feat: restructure dotfiles setup with bootstrap and setup scripts, enhance branch selection and backup processes

- Add scripts/ directory with numbered execution pattern
- Create 00-check-dependencies.sh for requirement validation
- Create 10-backup-files.sh for conflict handling
- Create 20-setup-stow.sh for symlink creation
- Create 90-post-install.sh for cleanup tasks
- Add scripts/utils.sh with colored logging functions
- Update install.sh to auto-discover and execute numbered scripts
- Remove hardcoded logic in favor of flexible script discovery

Benefits:
- Clean separation of concerns (each script has one job)
- Numbered execution order (SSH/systemd convention)
- Colored output for better UX
- Easy to extend with additional scripts
- Same entry point for all branches

README.md

@@ -15,23 +15,43 @@ A comprehensive dotfiles repository for SSH, remote environments, and developmen
 │   ├── cli-tools.txt     # Nice-to-haves - Enhanced CLI tools
 │   ├── dev.txt           # Development tools (docker, node, etc)
 │   └── gui.txt           # Desktop applications
-├── install.sh            # Bootstrap script with package management
+├── bootstrap.sh          # Get repo and select branch
+├── setup.sh              # Main orchestrator - runs all configuration
 └── README.md             # Documentation
 ```
 
 ## Install
 
+**From internet:**
+
 ```bash
 bash <(curl -sL https://ryans.tools/dotfiles)
 ```
 
+**From local copy (USB drive, etc.):**
+
+```bash
+./bootstrap.sh
+```
+
 The installer will:
 
-1. Clone this repository to `~/.dotfiles`
-2. Prompt you to choose which package sets to install
-3. Backup any existing conflicting files
-4. Use GNU Stow to symlink configurations
-5. Set up bash aliases including the `dotpull` update alias
+1. **Bootstrap:** Clone repository (or use local copy), select branch if desired
+2. **Setup:** Check dependencies, backup conflicts, install packages, configure with GNU Stow
+
+## Updates
+
+**Regular updates (recommended):**
+
+```bash
+dotpull
+```
+
+**Branch switching or major re-setup:**
+
+```bash
+cd ~/.dotfiles && ./bootstrap.sh
+```
 
 ## Package Categories
 

bootstrap.sh

@@ -0,0 +1,71 @@
+#!/bin/bash
+set -euo pipefail
+
+DOTFILES_REPO="https://gitea.purpleraft.com/ryan/dotfiles"
+DOTFILES_DIR="$HOME/.dotfiles"
+
+echo "Starting dotfiles bootstrap..."
+
+# Clone repo (new installs) or update for branch switching
+if [ -d "$DOTFILES_DIR/.git" ]; then
+    echo "Updating existing dotfiles repo..."
+    git -C "$DOTFILES_DIR" pull --quiet
+else
+    echo "Cloning dotfiles into $DOTFILES_DIR..."
