init wrapper-module config

overlays/README.md

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+# Overlays
+
+This directory contains composable Nix overlays used by the Neovim wrapper configuration. Each overlay is small and focused, so you can reuse or override them downstream.
+
+## Files
+
+- `r.nix`  
+  R-related overrides (rix overlay). Exposes `pkgs.rpkgs` from rstats-on-nix and creates pre-configured `rWrapper` and `quarto` with standard R packages.
+
+- `python.nix`  
+  Python-related overrides and package additions (e.g., extra Python packages).
+
+- `plugins.nix`  
+  Neovim plugin overrides (e.g., patching or pinning plugin derivations).
+
+- `default.nix`  
+  Aggregates and exports the overlays in a composable way. Includes the fran overlay for custom R packages.
+
+## Exports from `default.nix`
+
+`overlays/default.nix` exposes:
+
+- `rOverlay` - rix overlay for R packages from rstats-on-nix
+- `franOverlay` - fran overlay for custom R packages and tools  
+- `pythonOverlay`  
+- `pluginsOverlay`  
+- `dependencyOverlays` (list of overlays in order)  
+- `dependencyOverlay` (composed overlay via `lib.composeManyExtensions`)  
+- `default` (alias of `dependencyOverlay`)  
+- `dependencies` (alias of `dependencyOverlays`)
+
+## Downstream usage examples
+
+### Use the composed default overlay
+
+```/dev/null/example.nix#L1-18
+{
+  inputs,
+  ...
+}:
+let
+  overlayDefs = import ./overlays/default.nix inputs;
+in {
+  nixpkgs.overlays = [
+    overlayDefs.default
+  ];
+}
+```
+
+### Use specific overlays only
+
+```/dev/null/example.nix#L1-22
+{
+  inputs,
+  ...
+}:
+let
+  overlayDefs = import ./overlays/default.nix inputs;
+in {
+  nixpkgs.overlays = [
+    overlayDefs.rOverlay
+    overlayDefs.pluginsOverlay
+  ];
+}
+```
+
+### Extend with your own overlay (composition)
+
+```/dev/null/example.nix#L1-29
+{
+  inputs,
+  ...
+}:
+let
+  overlayDefs = import ./overlays/default.nix inputs;
+  myOverlay = final: prev: {
+    # Example: override a package
+    myTool = prev.myTool.override { /* ... */ };
+  };
+in {
+  nixpkgs.overlays = [
+    overlayDefs.default
+    myOverlay
+  ];
+}
+```
+
+## Adding a new overlay
+
+1. Create a new overlay file in this directory (e.g., `foo.nix`).
+2. Import it in `overlays/default.nix` and add it to `dependencyOverlays`.
+3. Optionally expose it as a named export (e.g., `fooOverlay`) for downstream reuse.
+
+## Notes
+
+- Keep overlays composable and focused.
+- Avoid monolithic overlays; prefer small, purpose-specific overlays.
+- When overriding plugins, keep patches minimal and document the intent.

overlays/default.nix

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+{ nixpkgs, ... }@inputs:
+let
+  lib = nixpkgs.lib;
+
+  rOverlay = import ./r.nix inputs;
+  franOverlay = inputs.fran.overlays.default;
+  pythonOverlay = import ./python.nix inputs;
+  pluginsOverlay = import ./plugins.nix inputs;
+
+  dependencyOverlays = [
+    rOverlay
+    franOverlay
+    pythonOverlay
+    pluginsOverlay
+  ];
+  dependencyOverlay = lib.composeManyExtensions dependencyOverlays;
+in
+{
+  inherit
+    rOverlay
+    franOverlay
+    pythonOverlay
+    pluginsOverlay
+    dependencyOverlays
+    dependencyOverlay;
+
+  # Named exports for downstream composition.
+  default = dependencyOverlay;
+  dependencies = dependencyOverlays;
+
+  overlays = {
+    inherit
+      rOverlay
+      franOverlay
+      pythonOverlay
+      pluginsOverlay
+      dependencyOverlays
+      dependencyOverlay;
+    default = dependencyOverlay;
+    dependencies = dependencyOverlays;
+  };
+}

overlays/plugins.nix

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+{ ... }:
+final: prev:
+{
+  codecompanion-nvim = prev.vimPlugins.codecompanion-nvim.overrideAttrs {
+    checkInputs = with prev.vimPlugins; [
+      blink-cmp
+      mini-nvim
+    ];
+    dependencies = [ prev.vimPlugins.plenary-nvim ];
+    nvimSkipModules = [
+      "codecompanion.actions.static"
+      "codecompanion.actions.init"
+      "minimal"
+      "codecompanion.providers.actions.fzf_lua"
+      "codecompanion.providers.completion.cmp.setup"
+      "codecompanion.providers.actions.telescope"
+      "codecompanion.providers.actions.snacks"
+    ];
+  };
+  zk-nvim = prev.vimPlugins.zk-nvim.overrideAttrs {
+    nvimSkipModules = [
+      "zk.pickers.fzf_lua"
+    ];
+  };
+}

overlays/python.nix

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+{ ... }:
+final: prev:
+let
+  reqPkgs = pyPackages:
+    with pyPackages; [
+      numpy
+    ];
+in
+{
+  basePythonPackages = reqPkgs;
+  python = prev.python3.withPackages reqPkgs;
+}

overlays/r.nix

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+# R packages overlay (rix)
+#
+# This overlay provides access to R packages from rstats-on-nix.
+#
+# rstats-on-nix maintains snapshots of CRAN packages built with Nix:
+# - Provides reproducible R package versions
+# - Ensures binary cache availability for faster builds
+# - Maintained by the rstats-on-nix community
+#
+# Available attributes after applying this overlay:
+#   - pkgs.rpkgs: R packages from rstats-on-nix
+#   - pkgs.rpkgs.rPackages: All CRAN packages
+#   - pkgs.rpkgs.quarto: Quarto publishing system
+#   - pkgs.rpkgs.rWrapper: R with package management
+#   - pkgs.rWrapper: R wrapper with standard packages pre-configured
+#   - pkgs.quarto: Quarto with R integration and standard packages
+#
+# Custom R packages and tools (radianWrapper, air-formatter) come from
+# the fran overlay which should be applied separately.
+#
+# To use specific R packages, reference them via:
+#   with pkgs.rpkgs.rPackages; [ package1 package2 ]
+#
+# Update the R snapshot date in flake.nix inputs section:
+#   rixpkgs.url = "github:rstats-on-nix/nixpkgs/YYYY-MM-DD"
+{rixpkgs, ...}: final: prev: let
+  # R packages from rstats-on-nix for the current system
+  rpkgs = rixpkgs.legacyPackages.${prev.stdenv.hostPlatform.system};
+
+  # Standard R packages used by default in rWrapper and quarto
+  reqPkgs = with rpkgs.rPackages; [
+    languageserver
+  ];
+in {
+  inherit rpkgs;
+  baseRPackages = reqPkgs;
+
+  # R wrapper with standard packages
+  rWrapper = rpkgs.rWrapper.override {packages = reqPkgs;};
+
+  # Quarto with R integration
+  quarto = rpkgs.quarto.override {extraRPackages = reqPkgs;};
+
+  # Update helper for rix
+  updateR = import ../scripts/updater.nix { pkgs = final; };
+}