diff --git a/modules/common/neovim/config/misc.nix b/modules/common/neovim/config/misc.nix
index 2319c00..906016b 100644
--- a/modules/common/neovim/config/misc.nix
+++ b/modules/common/neovim/config/misc.nix
@@ -10,6 +10,7 @@
     pkgs.vimPlugins.which-key-nvim # Keybind helper
   ];
 
+  # Initialize some plugins
   setup.Comment = { };
   setup.colorizer = { };
   setup.glow = { };
diff --git a/modules/common/neovim/config/telescope.nix b/modules/common/neovim/config/telescope.nix
index 1bd5b5c..01c29a4 100644
--- a/modules/common/neovim/config/telescope.nix
+++ b/modules/common/neovim/config/telescope.nix
@@ -1,5 +1,7 @@
 { pkgs, dsl, ... }: {
 
+  # Telescope is a fuzzy finder that can work with different sub-plugins
+
   plugins = [
     pkgs.vimPlugins.telescope-nvim
     pkgs.vimPlugins.project-nvim
diff --git a/modules/common/neovim/config/toggleterm.lua b/modules/common/neovim/config/toggleterm.lua
index 7499132..2e9c6cb 100644
--- a/modules/common/neovim/config/toggleterm.lua
+++ b/modules/common/neovim/config/toggleterm.lua
@@ -12,6 +12,8 @@ vim.api.nvim_create_autocmd("TermOpen", {
     end,
 })
 
+-- These are all the different types of terminals we can trigger
+
 local terminal = require("toggleterm.terminal").Terminal
 
 local basicterminal = terminal:new()
diff --git a/modules/common/neovim/config/toggleterm.nix b/modules/common/neovim/config/toggleterm.nix
index ee67302..8dac46f 100644
--- a/modules/common/neovim/config/toggleterm.nix
+++ b/modules/common/neovim/config/toggleterm.nix
@@ -1,5 +1,7 @@
 { pkgs, dsl, ... }: {
 
+  # Toggleterm provides a floating terminal inside the editor for quick access
+
   plugins = [ pkgs.vimPlugins.toggleterm-nvim ];
 
   use.toggleterm.setup = dsl.callWith {
diff --git a/modules/common/neovim/config/tree.nix b/modules/common/neovim/config/tree.nix
index 60825c6..4a625d1 100644
--- a/modules/common/neovim/config/tree.nix
+++ b/modules/common/neovim/config/tree.nix
@@ -1,5 +1,7 @@
 { pkgs, dsl, ... }: {
 
+  # This plugin creates a side drawer for navigating the current project
+
   plugins = [ pkgs.vimPlugins.nvim-tree-lua pkgs.vimPlugins.nvim-web-devicons ];
 
   # Disable netrw eagerly
@@ -10,16 +12,16 @@
   };
 
   setup.nvim-tree = {
-    disable_netrw = true;
-    hijack_netrw = true;
-    sync_root_with_cwd = true;
-    respect_buf_cwd = true;
-    update_focused_file = {
+    disable_netrw = true; # Disable the built-in file manager
+    hijack_netrw = true; # Works as the file manager
+    sync_root_with_cwd = true; # Change project whenever currend dir changes
+    respect_buf_cwd = true; # Change to exact location of focused buffer
+    update_focused_file = { # Change project based on the focused buffer
       enable = true;
       update_root = true;
       ignore_list = { };
     };
-    diagnostics = {
+    diagnostics = { # Enable LSP and linter integration
       enable = true;
       icons = {
         hint = "";
@@ -28,7 +30,7 @@
         error = "";
       };
     };
-    renderer = {
+    renderer = { # Show files with changes vs. current commit
       icons = {
         glyphs = {
           git = {
@@ -43,6 +45,7 @@
         };
       };
     };
+    # Set keybinds and initialize program
     on_attach = dsl.rawLua ''
       function (bufnr)
         local api = require('nvim-tree.api')
@@ -58,7 +61,7 @@
         vim.keymap.set('n', 'v', api.node.open.vertical, opts('Open: Vertical Split'))
       end
     '';
-    view = {
+    view = { # Set look and feel
       width = 30;
       hide_root_folder = false;
       side = "left";
@@ -67,6 +70,7 @@
     };
   };
 