+    git clone "$DOTFILES_REPO" "$DOTFILES_DIR"
+fi
+
+cd "$DOTFILES_DIR"
+
+# Branch selection - allows choosing which version of dotfiles to install
+# - New installs: git clone defaults to 'main', but you can switch to any branch
+# - Existing installs: switch from current branch to a different one
+# - Only runs in interactive terminals (skipped in automated/CI environments)
+if [ -t 0 ] && [ -t 1 ] && [ -d ".git" ]; then
+    current_branch=$(git branch --show-current 2>/dev/null || echo "unknown")
+    echo "Current branch: $current_branch"
+    
+    echo
+    read -p "Switch to a different branch? (y/N): " -n 1 -r
+    echo
+    
+    if [[ $REPLY =~ ^[Yy]$ ]]; then
+        echo "Available branches:"
+        git branch -a --format="%(refname:short)" | grep -v "HEAD" | sed 's|^origin/||' | sort -u | nl -w2 -s'. '
+        
+        branches=($(git branch -a --format="%(refname:short)" | grep -v "HEAD" | sed 's|^origin/||' | sort -u))
+        
+        while true; do
+            read -p "Enter branch number (1-${#branches[@]}): " branch_num
+            
+            if [[ "$branch_num" =~ ^[0-9]+$ ]] && [ "$branch_num" -ge 1 ] && [ "$branch_num" -le "${#branches[@]}" ]; then
+                selected_branch="${branches[$((branch_num-1))]}"
+                echo "Switching to branch: $selected_branch"
+                
+                if git show-ref --verify --quiet "refs/heads/$selected_branch"; then
+                    git checkout "$selected_branch"
+                elif git show-ref --verify --quiet "refs/remotes/origin/$selected_branch"; then
+                    git checkout -b "$selected_branch" "origin/$selected_branch"
+                else
+                    echo "Error: Branch $selected_branch not found"
+                    exit 1
+                fi
+                
+                git pull --quiet || true
+                echo "Switched to branch: $selected_branch"
+                break
+            else
+                echo "Invalid selection. Please enter a number between 1 and ${#branches[@]}"
+            fi
+        done
+    fi
+fi
+
+# Hand off to setup
+if [ -f "setup.sh" ]; then
+    echo "Starting setup..."
+    exec "./setup.sh"
+else
+    echo "Error: No setup.sh found!"
+    exit 1
+fi

install.sh

@@ -1,188 +0,0 @@
-#!/bin/bash
-set -euo pipefail
-
-DOTFILES_REPO="https://gitea.purpleraft.com/ryan/dotfiles"
-DOTFILES_DIR="$HOME/.dotfiles"
-
-# Handle branch selection
-if [ $# -eq 0 ]; then
-    echo "🌿 Fetching available branches..."
-    
-    # Get list of remote branches
-    branches=$(git ls-remote --heads "$DOTFILES_REPO" | sed 's/.*refs\/heads\///' | sort)
-    
-    if [ -z "$branches" ]; then
-        echo "⚠️  Could not fetch branches, using default 'main'"
-        BRANCH="main"
-    else
-        echo "Available branches:"
-        branch_array=()
-        i=1
-        while IFS= read -r branch; do
-            echo "$i. $branch"
-            branch_array+=("$branch")
-            ((i++))
-        done <<< "$branches"
-        
-        echo "$i. Enter custom branch name"
-        echo ""
-        read -p "Choose branch (1-$i) [default: main]: " branch_choice
-        
-        if [[ "$branch_choice" =~ ^[0-9]+$ ]] && [ "$branch_choice" -ge 1 ] && [ "$branch_choice" -lt "$i" ]; then
-            # Valid branch selection
-            BRANCH="${branch_array[$((branch_choice-1))]}"
-        elif [ "$branch_choice" -eq "$i" ]; then
-            # Custom branch name
-            read -p "Enter branch name: " custom_branch
-            BRANCH="$custom_branch"
-        else
-            # Default or invalid choice
-            if [[ " ${branch_array[*]} " =~ " main " ]]; then
-                BRANCH="main"
-            else
-                BRANCH="${branch_array[0]}"  # Use first available branch
-            fi
-            echo "Using default branch: $BRANCH"
-        fi
-    fi
-else
-    BRANCH="$1"
-fi
-
-# Function to install packages from a file
-install_packages() {
-    local package_file="$1"
-    local description="$2"
-    
-    if [ -f "$package_file" ]; then
-        echo "📦 Installing $description..."
