From 66cbb97f916e183ed91f79d7614801f5087d53e4 Mon Sep 17 00:00:00 2001
From: Ryan Hamilton <ryanehamil@outlook.com>
Date: Mon, 4 Aug 2025 19:16:02 -0500
Subject: [PATCH 1/8] feat: restructure dotfiles with GNU Stow organization

- Reorganize dotfiles into stow/ subdirectories (bash/, git/)
- Add package management system with categorized package lists
- Enhance install.sh with interactive package selection
- Fix package selection logic and improve error handling
- Update dotpull alias to work with new stow structure
- Add comprehensive documentation in README.md

Breaking Changes:
- Dotfiles moved from root to stow/ subdirectories
- Install script now requires user interaction for package selection
- Stow commands now target individual config directories
---
 README.md                                |  56 +++++++++-
 install.sh                               | 130 +++++++++++++++++++----
 packages/base.txt                        |  13 +++
 packages/cli-tools.txt                   |  11 ++
 packages/dev.txt                         |  15 +++
 packages/gui.txt                         |  10 ++
 .bash_aliases => stow/bash/.bash_aliases |   2 +-
 .bashrc => stow/bash/.bashrc             |   0
 .inputrc => stow/bash/.inputrc           |   0
 .gitconfig => stow/git/.gitconfig        |   0
 10 files changed, 216 insertions(+), 21 deletions(-)
 create mode 100644 packages/base.txt
 create mode 100644 packages/cli-tools.txt
 create mode 100644 packages/dev.txt
 create mode 100644 packages/gui.txt
 rename .bash_aliases => stow/bash/.bash_aliases (86%)
 rename .bashrc => stow/bash/.bashrc (100%)
 rename .inputrc => stow/bash/.inputrc (100%)
 rename .gitconfig => stow/git/.gitconfig (100%)

diff --git a/README.md b/README.md
index 01dee29..5db55be 100644
--- a/README.md
+++ b/README.md
@@ -1,8 +1,62 @@
 # Ryan's Dotfiles
 
-Minimal Bash dotfiles for SSH and remote environments.
+A comprehensive dotfiles repository for SSH, remote environments, and development setups.
+
+## Structure
+
+```
+~/.dotfiles/
+├── stow/                  # Configs organized for GNU Stow
+│   ├── bash/             # Bash configuration (.bashrc, .bash_aliases, .inputrc)
+│   ├── git/              # Git configuration (.gitconfig)
+│   └── [other configs]   # Additional configurations as needed
+├── packages/
+│   ├── base.txt          # MUST HAVE - Core system utilities
+│   ├── 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
+└── README.md             # Documentation
+```
 
 ## Install
 
 ```bash
 bash <(curl -sL https://ryans.tools/dotfiles)
+```
+
+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
+
+## Package Categories
+
+- **Base**: Essential system utilities (curl, git, stow, vim, etc.)
+- **CLI Tools**: Enhanced command-line tools (bat, fzf, ripgrep, etc.)
+- **Development**: Programming languages and dev tools (nodejs, python, docker, etc.)
+- **GUI**: Desktop applications (firefox, code, vlc, etc.)
+
+## Updating
+
+After initial installation, use the `dotpull` alias to update your dotfiles:
+
+```bash
+dotpull
+```
+
+This alias will pull the latest changes and re-stow all configurations.
+
+## Manual Management
+
+To manage individual configurations:
+
+```bash
+cd ~/.dotfiles/stow
+stow -t ~ bash    # Link bash config
+stow -t ~ git     # Link git config
+stow -D bash      # Unlink bash config
+```
diff --git a/install.sh b/install.sh
index 2da1367..c4a2832 100644
--- a/install.sh
+++ b/install.sh
@@ -4,6 +4,50 @@ set -euo pipefail
 DOTFILES_REPO="https://gitea.purpleraft.com/ryan/dotfiles"
 DOTFILES_DIR="$HOME/.dotfiles"
 
+# 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:"
@@ -15,33 +59,81 @@ fi
 
 # Clone or update the repo
 if [ -d "$DOTFILES_DIR/.git" ]; then
-  echo "Updating existing dotfiles repo..."
+  echo "🔄 Updating existing dotfiles repo..."
   git -C "$DOTFILES_DIR" pull --quiet
 else
-  echo "Cloning dotfiles into $DOTFILES_DIR..."
