Add comprehensive inline documentation to all modules and enhance README

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

templates/rde/lib/mini-notify-config.lua

@@ -1,16 +1,42 @@
--- Configuration for mini.notify
--- Filters out some verbose LSP progress notifications
+-- Neovim notification configuration using mini.notify
+--
+-- This file configures the mini.notify plugin to filter out verbose LSP messages.
+-- It reduces noise from the Lua language server during development.
+--
+-- What it does:
+--   - Sets up mini.notify as the notification handler
+--   - Filters out "Diagnosing" and "semantic tokens" messages from lua_ls
+--   - Keeps all other notifications visible
+--
+-- Usage:
+--   Loaded automatically via flake.nix:
+--   optionalLuaPreInit.project = [(builtins.readFile ./lib/mini-notify-config.lua)]
+--
+-- Customization:
+--   - Add more patterns to filter in the predicate function
+--   - Filter notifications from other LSP servers by client_name
+--   - Adjust notification display settings in setup() call
+
+-- Predicate function to filter notifications
+-- Returns true if notification should be shown, false to hide it
 local predicate = function(notif)
+  -- Keep all non-LSP notifications
   if not (notif.data.source == "lsp_progress" and notif.data.client_name == "lua_ls") then
     return true
   end
-  -- Filter out some LSP progress notifications from 'lua_ls'
+  -- Filter out specific verbose LSP progress notifications from lua_ls
+  -- These messages are too frequent and not useful during development
   return notif.msg:find("Diagnosing") == nil and notif.msg:find("semantic tokens") == nil
 end
 
+-- Custom sort function that applies filtering
+-- Filters notification array before sorting
 local custom_sort = function(notif_arr)
   return MiniNotify.default_sort(vim.tbl_filter(predicate, notif_arr))
 end
 
+-- Initialize mini.notify with custom configuration
 require("mini.notify").setup({ content = { sort = custom_sort } })
+
+-- Set mini.notify as the default notification handler
 vim.notify = MiniNotify.make_notify()

templates/rde/lib/shell-hook.nix

@@ -1,8 +1,27 @@
 # Shell hook configuration
+#
+# This module generates the welcome message displayed when entering the dev shell.
+# It provides information about available commands and how to get started.
+#
+# The message includes:
+#   - Project name and welcome banner
+#   - Quick start instructions (initProject, updateDeps)
+#   - List of all available commands based on enabled languages
+#   - Instructions for editing configuration
+#
+# Commands are conditionally shown based on config.enabledLanguages settings.
+# This ensures users only see commands relevant to their configuration.
+#
+# Usage:
+#   Imported in flake.nix as:
+#   shellHook = import ./lib/shell-hook.nix config pkgs;
+#
 # Generates the help message displayed when entering the dev shell
 config: pkgs: let
   inherit (config) defaultPackageName enabledLanguages enabledPackages;
   
+  # Build dynamic list of available commands based on enabled languages
+  # Filters out empty strings for disabled languages
   shellCmds = pkgs.lib.concatLines (pkgs.lib.filter (cmd: cmd != "") [
     (pkgs.lib.optionalString enabledLanguages.r "  - ${defaultPackageName}-r: Launch R console")
     (pkgs.lib.optionalString enabledLanguages.julia "  - ${defaultPackageName}-jl: Launch Julia REPL")