-        
-        # Read packages into array, skipping comments and empty lines
-        packages=()
-        while IFS= read -r line; do
-            # Skip comments and empty lines
-            [[ "$line" =~ ^[[:space:]]*# ]] && continue
-            [[ -z "${line// }" ]] && continue
-            packages+=("$line")
-        done < "$package_file"
-        
-        if [ ${#packages[@]} -eq 0 ]; then
-            echo "  No packages found in $package_file"
-            return
-        fi
-        
-        # Detect package manager and install packages
-        if command -v apt &> /dev/null; then
-            # Debian/Ubuntu
-            sudo apt update && sudo apt install -y "${packages[@]}"
-        elif command -v yum &> /dev/null; then
-            # RHEL/CentOS
-            sudo yum install -y "${packages[@]}"
-        elif command -v dnf &> /dev/null; then
-            # Fedora
-            sudo dnf install -y "${packages[@]}"
-        elif command -v pacman &> /dev/null; then
-            # Arch Linux
-            sudo pacman -S --noconfirm "${packages[@]}"
-        elif command -v brew &> /dev/null; then
-            # macOS
-            brew install "${packages[@]}"
-        else
-            echo "⚠️  No supported package manager found. Please install packages manually from $package_file"
-        fi
-    fi
-}
-
-# Check if stow is installed
-if ! command -v stow &> /dev/null; then
-    echo "❌ GNU Stow is not installed. Please install it first:"
-    echo "   Ubuntu/Debian: sudo apt install stow"
-    echo "   macOS: brew install stow"
-    echo "   Or use the alias: install_stow"
-    exit 1
-fi
-
-echo "🚀 Installing dotfiles from branch: $BRANCH"
-
-# Clone or update the repo
-if [ -d "$DOTFILES_DIR/.git" ]; then
-  echo "🔄 Updating existing dotfiles repo..."
-  git -C "$DOTFILES_DIR" fetch --quiet
-  git -C "$DOTFILES_DIR" checkout "$BRANCH" --quiet
-  git -C "$DOTFILES_DIR" pull --quiet
-else
-  echo "📥 Cloning dotfiles into $DOTFILES_DIR..."
-  git clone -b "$BRANCH" "$DOTFILES_REPO" "$DOTFILES_DIR"
-fi
-
-cd "$DOTFILES_DIR"
-
-# Install packages (with user confirmation)
-echo ""
-echo "Package installation options:"
-echo "1. Base packages (MUST HAVE) - curl, git, stow, vim, etc."
-echo "2. CLI tools (Nice-to-haves) - bat, fzf, ripgrep, etc."
-echo "3. Development tools - nodejs, python, docker, etc."
-echo "4. GUI applications - firefox, code, vlc, etc."
-echo "5. Skip package installation"
-echo ""
-
-read -p "Choose packages to install (1-5, or comma-separated like 1,2): " package_choice
-
-# Install selected packages
-if [[ "$package_choice" == *"1"* ]]; then
-    install_packages "packages/base.txt" "base packages"
-fi
-if [[ "$package_choice" == *"2"* ]]; then
-    install_packages "packages/cli-tools.txt" "CLI tools"
-fi
-if [[ "$package_choice" == *"3"* ]]; then
-    install_packages "packages/dev.txt" "development tools"
-fi
-if [[ "$package_choice" == *"4"* ]]; then
-    install_packages "packages/gui.txt" "GUI applications"
-fi
-
-# Backup existing files that would conflict with stow
-echo ""
-echo "🔗 Setting up dotfile symlinks..."
-for config_dir in stow/*/; do
-    if [ -d "$config_dir" ]; then
-        config_name=$(basename "$config_dir")
-        echo "  Checking for conflicts with $config_name config..."
-        
-        # Find all files that would be stowed and backup if they exist
-        find "$config_dir" -type f | while read -r file; do
-            relative_file="${file#$config_dir}"
-            target_file="$HOME/$relative_file"
-            
-            if [ -f "$target_file" ] && [ ! -L "$target_file" ]; then
-                echo "    ⚠️  Backing up existing file: $target_file -> ${target_file}.bak"
-                mv "$target_file" "${target_file}.bak"
-            fi
-        done
-    fi
-done
-
-# Use stow to create symlinks for each configuration
-cd stow
-for config_dir in */; do
-    if [ -d "$config_dir" ]; then
-        config_name=$(basename "$config_dir")
-        echo "  🔗 Stowing $config_name configuration..."
