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/setup.sh b/setup.sh
index f141a6b..751f2ab 100644
--- a/setup.sh
+++ b/setup.sh
@@ -25,14 +25,12 @@ 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..."
             
-            if "$script" "$DOTFILES_DIR"; then
+            if bash "$script" "$DOTFILES_DIR"; then
                 log_success "✓ $script_name completed"
             else
                 log_error "✗ $script_name failed"
diff --git a/.bash_aliases b/stow/bash/.bash_aliases
similarity index 86%
rename from .bash_aliases
rename to stow/bash/.bash_aliases
index 1165872..7d11949 100644
--- a/.bash_aliases
+++ b/stow/bash/.bash_aliases
@@ -7,7 +7,7 @@ alias h='history'
 alias grep='grep --color=auto'
 alias d='docker'
 alias dc='docker compose'
-alias dotpull='echo "🔄 Updating dotfiles..." && git -C ~/.dotfiles pull && echo "🔗 Re-stowing dotfiles..." && (cd ~/.dotfiles && stow --adopt -t ~ . 2>/dev/null || stow -t ~ .) && echo "✅ Done."'
+alias dotpull='echo "🔄 Updating dotfiles..." && git -C ~/.dotfiles pull && echo "🔗 Re-stowing dotfiles..." && (cd ~/.dotfiles/stow && for dir in */; do if [ -d "$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