+  echo "📥 Cloning dotfiles into $DOTFILES_DIR..."
   git clone "$DOTFILES_REPO" "$DOTFILES_DIR"
 fi
 
-# Backup existing files that would conflict with stow (excluding SSH config - it's machine-specific)
-for file in .bashrc .bash_aliases .inputrc .gitconfig; do
-  if [ -f "$HOME/$file" ] && [ ! -L "$HOME/$file" ]; then
-    echo "⚠️  Backing up existing file: $HOME/$file -> $HOME/${file}.bak"
-    mv "$HOME/$file" "$HOME/${file}.bak"
-  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
 
-# Change to dotfiles directory and use stow to create symlinks
-cd "$DOTFILES_DIR"
-echo "🔗 Using Stow to symlink dotfiles..."
-if ! stow --adopt -t "$HOME" . 2>/dev/null; then
-    echo "🔄 Adopting failed, trying regular stow..."
-    stow -t "$HOME" .
-fi
+# Use stow to create symlinks for each configuration
+cd stow
+for config_dir in */; do
+    if [ -d "$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* ]]; then
-  echo "Reloading Bash config..."
-  source ~/.bashrc
+if [[ $- == *i* ]] && [ -f "$HOME/.bashrc" ]; then
+    echo "🔄 Reloading Bash config..."
+    source ~/.bashrc
 fi
 
-echo "✅ Dotfiles install complete."
+echo ""
+echo "✅ Dotfiles install complete!"
+echo "💡 Use 'dotpull' alias to update your dotfiles in the future."
diff --git a/packages/base.txt b/packages/base.txt
new file mode 100644
index 0000000..8131853
--- /dev/null
+++ b/packages/base.txt
@@ -0,0 +1,13 @@
+# Base packages - MUST HAVE
+# Core system utilities
+curl
+wget
+git
+stow
+vim
+nano
+bash-completion
+tree
+htop
+unzip
+zip
diff --git a/packages/cli-tools.txt b/packages/cli-tools.txt
new file mode 100644
index 0000000..1b3f2c0
--- /dev/null
+++ b/packages/cli-tools.txt
@@ -0,0 +1,11 @@
+# CLI Tools - Nice-to-haves
+# Enhanced command line tools
+bat
+fd-find
+ripgrep
+fzf
+tmux
+screen
+jq
+ncdu
+exa
diff --git a/packages/dev.txt b/packages/dev.txt
new file mode 100644
index 0000000..d70da8a
--- /dev/null
+++ b/packages/dev.txt
@@ -0,0 +1,15 @@
+# Development Tools
+# Programming languages and tools
+nodejs
+npm
+python3
+python3-pip
+docker
+docker-compose
+build-essential
+make
+gcc
+g++
+golang-go
+rust
+cargo
diff --git a/packages/gui.txt b/packages/gui.txt
new file mode 100644
index 0000000..ad45e98
--- /dev/null
+++ b/packages/gui.txt
@@ -0,0 +1,10 @@
+# GUI Applications
+# Desktop applications (for systems with GUI)
+firefox
+code
+vlc
+gimp
+thunderbird
+libreoffice
+chromium-browser
+terminator
diff --git a/.bash_aliases b/stow/bash/.bash_aliases
similarity index 86%
rename from .bash_aliases
rename to stow/bash/.bash_aliases
index 1165872..7d11949 100644
--- a/.bash_aliases
+++ b/stow/bash/.bash_aliases
@@ -7,7 +7,7 @@ alias h='history'
 alias grep='grep --color=auto'
 alias d='docker'
 alias dc='docker compose'
-alias dotpull='echo "🔄 Updating dotfiles..." && git -C ~/.dotfiles pull && echo "🔗 Re-stowing dotfiles..." && (cd ~/.dotfiles && stow --adopt -t ~ . 2>/dev/null || stow -t ~ .) && echo "✅ Done."'
+alias dotpull='echo "🔄 Updating dotfiles..." && git -C ~/.dotfiles pull && echo "🔗 Re-stowing dotfiles..." && (cd ~/.dotfiles/stow && for dir in */; do if [ -d "$dir" ]; then echo "  Stowing $dir..." && stow -R -t ~ "$dir" || echo "    ⚠️  Failed to stow $dir"; fi; done) && echo "✅ Done."'