-        if ! stow -t "$HOME" "$config_name" 2>/dev/null; then
-            echo "    ⚠️  Stow failed for $config_name, trying with --adopt..."
-            stow --adopt -t "$HOME" "$config_name"
-        fi
-    fi
-done
-
-# Optionally source the new bashrc
-if [[ $- == *i* ]] && [ -f "$HOME/.bashrc" ]; then
-    echo "🔄 Reloading Bash config..."
-    source ~/.bashrc
-fi
-
-echo ""
-echo "✅ Dotfiles install complete!"
-echo "💡 Use 'dotpull' alias to update your dotfiles in the future."

scripts/00-check-dependencies.sh

@@ -0,0 +1,57 @@
+#!/bin/bash
+# scripts/00-check-dependencies.sh - Check for required dependencies
+
+set -euo pipefail
+
+# Source utilities
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+source "$SCRIPT_DIR/utils.sh"
+
+check_dependencies() {
+    log_info "Checking dependencies..."
+    
+    local missing_deps=()
+    
+    # Check for git
+    if ! command_exists git; then
+        missing_deps+=("git")
+    fi
+    
+    # Check for stow
+    if ! command_exists stow; then
+        missing_deps+=("stow")
+    fi
+    
+    if [ ${#missing_deps[@]} -gt 0 ]; then
+        log_error "Missing required dependencies: ${missing_deps[*]}"
+        echo ""
+        echo "Please install the missing dependencies:"
+        
+        for dep in "${missing_deps[@]}"; do
+            case "$dep" in
+                "git")
+                    echo "  Git:"
+                    echo "    Ubuntu/Debian: sudo apt install git"
+                    echo "    macOS: brew install git"
+                    echo "    Or visit: https://git-scm.com/downloads"
+                    ;;
+                "stow")
+                    echo "  GNU Stow:"
+                    echo "    Ubuntu/Debian: sudo apt install stow"
+                    echo "    macOS: brew install stow"
+                    echo "    Or use the alias: install_stow"
+                    ;;
+            esac
+            echo ""
+        done
+        
+        exit 1
+    fi
+    
+    log_success "All dependencies satisfied"
+}
+
+# Run if called directly
+if [[ "${BASH_SOURCE[0]}" == "${0}" ]]; then
+    check_dependencies
+fi

scripts/05-branch-selection.sh

@@ -0,0 +1,100 @@
+#!/bin/bash
+# scripts/05-branch-selection.sh - Allow user to select git branch
+
+set -euo pipefail
+
+# Source utilities
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+source "$SCRIPT_DIR/utils.sh"
+
+select_branch() {
+    local dotfiles_dir="$1"
+    
+    # Change to dotfiles directory
+    cd "$dotfiles_dir"
+    
+    # Get current branch
+    local current_branch
+    current_branch=$(git branch --show-current 2>/dev/null || echo "unknown")
+    
+    log_info "Current branch: $current_branch"
+    
+    # Only prompt if we're in an interactive terminal
+    if ! is_interactive; then
+        log_info "Non-interactive mode, staying on current branch: $current_branch"
+        return 0
+    fi
+    
+    # Get available branches (both local and remote)
+    log_info "Available branches:"
+    git branch -a --format="%(refname:short)" | grep -v "HEAD" | sort -u | nl -w2 -s'. '
+    
+    echo
+    read -p "Switch to a different branch? (y/N): " -n 1 -r
+    echo
+    
+    if [[ ! $REPLY =~ ^[Yy]$ ]]; then
+        log_info "Staying on current branch: $current_branch"
+        return 0
+    fi
+    
+    # Get list of branches for selection
+    local branches=()
+    while IFS= read -r branch; do
+        # Clean up branch names (remove origin/ prefix, etc.)
