Add comprehensive inline documentation to all modules and enhance README

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

templates/rde/hosts/r.nix

@@ -1,5 +1,26 @@
 # R-related host configurations
+#
+# This module defines R-related commands available in the dev shell.
+# R is configured with project-local package library and Quarto support.
+#
+# Available commands (when R is enabled):
+#   - <name>-r: Launch R console with packages
+#
+# How it works:
+#   - Uses rWrapper which includes all packages from overlays/r.nix
+#   - R_LIBS_USER=./.Rlibs enables project-local package installation
+#   - --no-save --no-restore ensures clean session startup
+#
+# Package management:
+#   - System packages: Edit overlays/r.nix
+#   - Project packages: Install with install.packages() in R
+#   - Custom packages: Create r-packages.nix in project root
+#
+# Dependencies: rWrapper, quarto, air-formatter (configured in flake.nix)
 config: pkgs: {
+  # r: R console with pre-configured packages
+  # Includes tidyverse, data.table, and other common packages
+  # Session starts without saving/restoring workspace
   r = {
     enable = config.enabledLanguages.r;
     path = {