 
 alias reloadbash='source ~/.bashrc && echo "Bash config reloaded."'
 
diff --git a/.bashrc b/stow/bash/.bashrc
similarity index 100%
rename from .bashrc
rename to stow/bash/.bashrc
diff --git a/.inputrc b/stow/bash/.inputrc
similarity index 100%
rename from .inputrc
rename to stow/bash/.inputrc
diff --git a/.gitconfig b/stow/git/.gitconfig
similarity index 100%
rename from .gitconfig
rename to stow/git/.gitconfig

From c11d8464028bf46e1f20bc88e651bda26ea8b774 Mon Sep 17 00:00:00 2001
From: Ryan Hamilton <ryanehamil@outlook.com>
Date: Mon, 4 Aug 2025 19:19:40 -0500
Subject: [PATCH 2/8] feat: enhance branch selection in install script with
 user prompts and default handling

---
 install.sh | 51 ++++++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 50 insertions(+), 1 deletion(-)

diff --git a/install.sh b/install.sh
index c4a2832..34d3bb9 100644
--- a/install.sh
+++ b/install.sh
@@ -4,6 +4,51 @@ 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"
@@ -57,13 +102,17 @@ if ! command -v stow &> /dev/null; then
     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 $DOTFILES_DIR..."
-  git clone "$DOTFILES_REPO" "$DOTFILES_DIR"
+  git clone -b "$BRANCH" "$DOTFILES_REPO" "$DOTFILES_DIR"
 fi
 
 cd "$DOTFILES_DIR"

From f824ca52d3eaa49f4762a960c65b40d9311786b3 Mon Sep 17 00:00:00 2001
From: Ryan Hamilton <ryanehamil@outlook.com>
Date: Mon, 4 Aug 2025 20:39:16 -0500
Subject: [PATCH 3/8] feat: restructure dotfiles setup with bootstrap and setup
 scripts, enhance branch selection and backup processes

---
 README.md                      |  32 +++++++--
 bootstrap.sh                   |  71 +++++++++++++++++++
 install.sh                     |  51 --------------
 scripts/05-branch-selection.sh | 100 ++++++++++++++++++++++++++
 scripts/10-backup-files.sh     |  42 ++++++++---
 scripts/20-setup-stow.sh       |  45 +++++++++---
 scripts/30-install-packages.sh | 125 +++++++++++++++++++++++++++++++++
 scripts/utils.sh               |  46 ++++++++++++
 setup.sh                       |  56 +++++++++++++++
 9 files changed, 493 insertions(+), 75 deletions(-)
 create mode 100644 bootstrap.sh
 delete mode 100644 install.sh
 create mode 100644 scripts/05-branch-selection.sh
 create mode 100644 scripts/30-install-packages.sh
 create mode 100644 setup.sh

diff --git a/README.md b/README.md
index 5db55be..d8b080c 100644
--- a/README.md
+++ b/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
 
diff --git a/bootstrap.sh b/bootstrap.sh
new file mode 100644
index 0000000..0aabd52
--- /dev/null
+++ b/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 ${#branches[@]}"
+            fi
+        done
+    fi
+fi
+
+# Hand off to setup
+if [ -f "setup.sh" ]; then
+    echo "Starting setup..."
+    exec "./setup.sh"
+else
+    echo "Error: No setup.sh found!"
+    exit 1
+fi
diff --git a/install.sh b/install.sh
deleted file mode 100644
index 6546502..0000000
--- a/install.sh
+++ /dev/null
@@ -1,51 +0,0 @@
-#!/bin/bash
-set -euo pipefail
-
-DOTFILES_REPO="https://gitea.purpleraft.com/ryan/dotfiles"
-DOTFILES_DIR="$HOME/.dotfiles"
-
-# Source utilities if available
-SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-if [ -f "$SCRIPT_DIR/scripts/utils.sh" ]; then
-    source "$SCRIPT_DIR/scripts/utils.sh"
-else
-    # Fallback logging functions if utils not available
-    log_info() { echo "ℹ️  $1"; }
-    log_success() { echo "✅ $1"; }
-    log_warning() { echo "⚠️  $1"; }
-    log_error() { echo "❌ $1"; }
-fi
-
-log_info "🚀 Starting dotfiles installation..."