+        clean_branch=$(echo "$branch" | sed 's|^origin/||' | sed 's|^remotes/origin/||')
+        # Skip HEAD and duplicates
+        if [[ "$clean_branch" != "HEAD" ]] && [[ ! " ${branches[@]} " =~ " ${clean_branch} " ]]; then
+            branches+=("$clean_branch")
+        fi
+    done < <(git branch -a --format="%(refname:short)" | grep -v "HEAD")
+    
+    # Sort branches
+    IFS=$'\n' branches=($(sort <<<"${branches[*]}"))
+    
+    echo "Select a branch:"
+    for i in "${!branches[@]}"; do
+        echo "$((i+1)). ${branches[i]}"
+    done
+    echo
+    
+    while true; do
+        read -p "Enter branch number (1-${#branches[@]}): " branch_num
+        
+        if [[ "$branch_num" =~ ^[0-9]+$ ]] && [ "$branch_num" -ge 1 ] && [ "$branch_num" -le "${#branches[@]}" ]; then
+            selected_branch="${branches[$((branch_num-1))]}"
+            break
+        else
+            log_warning "Invalid selection. Please enter a number between 1 and ${#branches[@]}"
+        fi
+    done
+    
+    # Switch to selected branch
+    log_info "Switching to branch: $selected_branch"
+    
+    if git show-ref --verify --quiet "refs/heads/$selected_branch"; then
+        # Local branch exists
+        git checkout "$selected_branch"
+    elif git show-ref --verify --quiet "refs/remotes/origin/$selected_branch"; then
+        # Remote branch exists, create local tracking branch
+        git checkout -b "$selected_branch" "origin/$selected_branch"
+    else
+        log_error "Branch $selected_branch not found"
+        return 1
+    fi
+    
+    # Pull latest changes
+    log_info "Pulling latest changes..."
+    git pull --quiet || true
+    
+    log_success "Switched to branch: $selected_branch"
+}
+
+# Run if called directly
+if [[ "${BASH_SOURCE[0]}" == "${0}" ]]; then
+    if [ $# -ne 1 ]; then
+        log_error "Usage: $0 <dotfiles_directory>"
+        exit 1
+    fi
+    select_branch "$1"
+fi

scripts/10-backup-files.sh

@@ -0,0 +1,65 @@
+#!/bin/bash
+# scripts/10-backup-files.sh - Backup existing files that would conflict
+
+set -euo pipefail
+
+# Source utilities
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+source "$SCRIPT_DIR/utils.sh"
+
+backup_files() {
+    local dotfiles_dir="$1"
+    
+    log_info "Checking for file conflicts..."
+    
+    local backed_up=()
+    
+    # Auto-discover files from stow directories
+    if [ -d "$dotfiles_dir/stow" ]; then
+        # Use new stow structure - scan all files in stow subdirectories
+        for config_dir in "$dotfiles_dir/stow"/*; do
+            if [ -d "$config_dir" ]; then
+                log_info "Checking $(basename "$config_dir") configuration for conflicts..."
