feat!: reorganize scripts into configure/, lib/, and sync/ directories

- Move configuration scripts from util/ to configure/
- Extract shared utilities into lib/ (colors, backup, packages)
- Move repo sync functionality to sync/ directory
- Add run.sh as main entry point replacing util/setup.sh
- Remove morning.sh (functionality moved to sync/repos.sh)
- Add tests for package management functions

Author: nickineering

MANUAL_STEPS.md

@@ -41,23 +41,18 @@ git config --global user.name "Your Name"
 git config --global user.email "Your email specifically for git"
 ```
 
-## Morning routine setup
+## GitLab repo sync setup
 
-To enable the `morning` command for GitLab repo syncing:
+To enable GitLab repo syncing:
 
-1. Create the work directory:
+1. Configure your GitLab group in `~/.env.sh`:
    ```bash
-   mkdir ~/work
+   export GITLAB_GROUP="your-group"
+   # Optional: exclude specific subdirectories (pipe-separated)
+   export GITLAB_EXCLUDE_DIRS="archived|sandbox"
    ```
 
-2. Configure your GitLab group in `~/.env.sh`:
-   ```bash
-   export MORNING_GITLAB_GROUP="your-group"
-   # Optional: exclude specific subdirectories
-   export MORNING_EXCLUDE_DIRS="unsynced|bugs"
-   ```
-
-3. Authenticate with GitLab:
+2. Authenticate with GitLab:
    ```bash
    glab auth login
    ```
@@ -112,9 +107,9 @@ sure to complete any steps noted:
 1. WhatsApp
 1. Zoom
 
-Finally, you need to run the following command in your terminal to finish the
-automated setups:
+Finally, after signing in to Firefox (to create the profile folder), run the
+following command to finish automated setup:
 
 ```bash
-chmod +x ~/projects/setup/util/after_signin.sh && ~/projects/setup/util/after_signin.sh
+~/projects/setup/configure/after_signin.sh
 ```

Makefile

@@ -8,7 +8,7 @@ test:
 	bats tests/
 
 setup:
-	./util/setup.sh
+	./run.sh
 
 fix:
 	shellharden --replace **/*.sh

bootstrap.sh

@@ -7,12 +7,15 @@
 # Bash strict mode
 set -euo pipefail
 
-# Print commands as they are run
-set -v
+# Guard: refuse to run as root
+if [ "$(id -u)" -eq 0 ]; then
+	echo "Error: Do not run this script as root" >&2
+	exit 1
+fi
 
 # Trap handler for cleanup on interruption
 CURRENT_STEP=""
-# shellcheck disable=SC2329  # Invoked by trap
+# shellcheck disable=SC2329 # Function appears unused but is invoked by trap
 cleanup_on_interrupt() {
 	echo "" >&2
 	echo "Bootstrap interrupted!" >&2
@@ -24,25 +27,22 @@ cleanup_on_interrupt() {
 }
 trap cleanup_on_interrupt INT TERM
 
-# Start running the print utility first so we can update the user on progress.
-# We must save the file first because we are on Bash 3.2
-if ! curl -fsSL https://raw.githubusercontent.com/nickineering/setup/master/util/print.sh >/tmp/print.sh; then
-	echo "Error: Failed to download print utility. Check your internet connection." >&2
-	exit 1
-fi
-# shellcheck source=util/print.sh
-source /tmp/print.sh
+# Colors for output
+green='\033[32m'
+yellow='\033[33m'
+cyan='\033[36m'
+bold='\033[1m'
+reset='\033[0m'
 
-print_green "Please leave everything closed and wait for your Mac to be configured. \
-This will take a while." "AUTOMATICALLY CONFIGURING MAC"
+echo -e "${bold}${cyan}=== AUTOMATICALLY CONFIGURING MAC ===${reset}"
+echo -e "${green}Please leave everything closed and wait for your Mac to be configured. This will take a while.${reset}"
 
 CURRENT_STEP="installing Homebrew"
 # Install Homebrew, a Mac package manager
 if command -v brew; then
-	brew upgrade || print_green "Warning: Some Homebrew packages failed to upgrade"
-	print_green "Upgraded Homebrew packages"
+	echo -e "${green}Homebrew already installed${reset}"
 else
-	print_green "Installing Homebrew..."