-
-# Clone or update the repo
-if [ -d "$DOTFILES_DIR/.git" ]; then
-    log_info "Updating existing dotfiles repo..."
-    git -C "$DOTFILES_DIR" pull --quiet
-else
-    log_info "Cloning dotfiles into $DOTFILES_DIR..."
-    git clone "$DOTFILES_REPO" "$DOTFILES_DIR"
-fi
-
-cd "$DOTFILES_DIR"
-
-# Auto-discover and run setup scripts
-if [ -d "scripts" ]; then
-    log_info "Running setup scripts..."
-    
-    # Look for numbered scripts and run them in order
-    for script in 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 $script_name..."
-            "$script" "$DOTFILES_DIR"
-        fi
-    done
-else
-    log_error "No scripts directory found! Something went wrong with the installation."
-    exit 1
-fi
-
-log_success "Dotfiles install complete!"
diff --git a/scripts/05-branch-selection.sh b/scripts/05-branch-selection.sh
new file mode 100644
index 0000000..a873513
--- /dev/null
+++ b/scripts/05-branch-selection.sh
@@ -0,0 +1,100 @@
+#!/bin/bash
+# scripts/05-branch-selection.sh - Allow user to select git branch
+
+set -euo pipefail
+
+# Source utilities
+SCRIPT_DIR="$(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
diff --git a/scripts/10-backup-files.sh b/scripts/10-backup-files.sh
index 84ef4f1..52b1c78 100644
--- a/scripts/10-backup-files.sh
+++ b/scripts/10-backup-files.sh
@@ -12,17 +12,41 @@ backup_files() {
     
     log_info "Checking for file conflicts..."
     
-    # Files that might conflict with stow
-    local files_to_check=(.bashrc .bash_aliases .inputrc .gitconfig)
     local backed_up=()
     
-    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+=("$file")
-        fi
-    done
+    # Auto-discover files from stow directories
+    if [ -d "$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): ${backed_up[*]}"
diff --git a/scripts/20-setup-stow.sh b/scripts/20-setup-stow.sh
index 3fbe526..cc1afb0 100644
--- a/scripts/20-setup-stow.sh
+++ b/scripts/20-setup-stow.sh
@@ -10,16 +10,43 @@ source "$SCRIPT_DIR/utils.sh"
 setup_stow() {
     local dotfiles_dir="$1"
     
-    # Change to dotfiles directory and use stow to create symlinks
-    cd "$dotfiles_dir"
-    log_info "Using Stow to symlink dotfiles..."
-    
-    if ! stow --adopt -t "$HOME" . 2>/dev/null; then
-        log_warning "Adopting failed, trying regular stow..."
-        stow -t "$HOME" .
+    if [ -d "$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
-    
-    log_success "Stow setup complete"
 }
 
 # Run if called directly
diff --git a/scripts/30-install-packages.sh b/scripts/30-install-packages.sh
new file mode 100644
index 0000000..3670279
--- /dev/null
+++ b/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
diff --git a/scripts/utils.sh b/scripts/utils.sh
index 465c702..0860494 100644
--- a/scripts/utils.sh
+++ b/scripts/utils.sh
@@ -34,3 +34,49 @@ command_exists() {
 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: $selected_branch"
+}
diff --git a/setup.sh b/setup.sh
new file mode 100644
index 0000000..f141a6b
--- /dev/null
+++ b/setup.sh
@@ -0,0 +1,56 @@
+#!/bin/bash
+# setup.sh - Main dotfiles setup orchestrator
+# Runs all numbered scripts in sequence
+
+set -euo pipefail
+
+# Get the absolute path to the directory containing this script
+# This handles symlinks and relative paths to always find the dotfiles root
+DOTFILES_DIR="$(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!"