+                
+                # Find all files that would be stowed
+                find "$config_dir" -type f | while read -r file; do
+                    # Get relative path from config directory
+                    relative_file="${file#$config_dir/}"
+                    target_file="$HOME/$relative_file"
+                    
+                    if [ -f "$target_file" ] && [ ! -L "$target_file" ]; then
+                        log_warning "Backing up existing file: $target_file -> ${target_file}.bak"
+                        mv "$target_file" "${target_file}.bak"
+                        backed_up+=("$relative_file")
+                    fi
+                done
+            fi
+        done
+    else
+        # Fallback to old structure - hardcoded file list
+        local files_to_check=(.bashrc .bash_aliases .inputrc .gitconfig)
+        
+        for file in "${files_to_check[@]}"; do
+            if [ -f "$HOME/$file" ] && [ ! -L "$HOME/$file" ]; then
+                log_warning "Backing up existing file: $HOME/$file -> $HOME/${file}.bak"
+                mv "$HOME/$file" "$HOME/${file}.bak"
+                backed_up+=("$file")
+            fi
+        done
+    fi
+    
+    if [ ${#backed_up[@]} -gt 0 ]; then
+        log_info "Backed up ${#backed_up[@]} file(s): ${backed_up[*]}"
+    else
+        log_info "No file conflicts found"
+    fi
+}
+
+# Run if called directly
+if [[ "${BASH_SOURCE[0]}" == "${0}" ]]; then
+    if [ $# -ne 1 ]; then
+        log_error "Usage: $0 <dotfiles_directory>"
+        exit 1
+    fi
+    backup_files "$1"
+fi

scripts/20-setup-stow.sh

@@ -0,0 +1,59 @@
+#!/bin/bash
+# scripts/20-setup-stow.sh - Handle GNU Stow operations
+
+set -euo pipefail
+
+# Source utilities
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+source "$SCRIPT_DIR/utils.sh"
+
+setup_stow() {
+    local dotfiles_dir="$1"
+    
+    if [ -d "$dotfiles_dir/stow" ]; then
+        # Use new stow structure - stow each subdirectory individually
+        cd "$dotfiles_dir/stow"
+        log_info "Using Stow to symlink dotfiles from stow/ subdirectories..."
+        
+        local stowed=()
+        
+        for config_dir in *; do
+            if [ -d "$config_dir" ]; then
+                log_info "Stowing $config_dir configuration..."
+                
+                if ! stow --adopt -t "$HOME" "$config_dir" 2>/dev/null; then
+                    log_warning "Adopting failed for $config_dir, trying regular stow..."
+                    stow -t "$HOME" "$config_dir"
+                fi
+                
+                stowed+=("$config_dir")
+            fi
+        done
+        
+        if [ ${#stowed[@]} -gt 0 ]; then
+            log_success "Stowed ${#stowed[@]} configuration(s): ${stowed[*]}"
+        else
+            log_warning "No stow subdirectories found in $dotfiles_dir/stow"
+        fi
+    else
+        # Fallback to old structure - stow entire directory
+        cd "$dotfiles_dir"
+        log_info "Using Stow to symlink dotfiles from root directory..."
+        
+        if ! stow --adopt -t "$HOME" . 2>/dev/null; then
+            log_warning "Adopting failed, trying regular stow..."
+            stow -t "$HOME" .
+        fi
+        
+        log_success "Stow setup complete"
+    fi
+}
+
+# Run if called directly
+if [[ "${BASH_SOURCE[0]}" == "${0}" ]]; then
+    if [ $# -ne 1 ]; then
+        log_error "Usage: $0 <dotfiles_directory>"
+        exit 1
+    fi
+    setup_stow "$1"
+fi

scripts/30-install-packages.sh

@@ -0,0 +1,125 @@
+#!/bin/bash
+# scripts/30-install-packages.sh - Install packages from package lists
+
+set -euo pipefail
+
+# Source utilities
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+source "$SCRIPT_DIR/utils.sh"
+
+# Detect package manager
+detect_package_manager() {
+    if command_exists apt; then
+        echo "apt"
+    elif command_exists yum; then
+        echo "yum"
+    elif command_exists dnf; then
+        echo "dnf"
+    elif command_exists pacman; then
+        echo "pacman"
+    elif command_exists brew; then
+        echo "brew"
+    else
+        echo "unknown"
+    fi
+}
+
+# Install packages with detected package manager
+install_packages() {
+    local package_manager="$1"
+    shift
+    local packages=("$@")
+    
+    if [ ${#packages[@]} -eq 0 ]; then
+        log_info "No packages to install"
+        return 0
+    fi
+    
+    case "$package_manager" in
+        apt)
+            log_info "Installing packages with apt..."
+            sudo apt update && sudo apt install -y "${packages[@]}"
+            ;;
+        yum)
+            log_info "Installing packages with yum..."
