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