+  # Toggle the sidebar
   lua = ''
     vim.keymap.set("n", "<Leader>e", ":NvimTreeFindFileToggle<CR>", { silent = true })
   '';
diff --git a/modules/common/neovim/default.nix b/modules/common/neovim/default.nix
index 8a7a9f7..8051c04 100644
--- a/modules/common/neovim/default.nix
+++ b/modules/common/neovim/default.nix
@@ -18,11 +18,16 @@ in {
 
         home.packages = [ neovim ];
 
+        # Use Neovim as the editor for git commit messages
         programs.git.extraConfig.core.editor = "nvim";
+
+        # Set Neovim as the default app for text editing and manual pages
         home.sessionVariables = {
           EDITOR = "nvim";
           MANPAGER = "nvim +Man!";
         };
+
+        # Create quick aliases for launching Neovim
         programs.fish = {
           shellAliases = { vim = "nvim"; };
           shellAbbrs = {
@@ -31,12 +36,20 @@ in {
             vll = "nvim -c 'Telescope oldfiles'";
           };
         };
+
+        # Set Neovim as the kitty terminal "scrollback" (vi mode) option.
+        # Requires removing some of the ANSI escape codes that are sent to the
+        # scrollback using sed and baleia, as well as removing several
+        # unnecessary features.
         programs.kitty.settings.scrollback_pager = ''
           $SHELL -c 'sed -r "s/[[:cntrl:]]\]133;[AC]..//g" | ${neovim}/bin/nvim -c "setlocal nonumber norelativenumber nolist laststatus=0" -c "lua baleia = require(\"baleia\").setup({}); baleia.once(0)" -c "map <silent> q :qa!<CR>" -c "autocmd VimEnter * normal G"' '';
 
+        # Create a desktop option for launching Neovim from a file manager
+        # (Requires launching the terminal and then executing Neovim)
         xdg.desktopEntries.nvim = lib.mkIf pkgs.stdenv.isLinux {
           name = "Neovim wrapper";
           exec = "kitty nvim %F";
+          mimeType = [ "text/plain" "text/markdown" ];
         };
         xdg.mimeApps.defaultApplications = lib.mkIf pkgs.stdenv.isLinux {
           "text/plain" = [ "nvim.desktop" ];
@@ -45,9 +58,6 @@ in {
 
       };
 
-    # # Used for icons in Vim
-    # fonts.fonts = with pkgs; [ nerdfonts ];
-
   };
 
 }
diff --git a/modules/common/repositories/dotfiles.nix b/modules/common/repositories/dotfiles.nix
index fda2dc1..eabb1e5 100644
--- a/modules/common/repositories/dotfiles.nix
+++ b/modules/common/repositories/dotfiles.nix
@@ -1,5 +1,7 @@
 { config, pkgs, lib, ... }: {
 
+  # Allows me to make sure I can work on my dotfiles locally
+
   options.dotfiles.enable = lib.mkEnableOption "Clone dotfiles.";
 
   config = lib.mkIf config.dotfiles.enable {
diff --git a/modules/common/repositories/notes.nix b/modules/common/repositories/notes.nix
index 47e521b..7439258 100644
--- a/modules/common/repositories/notes.nix
+++ b/modules/common/repositories/notes.nix
@@ -1,5 +1,8 @@
 { config, ... }: {
 
+  # This is just a placeholder as I expect to interact with my notes in a
+  # certain location
+
   home-manager.users.${config.user} = {
 
     home.sessionVariables = {
diff --git a/modules/common/shell/charm.nix b/modules/common/shell/charm.nix
index b2972cf..4ea98aa 100644
--- a/modules/common/shell/charm.nix
+++ b/modules/common/shell/charm.nix
@@ -1,5 +1,7 @@
 { config, pkgs, lib, ... }: {
 
+  # Convenience utilities from charm.sh
+
   options.charm.enable = lib.mkEnableOption "Charm utilities.";
 
   config.home-manager.users.${config.user} = lib.mkIf config.charm.enable {
diff --git a/modules/common/shell/direnv.nix b/modules/common/shell/direnv.nix
index b5f5165..daddb31 100644
--- a/modules/common/shell/direnv.nix
+++ b/modules/common/shell/direnv.nix
@@ -1,5 +1,6 @@
 { config, ... }: {
 
