nixpkgs",
-        "rev": "a4bf06618f0b5ee50f14ed8f0da77d34ecc19160",
+        "rev": "c6f52ebd45e5925c188d1a20119978aa4ffd5ef6",
         "type": "github"
       },
       "original": {
@@ -138,16 +141,16 @@
     },
     "rixpkgs": {
       "locked": {
-        "lastModified": 1776958221,
+        "lastModified": 1765802109,
-        "narHash": "sha256-cOHLrMWifj8HQMIG6gMhGowwPAkyX/kijDx38wK8kUM=",
+        "narHash": "sha256-Aru0TG1mEhIJiaXElFopn5lrAE+pyxfF0JelHOIY4FQ=",
         "owner": "rstats-on-nix",
         "repo": "nixpkgs",
-        "rev": "db90c554b7172188324b84deea35ed5975e20e44",
+        "rev": "bdfc55ed37f7d1228a856be0f57876596b04477a",
         "type": "github"
       },
       "original": {
         "owner": "rstats-on-nix",
-        "ref": "2026-04-22",
+        "ref": "2025-12-15",
         "repo": "nixpkgs",
         "type": "github"
       }

templates/rde/flake.nix

@@ -219,7 +219,7 @@
     });
   };
   inputs = {
-    rixpkgs.url = "github:rstats-on-nix/nixpkgs/2026-04-22";
+    rixpkgs.url = "github:rstats-on-nix/nixpkgs/2025-12-15";
     nixpkgs.url = "github:nixos/nixpkgs/nixos-25.11";
     nixCats = {
       url = "github:dwinkler1/nixCatsConfig";
@@ -237,6 +237,7 @@
       url = "github:dwinkler1/fran";
       inputs = {
         nixpkgs.follows = "rixpkgs";
+        nvimcom.follows = "plugins-r";
       };
     };
     ## Git Plugins