+            sudo yum install -y "${packages[@]}"
+            ;;
+        dnf)
+            log_info "Installing packages with dnf..."
+            sudo dnf install -y "${packages[@]}"
+            ;;
+        pacman)
+            log_info "Installing packages with pacman..."
+            sudo pacman -S --noconfirm "${packages[@]}"
+            ;;
+        brew)
+            log_info "Installing packages with brew..."
+            brew install "${packages[@]}"
+            ;;
+        *)
+            log_error "Unknown package manager. Please install packages manually."
+            return 1
+            ;;
+    esac
+}
+
+# Read packages from file
+read_package_file() {
+    local file="$1"
+    if [ -f "$file" ]; then
+        # Filter out comments and empty lines
+        grep -v '^#' "$file" | grep -v '^[[:space:]]*$' | tr '\n' ' '
+    fi
+}
+
+install_package_lists() {
+    local dotfiles_dir="$1"
+    local packages_dir="$dotfiles_dir/packages"
+    
+    if [ ! -d "$packages_dir" ]; then
+        log_warning "No packages directory found at $packages_dir"
+        return 0
+    fi
+    
+    local package_manager
+    package_manager=$(detect_package_manager)
+    
+    if [ "$package_manager" = "unknown" ]; then
+        log_error "No supported package manager found"
+        return 1
+    fi
+    
+    log_info "Detected package manager: $package_manager"
+    
+    # Install package lists in order
+    local package_files=("base.txt" "cli-tools.txt" "dev.txt" "gui.txt")
+    
+    for package_file in "${package_files[@]}"; do
+        local file_path="$packages_dir/$package_file"
+        if [ -f "$file_path" ]; then
+            log_info "Installing packages from $package_file..."
+            local packages
+            packages=$(read_package_file "$file_path")
+            
+            if [ -n "$packages" ]; then
+                # Convert space-separated string to array
+                read -ra package_array <<< "$packages"
+                install_packages "$package_manager" "${package_array[@]}"
+                log_success "Completed installation from $package_file"
+            else
+                log_info "No packages found in $package_file"
+            fi
+        else
+            log_info "Package file $package_file not found, skipping"
+        fi
+    done
+}
+
+# Run if called directly
+if [[ "${BASH_SOURCE[0]}" == "${0}" ]]; then
+    if [ $# -ne 1 ]; then
+        log_error "Usage: $0 <dotfiles_directory>"
+        exit 1
+    fi
+    install_package_lists "$1"
+fi

scripts/90-post-install.sh

@@ -0,0 +1,26 @@
+#!/bin/bash
+# scripts/90-post-install.sh - Post-installation tasks
+
+set -euo pipefail
+
+# Source utilities
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+source "$SCRIPT_DIR/utils.sh"
+
+post_install() {
+    log_info "Running post-installation tasks..."
+    
+    # Source the new bashrc if in interactive shell
+    if is_interactive && [ -f "$HOME/.bashrc" ]; then
+        log_info "Reloading Bash config..."
+        source "$HOME/.bashrc"
+    fi
+    
+    # Show completion message
+    log_success "Post-installation tasks complete"
+}
+
+# Run if called directly
+if [[ "${BASH_SOURCE[0]}" == "${0}" ]]; then
+    post_install
+fi

scripts/utils.sh

@@ -0,0 +1,82 @@
+#!/bin/bash
+# scripts/utils.sh - Shared utilities and functions
+
+# Colors for output
+RED='\033[0;31m'
+GREEN='\033[0;32m'
+YELLOW='\033[1;33m'
+BLUE='\033[0;34m'
+NC='\033[0m' # No Color
+
+# Logging functions
+log_info() {
+    echo -e "${BLUE}ℹ️  $1${NC}"
+}
+
+log_success() {
+    echo -e "${GREEN}✅ $1${NC}"
+}
+
+log_warning() {
+    echo -e "${YELLOW}⚠️  $1${NC}"
+}
+
+log_error() {
+    echo -e "${RED}❌ $1${NC}"
+}
+
+# Check if command exists
+command_exists() {
+    command -v "$1" &> /dev/null
+}
+
+# Check if we're in an interactive shell
+is_interactive() {
+    [[ $- == *i* ]]
+}
+
+# Branch selection utilities
+list_branches() {
+    local dotfiles_dir="$1"
+    cd "$dotfiles_dir"
+    
+    # Get available branches (both local and remote)
+    local branches=()
+    while IFS= read -r branch; do
+        # Clean up branch names (remove origin/ prefix, etc.)
