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

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

templates/rde/overlays/project-scripts.nix

@@ -0,0 +1,14 @@
+# Project scripts overlay
+config: final: prev: let
+  # Helper function to substitute config placeholders in scripts
+  substituteScript = scriptPath:
+    prev.lib.replaceStrings
+      ["@defaultPackageName@"]
+      [config.defaultPackageName]
+      (builtins.readFile scriptPath);
+in {
+  initPython = prev.writeShellScriptBin "initPython" (substituteScript ./scripts/initPython.sh);
+  initProject = prev.writeShellScriptBin "initProject" (substituteScript ./scripts/initProject.sh);
+  updateDeps = prev.writeShellScriptBin "updateDeps" (substituteScript ./scripts/updateDeps.sh);
+  activateDevenv = prev.writeShellScriptBin "activateDevenv" (substituteScript ./scripts/activateDevenv.sh);
+}

templates/rde/overlays/python.nix

@@ -0,0 +1,7 @@
+# Python packages overlay
+final: prev: {
+  python = prev.python3.withPackages (pyPackages:
+    with pyPackages; [
+      requests
+    ]);
+}

templates/rde/overlays/r.nix

@@ -0,0 +1,20 @@
+# R packages overlay
+final: prev: let
+  reqPkgs = with final.rpkgs.rPackages;
+    [
+      broom
+      data_table
+      janitor
+      languageserver
+      reprex
+      styler
+      tidyverse
+    ]
+    ++ (with final.extraRPackages; [
+      httpgd
+    ])
+    ++ (prev.lib.optional (builtins.pathExists ./r-packages.nix) (import ./r-packages.nix final.rpkgs));
+in {
+  quarto = final.rpkgs.quarto.override {extraRPackages = reqPkgs;};
+  rWrapper = final.rpkgs.rWrapper.override {packages = reqPkgs;};
+}

templates/rde/overlays/rix.nix

@@ -0,0 +1,4 @@
+# Rix overlay for R packages from rstats-on-nix
+inputs: final: prev: {
+  rpkgs = inputs.rixpkgs.legacyPackages.${prev.stdenv.hostPlatform.system};
+}

templates/rde/overlays/theme.nix

@@ -0,0 +1,12 @@
+# Extra theme packages overlay
+config: final: prev: let
+  extraTheme = {
+    plugin = prev.vimPlugins."${config.theme.extraColorschemePackage.plugin}";
+    name = config.theme.extraColorschemePackage.name;
+    config = {
+      lua = config.theme.extraColorschemePackage.extraLua;
+    };
+  };
+in {
+  inherit extraTheme;
+}