+	echo -e "${green}Installing Homebrew...${reset}"
 	HOMEBREW_INSTALL_SCRIPT=$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)
 	if [ "$HOMEBREW_INSTALL_SCRIPT" = "" ]; then
 		echo "Error: Failed to download Homebrew installer" >&2
@@ -53,7 +53,7 @@ else
 		exit 1
 	fi
 	eval "$(/opt/homebrew/bin/brew shellenv)"
-	print_green "Installed Homebrew"
+	echo -e "${green}Installed Homebrew${reset}"
 fi
 
 CURRENT_STEP="cloning setup repository"
@@ -62,14 +62,14 @@ mkdir -p ~/projects
 export SETUP=~/projects/setup
 brew install git # Use Homebrew so that updates are easy
 if [ -d "$SETUP" ]; then
-	git -C "$SETUP" pull || print_green "Warning: Failed to pull latest commits"
-	print_green "Pulled latest commits from repo"
+	git -C "$SETUP" pull || echo -e "${yellow}Warning: Failed to pull latest commits${reset}"
+	echo -e "${green}Pulled latest commits from repo${reset}"
 else
 	if ! git clone https://github.com/nickineering/setup.git "$SETUP"; then
 		echo "Error: Failed to clone setup repo" >&2
 		exit 1
 	fi
-	print_green "Cloned repo into projects directory"
+	echo -e "${green}Cloned setup repo into projects directory${reset}"
 fi
 
 CURRENT_STEP="installing modern Bash"
@@ -79,4 +79,4 @@ if ! brew install bash; then
 	echo "Error: Failed to install bash via Homebrew" >&2
 	exit 1
 fi
-source "$SETUP"/util/setup.sh
+"$SETUP"/run.sh

configure/after_signin.sh

@@ -0,0 +1,37 @@
+#!/opt/homebrew/bin/bash
+# shellcheck disable=SC2154 # Variables like $green are defined in lib/colors.sh
+#
+# Post-setup configuration for things that need apps to be launched first:
+# - Firefox: needs profile folder to exist (created on first launch)
+# - GitHub CLI: interactive authentication
+
+set -euo pipefail
+
+export SETUP=~/projects/setup
+export DOTFILES="$SETUP/linked"
+cd "$SETUP"
+
+source lib/colors.sh
+source lib/backup.sh
+
+echo -e "${bold}${cyan}=== Post-setup configuration ===${reset}"
+echo ""
+
+# Firefox settings (requires Firefox to have been launched once)
+source configure/firefox.sh
+if [[ "${FIREFOX_NEEDS_SETUP:-}" != "1" ]]; then
+	echo -e "${green}Configured Firefox${reset}"
+fi
+
+# GitHub CLI authentication
+if ! gh auth status &>/dev/null; then
+	echo ""
+	echo -e "${bold}GitHub CLI authentication${reset}"
+	gh auth login
+	echo -e "${green}Configured GitHub CLI${reset}"
+else
+	echo -e "${dim}GitHub CLI already authenticated${reset}"
+fi
+
+echo ""
+echo -e "${green}Done!${reset}"

util/configure_claude.sh configure/claude.shutil/configure_claude.sh renamed to configure/claude.sh

@@ -1,4 +1,6 @@
-#!/opt/homebrew/bin/bash
+# shellcheck shell=bash
+# shellcheck disable=SC2154 # Variables like $green are defined in lib/colors.sh
+# Sourced by run.sh
 
 # Configure Claude Code settings and instructions
 
@@ -10,20 +12,19 @@ CLAUDE_COPIED="$SETUP/copied/claude"
 mkdir -p "$CLAUDE_DIR"
 
 # Backup existing files
-source backup_or_delete.sh
 backup_or_delete "$CLAUDE_DIR/settings.json"
 backup_or_delete "$CLAUDE_DIR/CLAUDE.md"
 backup_or_delete "$CLAUDE_DIR/skills"
 
 # Symlink settings, instructions, and skills
-ln -s "$CLAUDE_DOTFILES/settings.json" "$CLAUDE_DIR/settings.json"
-ln -s "$CLAUDE_DOTFILES/CLAUDE.md" "$CLAUDE_DIR/CLAUDE.md"
-ln -s "$CLAUDE_DOTFILES/skills" "$CLAUDE_DIR/skills"
+ln -sf "$CLAUDE_DOTFILES/settings.json" "$CLAUDE_DIR/settings.json"
+ln -sf "$CLAUDE_DOTFILES/CLAUDE.md" "$CLAUDE_DIR/CLAUDE.md"
+ln -sfn "$CLAUDE_DOTFILES/skills" "$CLAUDE_DIR/skills"
 
 # Copy CLAUDE.local.md template if it doesn't exist
 if [ ! -f "$CLAUDE_DIR/CLAUDE.local.md" ]; then
 	cp "$CLAUDE_COPIED/CLAUDE.local.md" "$CLAUDE_DIR/CLAUDE.local.md"
-	print_green "Created Claude local instructions template"
+	echo -e "${green}Created Claude local instructions template${reset}"
 fi
 
-print_green "Configured Claude Code"