+  # Enables quickly entering Nix shells when changing directories
   home-manager.users.${config.user}.programs.direnv = {
     enable = true;
     nix-direnv.enable = true;
diff --git a/modules/common/shell/fzf.nix b/modules/common/shell/fzf.nix
index 1f9819b..a36b0bb 100644
--- a/modules/common/shell/fzf.nix
+++ b/modules/common/shell/fzf.nix
@@ -1,5 +1,7 @@
 { config, ... }: {
 
+  # FZF is a fuzzy-finder for the terminal
+
   home-manager.users.${config.user} = {
 
     programs.fzf.enable = true;
diff --git a/modules/nixos/applications/calibre.nix b/modules/nixos/applications/calibre.nix
index 1a65f0f..4a95223 100644
--- a/modules/nixos/applications/calibre.nix
+++ b/modules/nixos/applications/calibre.nix
@@ -14,6 +14,8 @@
       home.packages = with pkgs; [ calibre ];
       # home.sessionVariables = { CALIBRE_USE_DARK_PALETTE = 1; };
     };
+
+    # Forces Calibre to use dark mode
     environment.sessionVariables = { CALIBRE_USE_DARK_PALETTE = "1"; };
   };
 }
diff --git a/modules/nixos/applications/nautilus.nix b/modules/nixos/applications/nautilus.nix
index cea607e..46223ee 100644
--- a/modules/nixos/applications/nautilus.nix
+++ b/modules/nixos/applications/nautilus.nix
@@ -18,12 +18,14 @@
 
     home-manager.users.${config.user} = {
 
+      # Quick button for launching nautilus
       xsession.windowManager.i3.config.keybindings = {
         "${
           config.home-manager.users.${config.user}.xsession.windowManager.i3.config.modifier
         }+n" = "exec --no-startup-id ${pkgs.gnome.nautilus}/bin/nautilus";
       };
 
+      # Generates a QR code and previews it with sushi
       programs.fish.functions = {
         qr = {
           body =
@@ -31,7 +33,7 @@
         };
       };
 
-      # Set default for opening directories
+      # Set Nautilus as default for opening directories
       xdg.mimeApps = {
         associations.added."inode/directory" = [ "org.gnome.Nautilus.desktop" ];
         # associations.removed = {
diff --git a/modules/nixos/system/auto-upgrade.nix b/modules/nixos/system/auto-upgrade.nix
new file mode 100644
index 0000000..0612042
--- /dev/null
+++ b/modules/nixos/system/auto-upgrade.nix
@@ -0,0 +1,47 @@
+{ config, pkgs, lib, ... }: {
+
+  # This setting only applies to NixOS, different on Darwin
+  nix.gc.dates = "03:03"; # Run every morning (but before upgrade)
+
+  # Update the system daily by pointing it at the flake repository
+  system.autoUpgrade = {
+    enable = config.server; # Only auto upgrade servers
+    dates = "03:33";
+    flake = "git+${config.dotfilesRepo}";
+    randomizedDelaySec = "25min";
+    operation = "switch";
+    allowReboot = true;
+    rebootWindow = {
+      lower = "00:01";
+      upper = "06:00";
+    };
+  };
+
+  # Create an email notification service for failed jobs
+  systemd.services."notify-email@" =
+    let address = "system@${config.mail.server}";
+    in {
+      enable = config.mail.enable;
+      environment.SERVICE_ID = "%i";
+      script = ''
+        TEMPFILE=$(mktemp)
+        echo "From: ${address}" > $TEMPFILE
+        echo "To: ${address}" >> $TEMPFILE
+        echo "Subject: Failure in $SERVICE_ID" >> $TEMPFILE
+        echo -e "\nGot an error with $SERVICE_ID\n\n" >> $TEMPFILE
+        set +e
+        systemctl status $SERVICE_ID >> $TEMPFILE
+        set -e
+        ${pkgs.msmtp}/bin/msmtp \
+            --file=${config.homePath}/.config/msmtp/config \
+            --account=system \
+            ${address} < $TEMPFILE
+      '';
+    };
+
+  # Send an email whenever auto upgrade fails
+  systemd.services.nixos-upgrade.onFailure =
+    lib.mkIf config.systemd.services."notify-email@".enable
+    [ "notify-email@%i.service" ];
+
+}
diff --git a/modules/nixos/system/default.nix b/modules/nixos/system/default.nix
index 8a6e27f..64757f0 100644
--- a/modules/nixos/system/default.nix
+++ b/modules/nixos/system/default.nix
@@ -1,6 +1,7 @@
 { config, pkgs, lib, ... }: {
 