From 67504dccffc4c0b6627bad886288cce45d958131 Mon Sep 17 00:00:00 2001
From: Ryan Hamilton <ryanehamil@outlook.com>
Date: Mon, 4 Aug 2025 20:44:53 -0500
Subject: [PATCH 4/8] remove: standalone branch selection script -
 functionality moved to bootstrap.sh

---
 scripts/05-branch-selection.sh | 100 ---------------------------------
 1 file changed, 100 deletions(-)
 delete mode 100644 scripts/05-branch-selection.sh

diff --git a/scripts/05-branch-selection.sh b/scripts/05-branch-selection.sh
deleted file mode 100644
index a873513..0000000
--- a/scripts/05-branch-selection.sh
+++ /dev/null
@@ -1,100 +0,0 @@
-#!/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

From 2ef00a0dd9ec218eece0fc0026a64b0c0b52db97 Mon Sep 17 00:00:00 2001
From: Ryan Hamilton <ryanehamil@outlook.com>
Date: Mon, 4 Aug 2025 20:51:13 -0500
Subject: [PATCH 5/8] fix: enhance git pull handling in bootstrap script to
 manage local changes

---
 bootstrap.sh | 19 ++++++++++++++++---
 1 file changed, 16 insertions(+), 3 deletions(-)

diff --git a/bootstrap.sh b/bootstrap.sh
index 0aabd52..e8a1719 100644
--- a/bootstrap.sh
+++ b/bootstrap.sh
@@ -9,14 +9,27 @@ 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
+    cd "$DOTFILES_DIR"
+    
+    # Handle local changes if they exist
+    if ! git diff-index --quiet HEAD --; then
+        echo "Local changes detected:"
+        echo "1) Discard  2) Stash  3) Abort"
+        read -p "Choice (1-3): " choice
+        case $choice in
+            1) git reset --hard HEAD ;;
+            2) git stash push -m "Bootstrap $(date +%Y%m%d-%H%M)" ;;
+            *) echo "Aborted. Check 'git status' in $DOTFILES_DIR"; exit 1 ;;
+        esac
+    fi
+    
+    git pull --quiet || { echo "Error: Failed to update repository"; exit 1; }
 else
     echo "Cloning dotfiles into $DOTFILES_DIR..."
     git clone "$DOTFILES_REPO" "$DOTFILES_DIR"
+    cd "$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

From b08c9acb29cc19156e7df116e4088b96b8613fa6 Mon Sep 17 00:00:00 2001
From: Ryan Hamilton <ryanehamil@outlook.com>
Date: Mon, 4 Aug 2025 20:53:09 -0500
Subject: [PATCH 6/8] fix: update setup script execution method for improved
 compatibility

---
 bootstrap.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/bootstrap.sh b/bootstrap.sh
index e8a1719..fbeb216 100644
--- a/bootstrap.sh
+++ b/bootstrap.sh
@@ -77,7 +77,8 @@ fi
 # Hand off to setup
 if [ -f "setup.sh" ]; then
     echo "Starting setup..."
-    exec "./setup.sh"
+    chmod +x setup.sh 2>/dev/null || true
+    bash setup.sh
 else
     echo "Error: No setup.sh found!"
     exit 1

From a245bebffbe58263082fc45c44ccd4d4e2f8e123 Mon Sep 17 00:00:00 2001
From: Ryan Hamilton <ryanehamil@outlook.com>
Date: Mon, 4 Aug 2025 20:59:04 -0500
Subject: [PATCH 7/8] fix: ensure setup scripts are executed with bash for
 compatibility

---
 setup.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.sh b/setup.sh
index f141a6b..575a937 100644
--- a/setup.sh
+++ b/setup.sh
@@ -32,7 +32,7 @@ if [ -d "$DOTFILES_DIR/scripts" ]; then
             script_name=$(basename "$script")
             log_info "Running $script_name..."
             
-            if "$script" "$DOTFILES_DIR"; then
+            if bash "$script" "$DOTFILES_DIR"; then
                 log_success "✓ $script_name completed"
             else
                 log_error "✗ $script_name failed"

From 4b50becf6f124468e0909691ab8417cf59536ddb Mon Sep 17 00:00:00 2001
From: Ryan Hamilton <ryanehamil@outlook.com>
Date: Mon, 4 Aug 2025 21:03:46 -0500
Subject: [PATCH 8/8] fix: correct script path in setup.sh for proper execution

---
 setup.sh | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/setup.sh b/setup.sh
index 575a937..751f2ab 100644
--- a/setup.sh
+++ b/setup.sh
@@ -25,10 +25,8 @@ if [ -d "$DOTFILES_DIR/scripts" ]; then
     
     # Look for numbered scripts and run them in order
     script_count=0
-    for script in "$DOTFILES_DIR/scripts"/[0-9][0-9]-*.sh; do
+    for script in "$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..."