+        clean_branch=$(echo "$branch" | sed 's|^origin/||' | sed 's|^remotes/origin/||')
+        # Skip HEAD and duplicates
+        if [[ "$clean_branch" != "HEAD" ]] && [[ ! " ${branches[@]} " =~ " ${clean_branch} " ]]; then
+            branches+=("$clean_branch")
+        fi
+    done < <(git branch -a --format="%(refname:short)" | grep -v "HEAD")
+    
+    # Sort and return branches
+    printf '%s\n' "${branches[@]}" | sort
+}
+
+switch_to_branch() {
+    local dotfiles_dir="$1"
+    local selected_branch="$2"
+    
+    cd "$dotfiles_dir"
+    
+    log_info "Switching to branch: $selected_branch"
+    
+    if git show-ref --verify --quiet "refs/heads/$selected_branch"; then
+        # Local branch exists
+        git checkout "$selected_branch"
+    elif git show-ref --verify --quiet "refs/remotes/origin/$selected_branch"; then
+        # Remote branch exists, create local tracking branch
+        git checkout -b "$selected_branch" "origin/$selected_branch"
+    else
+        log_error "Branch $selected_branch not found"
+        return 1
+    fi
+    
+    # Pull latest changes
+    log_info "Pulling latest changes..."
+    git pull --quiet || true
+    
+    log_success "Switched to branch: $selected_branch"
+}

setup.sh

@@ -0,0 +1,56 @@
+#!/bin/bash
+# setup.sh - Main dotfiles setup orchestrator
+# Runs all numbered scripts in sequence
+
+set -euo pipefail
+
+# Get the absolute path to the directory containing this script
+# This handles symlinks and relative paths to always find the dotfiles root
+DOTFILES_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+
+# Source utilities with fallback
+if [ -f "$DOTFILES_DIR/scripts/utils.sh" ]; then
+    source "$DOTFILES_DIR/scripts/utils.sh"
+else
+    echo "Error: scripts/utils.sh not found! Repository structure is corrupted."
+    exit 1
+fi
+
+log_info "🔧 Starting dotfiles setup..."
+log_info "Working directory: $DOTFILES_DIR"
+
+# Auto-discover and run setup scripts
+if [ -d "$DOTFILES_DIR/scripts" ]; then
+    log_info "Running setup scripts..."
+    
+    # Look for numbered scripts and run them in order
+    script_count=0
+    for script in "$DOTFILES_DIR/scripts"/[0-9][0-9]-*.sh; do
+        if [ -f "$script" ]; then
+            # Make executable and run
+            chmod +x "$script" 2>/dev/null || true
+            script_name=$(basename "$script")
+            log_info "Running $script_name..."
+            
+            if "$script" "$DOTFILES_DIR"; then
+                log_success "✓ $script_name completed"
+            else
+                log_error "✗ $script_name failed"
+                exit 1
+            fi
+            
+            ((script_count++))
+        fi
+    done
+    
+    if [ $script_count -eq 0 ]; then
+        log_warning "No numbered scripts found in scripts/ directory"
+    else
+        log_success "Completed $script_count setup script(s)"
+    fi
+else
+    log_error "No scripts directory found! Something went wrong with the installation."
+    exit 1
+fi
+
+log_success "🎉 Dotfiles setup complete!"