diff --git a/install.sh b/install.sh
index 3ad15b3..fdb7921 100755
--- a/install.sh
+++ b/install.sh
@@ -35,6 +35,9 @@ PURPLE='\033[0;35m'
 # Other params
 PROMPT_TIMEOUT=15 # When user is prompted for input, skip after x seconds
 
+# Clear the screen
+clear
+
 # Start timer
 start_time=`date +%s`
 
@@ -54,6 +57,23 @@ make_banner () {
   echo -e "\n${banner}\n${RESET}"
 }
 
+# Explain to the user what changes will be made
+make_intro () {
+  C2="\033[0;35m"
+  C3="\x1b[2m"
+  echo -e "${CYAN_B}The seup script will do the following:${RESET}"
+  echo -e "${C2}(1) Pre-Setup Tasls"
+  echo -e "  ${C3}- Check that all requirements are met, and system is compatible"
+  echo -e "${C2}(2) Setup Dotfiles"
+  echo -e "  ${C3}- Clone or update dotfiles from git, and apply symlinks"
+  echo -e "${C2}(3) Install packages"
+  echo -e "  ${C3}- Update packeges, and prompt to install apps"
+  echo -e "${C2}(4) Configure sytstem"
+  echo -e "  ${C3}- Setup Vim, Tmux and ZSH plugins"
+  echo -e "  ${C3}- Configure OS and apply app user preferences"
+  echo -e "\n${PURPLE}You will be prompted at each stage, before any changes are made.${RESET}"
+}
+
 # Checks if a given package is installed
 command_exists () {
   hash "$1" 2> /dev/null
@@ -83,6 +103,18 @@ function pre_setup_tasks () {
   # Show starting banner
   make_banner "${TITLE}" "${CYAN_B}" 1
 
+  # Print list of what will be applied
+  make_intro
+
+  # Confirm user would like to proceed
+  echo -e "\n${CYAN_B}Are you happy to continue? (y/N)${RESET}"
+  read -t $PROMPT_TIMEOUT -n 1 -r
+  if [[ ! $REPLY =~ ^[Yy]$ ]]; then
+    echo -e "\n${PURPLE}No worries, feel free to come back another time.\nTerminating...${RESET}"
+    exit 0
+  fi
+  echo
+
   # Verify required packages are installed
   system_verify "git" true
   system_verify "zsh" false
@@ -145,10 +177,21 @@ function apply_preferences () {
   sh "${TMUX_PLUGIN_MANAGER_PATH}/tpm/bin/install_plugins"
   sh "${XDG_DATA_HOME}/tmux/plugins/tpm/bin/install_plugins"
   
-
   # Install / update ZSH plugins with Antigen
   echo -e "${PURPLE}Installing ZSH Plugins${RESET}"
   /bin/zsh -i -c "antigen update && antigen-apply"
+
+  # Apply general system, app and OS security preferences (prompt user first)
+  read -t $PROMPT_TIMEOUT -p "$(echo -e $CYAN_B)Would you like to apply system preferences? (y/N)" -n 1 -r
+  if [[ $REPLY =~ ^[Yy]$ ]]; then
+    if [ "$system_type" = "Darwin" ]; then
+      echo -e "\n${PURPLE}Applying MacOS system preferences, ensure you've understood before proceeding${RESET}\n"
+      macos_settings_dir="$DOTFILES_DIR/system-specific/macos/system-settings"
+      for macScript in "macos-security.sh" "macos-preferences.sh" "macos-apps.sh"; do
+        chmod +x $macos_settings_dir/$macScript && $macos_settings_dir/$macScript --quick-exit
+      done
+    fi
+  fi
 }
 