+echo -e "${dim}Configured Claude Code${reset}"

configure/firefox.sh

@@ -0,0 +1,21 @@
+# shellcheck shell=bash
+# shellcheck disable=SC2154 # Variables like $yellow defined in lib/colors.sh
+# Sourced by run.sh (requires lib/colors.sh, lib/backup.sh)
+
+# Install custom Firefox settings
+FIREFOX_FOLDER="$HOME/Library/Application Support/Firefox/Profiles"
+if [ ! -d "$FIREFOX_FOLDER" ]; then
+	# Firefox not launched yet - run.sh will remind user at the end
+	export FIREFOX_NEEDS_SETUP=1
+else
+	FIREFOX_PROFILE=$(find "$FIREFOX_FOLDER" -maxdepth 1 -name '*.dev-edition-default' 2>/dev/null | head -n1)
+	if [ "$FIREFOX_PROFILE" = "" ]; then
+		echo -e "${dim}Could not find Firefox profile folder. Skipping Firefox settings...${reset}"
+	else
+
+		backup_or_delete "$FIREFOX_PROFILE/user.js"
+		if ! ln -sf "$DOTFILES/user.js" "$FIREFOX_PROFILE/user.js"; then
+			echo -e "${yellow}Warning: Failed to link Firefox user.js${reset}"
+		fi
+	fi
+fi

util/configure_macos.sh configure/macos.shutil/configure_macos.sh renamed to configure/macos.sh

@@ -1,4 +1,5 @@
-#!/opt/homebrew/bin/bash
+# shellcheck shell=bash
+# Sourced by run.sh - configure macOS system preferences and Dock
 
 # Disable screensaver
 defaults -currentHost write com.apple.screensaver idleTime 0
@@ -21,8 +22,15 @@ defaults write com.apple.dock enable-spring-load-actions-on-all-items -bool true
 # Speeds up window minimizing and maximizing
 defaults write com.apple.dock mineffect -string "scale"
 
-# Remove all apps kept in Dock by default
-defaults write com.apple.dock persistent-apps -array
+# Clear Dock apps only if Dock is at default (has Mail/Safari) - skip on re-runs
+current_dock=$(defaults read com.apple.dock persistent-apps 2>/dev/null | grep -c "file-label") || current_dock=0
+if [[ "$current_dock" -gt 0 ]]; then
+	# Check if it looks like default Dock (has Safari)
+	has_safari=$(defaults read com.apple.dock persistent-apps 2>/dev/null | grep -c "Safari") || has_safari=0
+	if [[ "$has_safari" -gt 0 ]]; then
+		defaults write com.apple.dock persistent-apps -array
+	fi
+fi
 
 # Don't show recent apps not presently open in the dock
 defaults write com.apple.dock show-recents -bool FALSE
@@ -77,27 +85,32 @@ defaults write NSGlobalDomain AppleShowAllExtensions -bool true
 defaults write kCFPreferencesAnyApplication TSMLanguageIndicatorEnabled 0
 
 # Import `add_to_dock` function
-source add_to_dock.sh
+source "$SETUP/lib/add_to_dock.sh"
 
 # Add the following applications to the Mac dock
-add_to_dock "1Password"
-add_to_dock "Boop"
-add_to_dock "Calculator" "System"
-add_to_dock "Firefox Developer Edition"
-add_to_dock "Google Chrome"
-add_to_dock "iPhone Mirroring" "System"
-add_to_dock "iTerm"
-add_to_dock "NordVPN"
-add_to_dock "Notes" "System"
-add_to_dock "Photo Booth" "System"
-add_to_dock "Reminders" "System"
-add_to_dock "Spotify"
-add_to_dock "Utilities/Activity Monitor" "System"
-add_to_dock "Visual Studio Code"
-add_to_dock "Weather" "System"
-# Required to make changes to the Dock and Finder take effect
-killall Dock
-killall Finder
+# Track if any apps were added (return 0 = added, 2 = already present)
+dock_changed=false
+add_to_dock "1Password" && dock_changed=true
+add_to_dock "Boop" && dock_changed=true
+add_to_dock "Calculator" "System" && dock_changed=true
+add_to_dock "Firefox Developer Edition" && dock_changed=true
+add_to_dock "Google Chrome" && dock_changed=true
+add_to_dock "iPhone Mirroring" "System" && dock_changed=true
+add_to_dock "iTerm" && dock_changed=true
+add_to_dock "NordVPN" && dock_changed=true
+add_to_dock "Notes" "System" && dock_changed=true
+add_to_dock "Photo Booth" "System" && dock_changed=true
+add_to_dock "Reminders" "System" && dock_changed=true
+add_to_dock "Spotify" && dock_changed=true
+add_to_dock "Utilities/Activity Monitor" "System" && dock_changed=true