-  imports = [ ./doas.nix ./journald.nix ./user.nix ./timezone.nix ];
+  imports =
+    [ ./auto-upgrade.nix ./doas.nix ./journald.nix ./user.nix ./timezone.nix ];
 
   config = lib.mkIf pkgs.stdenv.isLinux {
 
@@ -8,54 +9,6 @@
     system.stateVersion =
       config.home-manager.users.${config.user}.home.stateVersion;
 
-    # This setting only applies to NixOS, different on Darwin
-    nix.gc.dates = "weekly";
-
-    systemd.timers.nix-gc.timerConfig = { WakeSystem = true; };
-    systemd.services.nix-gc.postStop =
-      lib.mkIf (!config.server) "systemctl suspend";
-
-    # Update the system daily
-    system.autoUpgrade = {
-      enable = config.server; # Only auto upgrade servers
-      dates = "03:33";
-      flake = "git+${config.dotfilesRepo}";
-      randomizedDelaySec = "45min";
-      operation = "switch";
-      allowReboot = config.server; # Reboot servers
-      rebootWindow = {
-        lower = "00:01";
-        upper = "06:00";
-      };
-    };
-
-    # Create an email notification service for failed jobs
-    systemd.services."notify-email@" =
-      let address = "system@${config.mail.server}";
-      in {
-        enable = config.mail.enable;
-        environment.SERVICE_ID = "%i";
-        script = ''
-          TEMPFILE=$(mktemp)
-          echo "From: ${address}" > $TEMPFILE
-          echo "To: ${address}" >> $TEMPFILE
-          echo "Subject: Failure in $SERVICE_ID" >> $TEMPFILE
-          echo -e "\nGot an error with $SERVICE_ID\n\n" >> $TEMPFILE
-          set +e
-          systemctl status $SERVICE_ID >> $TEMPFILE
-          set -e
-          ${pkgs.msmtp}/bin/msmtp \
-              --file=${config.homePath}/.config/msmtp/config \
-              --account=system \
-              ${address} < $TEMPFILE
-        '';
-      };
-
-    # Send an email whenever auto upgrade fails
-    systemd.services.nixos-upgrade.onFailure =
-      lib.mkIf config.systemd.services."notify-email@".enable
-      [ "notify-email@%i.service" ];
-
   };
 
 }
diff --git a/modules/nixos/system/doas.nix b/modules/nixos/system/doas.nix
index f2cff94..ff61572 100644
--- a/modules/nixos/system/doas.nix
+++ b/modules/nixos/system/doas.nix
@@ -13,11 +13,11 @@
       doas = {
         enable = true;
 
-        # No password required
+        # No password required for trusted users
         wheelNeedsPassword = false;
 
         # Pass environment variables from user to root
-        # Also requires removing password here
+        # Also requires specifying that we are removing password here
         extraRules = [{
           groups = [ "wheel" ];
           noPass = true;
@@ -26,6 +26,7 @@
       };
     };
 
+    # Alias sudo to doas for convenience
     home-manager.users.${config.user}.programs.fish.shellAliases = {
       sudo = "doas";
     };
diff --git a/modules/nixos/system/journald.nix b/modules/nixos/system/journald.nix
index fe94a19..2b8582f 100644
--- a/modules/nixos/system/journald.nix
+++ b/modules/nixos/system/journald.nix
@@ -1,6 +1,7 @@
 { ... }: {
 
   # How long to keep journalctl entries
+  # This helps to make sure log disk usage doesn't grow too unwieldy
   services.journald.extraConfig = ''
     SystemMaxUse=100M
     MaxFileSec=1month
diff --git a/modules/nixos/system/user.nix b/modules/nixos/system/user.nix
index 3d2f09e..f86c685 100644
--- a/modules/nixos/system/user.nix
+++ b/modules/nixos/system/user.nix
@@ -1,4 +1,4 @@
-{ config, pkgs, lib, ... }: {
+{ config, lib, ... }: {
 
   options = {
 
@@ -11,7 +11,7 @@
 
   };
 
-  config = lib.mkIf (pkgs.stdenv.isLinux) {
+  config = {
 
     # Allows us to declaritively set password
     users.mutableUsers = false;