 # Setup Brew, install / update packages, organize launchpad and checks for macOS updates
@@ -164,9 +207,9 @@ function intall_macos_packages () {
     fi
   fi
   # Update / Install the Homebrew packages in ~/.Brewfile
-  if command_exists brew && [ -f "$HOME/.Brewfile" ]
+  if command_exists brew && [ -f "$DOTFILES_DIR/installs/Brewfile" ]
   then
-    echo -e "${PURPLE}Updating homebrew and packages...${RESET}"
+    echo -e "\n${PURPLE}Updating homebrew and packages...${RESET}"
     brew update
     brew upgrade
     brew bundle --global --file $HOME/.Brewfile
@@ -175,17 +218,20 @@ function intall_macos_packages () {
     echo -e "${PURPLE}Skipping Homebrew as requirements not met${RESET}"
   fi
   # Restore launchpad structure with lporg
-  if ! command_exists lporg && [ -f "$DOTFILES_DIR/configs/macos/launchpad.yml" ]; then
+  launchpad_layout="${DOTFILES_DIR}/system-specific/macos/app-configs/launchpad.yml"
+  if command_exists lporg && [ -f $launchpad_layout ]; then
     echo -e "${PURPLE}Restoring Launchpad Layout...${RESET}"
-    lporg load "$DOTFILES_DIR/configs/macos/launchpad.yml"
+    lporg load $launchpad_layout
   fi
   # Check for MacOS software updates, and ask user if they'd like to install
   echo -e "${PURPLE}Checking for software updates...${RESET}"
   pending_updates=$(softwareupdate -l 2>&1)
   if [[ ! $pending_updates == *"No new software available."* ]]; then
-    read -t $PROMPT_TIMEOUT -p "$(echo -e $CYAN_B)A new macOS software update is available.\
-    Would you like to install it now?$(echo -e $RESET) (y/N)" -n 1 -r
+    echo -e "${PURPLE}A new version of Mac OS is availbile${RESET}"
+    read -t $PROMPT_TIMEOUT -p "$(echo -e $CYAN_B)Would you like to update to the latest version of MacOS? (y/N)" -n 1 -r
+    echo -e "${RESET}"
     if [[ $REPLY =~ ^[Yy]$ ]]; then
+      echo "${PURPLE}Updating MacOS${RESET}"
       softwareupdate -i -a
     fi
   else
@@ -196,16 +242,11 @@ function intall_macos_packages () {
 
 # Based on system type, uses appropriate package manager to install / updates apps
 function install_packages () {
-
   read -t $PROMPT_TIMEOUT -p "$(echo -e $CYAN_B)Would you like to install / update system packages? (y/N) " -n 1 -r
   if [[ ! $REPLY =~ ^[Yy]$ ]]; then
     echo -e "\n${PURPLE}Skipping package installs${RESET}"
     return
   fi
-  # Ask for users password
-  echo -e "\n${PURPLE}Some install steps may require elevated permissions.${CYAN_B}\n\
-  You can enter your password now, to avoid typing it for each stage, or Ctrl+C to skip.${RESET}"
-  sudo -v
   # Mac OS
   if [ "$system_type" = "Darwin" ]; then
     intall_macos_packages
@@ -220,15 +261,25 @@ function finishing_up () {
   # Print success message, and time taken
   total_time=$((`date +%s`-start_time))
   make_banner "✨ Dotfiles configured succesfully in $total_time seconds" ${GREEN_B} 1
+  echo -e "\033[0;92m     .--.\n    |o_o |\n    |:_/ |\n   // \
+  \ \\ \n  (|     | ) \n /'\_   _/\`\\ \n \\___)=(___/\n"
   
   # Exit script with success code
+  echo -e "${CYAN_B}Press any key to exit.${RESET}\n"
+  read -t $PROMPT_TIMEOUT -n 1 -s
   exit 0
 }
 
+# If --help flag passed in, just show the help menu
+if [[ $* == "--help" ]]; then
+  make_intro
+  exit 0
+fi
+
 # Let's Begin!
 pre_setup_tasks   # Print start message, and check requirements are met
 setup_dot_files   # Clone / updatae dotfiles, and create the symlinks
-apply_preferences # Apply settings for individual applications
 install_packages  # Prompt to install / update OS-specific packages
+apply_preferences # Apply settings for individual applications
 finishing_up      # Refresh current session, print summary and exit
 # All done :)