+add_to_dock "Visual Studio Code" && dock_changed=true
+add_to_dock "Weather" "System" && dock_changed=true
+
+# Only restart Dock if apps were added
+if [[ "$dock_changed" == "true" ]]; then
+	killall Dock
+fi
+# Finder settings apply on next window open, no restart needed
 
 # Add directories to Finder favorites
 # brew install --cask mysides

configure/node.sh

@@ -0,0 +1,39 @@
+# shellcheck shell=bash
+# shellcheck disable=SC2154 # Variables like $yellow defined in lib/colors.sh
+# Sourced by run.sh after verifying nvm exists
+
+# Setup Node Version Manager (NVM) for local JavaScript
+mkdir -p ~/.nvm
+export NVM_DIR="$HOME/.nvm"
+
+NVM_SCRIPT="$(brew --prefix)/opt/nvm/nvm.sh"
+
+# nvm.sh has unset variables, so temporarily disable strict mode
+# Use trap to ensure we always re-enable it
+_restore_strict_mode() { set -u; }
+trap _restore_strict_mode RETURN
+
+set +u
+# shellcheck disable=SC1090 # Can't follow dynamic source path
+\. "$NVM_SCRIPT"
+
+PREVIOUS_NODE_VERSION=$(nvm current)
+# shellcheck disable=SC1090 # nvm is a shell function, not a file
+if ! nvm install --lts; then
+	echo -e "${yellow}Warning: Failed to install Node LTS${reset}" >&2
+	return 0
+fi
+
+NEW_NODE_VERSION=$(nvm current)
+if [ "$PREVIOUS_NODE_VERSION" != "$NEW_NODE_VERSION" ] && [ "$PREVIOUS_NODE_VERSION" != "none" ] && [ "$PREVIOUS_NODE_VERSION" != "system" ]; then
+	echo -n "Uninstall old Node version ${PREVIOUS_NODE_VERSION}? [y/N]: "
+	read -r -n 1 confirm </dev/tty
+	echo ""
+	if [[ "$confirm" =~ ^[Yy]$ ]]; then
+		nvm uninstall "$PREVIOUS_NODE_VERSION" || echo -e "${yellow}Warning: Failed to uninstall previous Node version${reset}"
+	else
+		echo -e "${dim}Kept ${PREVIOUS_NODE_VERSION}${reset}"
+	fi
+fi
+
+npm install -g npm || echo -e "${yellow}Warning: Failed to upgrade npm${reset}"

configure/python.sh

@@ -0,0 +1,11 @@
+# shellcheck shell=bash
+# shellcheck disable=SC2154 # Variables like $yellow defined in lib/colors.sh
+# Sourced by run.sh after checking `command -v uv`
+
+# --default sets python/python3 commands (experimental, acknowledged via --preview-features)
+if ! uv python install --default --preview-features python-install-default; then
+	echo -e "${yellow}Warning: Failed to install Python via uv${reset}" >&2
+fi
+
+# Upgrade can fail gracefully - it's not a critical install
+uv python upgrade || echo -e "${yellow}Warning: Failed to upgrade Python${reset}"

configure/ruff.sh

@@ -0,0 +1,35 @@
+# shellcheck shell=bash
+# shellcheck disable=SC2154 # Variables like $yellow defined in lib/colors.sh
+# Sourced by run.sh
+
+export RUFF_CONFIG=~/projects/ruff-config
+if [ -d "$RUFF_CONFIG" ]; then
+	git -C "$RUFF_CONFIG" pull || echo -e "${yellow}Warning: Failed to update Ruff config${reset}"
+	echo -e "${dim}Pulled the latest commits for Ruff config${reset}"
+else
+	if ! git clone https://github.com/nickineering/ruff-config "$RUFF_CONFIG"; then
+		echo -e "${yellow}Warning: Failed to clone Ruff config repo, skipping Ruff setup${reset}" >&2
+		return 0
+	fi
+	echo -e "${green}Cloned Ruff config repo${reset}"
+fi
+
+# Per platform determined by Rust: https://docs.rs/dirs/4.0.0/dirs/fn.config_dir.html
+RUFF_DIR="$HOME/Library/Application Support/ruff/"
+RUFF_BASE="$RUFF_CONFIG/nickineering_ruff_config/nickineering-ruff-base.toml"
+
+if [ ! -f "$RUFF_BASE" ]; then
+	echo -e "${yellow}Warning: Ruff base config not found at $RUFF_BASE${reset}" >&2
+	return 0
+fi
+
+mkdir -p "$RUFF_DIR"
+if ! ln -sf "$RUFF_BASE" "$RUFF_DIR/ruff.toml"; then
+	echo -e "${yellow}Warning: Failed to link Ruff config${reset}" >&2
+fi
+
+# Install shell completions for ruff - requires code in .zshrc
+mkdir -p ~/.zfunc
+if ! ruff generate-shell-completion zsh >~/.zfunc/_ruff; then
+	echo -e "${yellow}Warning: Failed to generate Ruff shell completions${reset}"
+fi