diff --git a/install-deps.sh b/install-deps.sh
new file mode 100755
index 0000000..4a7b1fe
--- /dev/null
+++ b/install-deps.sh
@@ -0,0 +1,205 @@
+#!/usr/bin/env bash
+# install-deps.sh: Install all system and tooling dependencies.
+# Run this after cloning on a new machine (before install-stow.sh).
+
+set -euo pipefail
+
+DOTFILES_DIR="$(cd "$(dirname "$0")" && pwd)"
+
+# ---------------------------------------------------------------------------
+# Helpers
+# ---------------------------------------------------------------------------
+
+ok()   { echo "  ✓ $*"; }
+info() { echo "  → $*"; }
+warn() { echo "  ⚠ $*"; }
+header() { echo ""; echo "==> $*"; }
+
+have() { command -v "$1" &>/dev/null; }
+
+# ---------------------------------------------------------------------------
+# Detect Linux distribution
+# ---------------------------------------------------------------------------
+
+detect_distro() {
+  if [[ -f /etc/os-release ]]; then
+    # shellcheck source=/dev/null
+    . /etc/os-release
+    echo "$ID"
+  else
+    echo "unknown"
+  fi
+}
+
+DISTRO=$(detect_distro)
+
+# ---------------------------------------------------------------------------
+# System packages
+# ---------------------------------------------------------------------------
+
+header "System packages"
+
+COMMON_PACKAGES=(
+  stow
+  swayidle
+  mako
+  libnotify
+  fuzzel
+  wireplumber
+  brightnessctl
+  alsa-utils
+  wf-recorder
+  slurp
+  zenity
+  jq
+  firefox
+  zoxide
+)
+
+case "$DISTRO" in
+  endeavouros|arch)
+    DISTRO_PACKAGES=(
+      pipewire-pulse
+      ffmpeg
+    )
+    PACKAGES=("${COMMON_PACKAGES[@]}" "${DISTRO_PACKAGES[@]}")
+
+    # Warn about pending upgrades (partial upgrades are unsupported on Arch)
+    sudo pacman -Sy --noconfirm &>/dev/null
+    updates=$(pacman -Qu 2>/dev/null | wc -l)
+    if [[ "$updates" -gt 0 ]]; then
+      warn "$updates system package(s) are out of date."
+      warn "If pacman fails with dependency conflicts, run 'sudo pacman -Syu'"
+      warn "locally (not over SSH) then re-run this script."
+      echo ""
+    fi
+
+    # Only install packages that aren't already present
+    MISSING=()
+    for pkg in "${PACKAGES[@]}"; do
+      if ! pacman -Q "$pkg" &>/dev/null; then
+        MISSING+=("$pkg")
+      else
+        ok "$pkg"
+      fi
+    done
+    if [[ ${#MISSING[@]} -gt 0 ]]; then
+      info "Installing: ${MISSING[*]}"
+      sudo pacman -S --noconfirm "${MISSING[@]}"
+    fi
+    ;;
+
+  fedora|fedora-asahi-remix)
+    DISTRO_PACKAGES=(
+      pipewire-utils
+      ffmpeg
+    )
+    PACKAGES=("${COMMON_PACKAGES[@]}" "${DISTRO_PACKAGES[@]}")
+
+    MISSING=()
+    for pkg in "${PACKAGES[@]}"; do
+      if rpm -q "$pkg" &>/dev/null; then
+        ok "$pkg"
+      else
+        MISSING+=("$pkg")
+      fi
+    done
+    if [[ ${#MISSING[@]} -gt 0 ]]; then
+      info "Installing: ${MISSING[*]}"
+      sudo dnf install -y "${MISSING[@]}"
+    fi
+    ;;
+
+  *)
+    warn "Unsupported distribution: $DISTRO — skipping system packages."
+    ;;
+esac
+
+# ---------------------------------------------------------------------------
+# Tools not in distro repos — warn if missing
+# ---------------------------------------------------------------------------
+
+header "Optional tools (manual install)"
+
+warn_missing() {
+  local cmd="$1" msg="$2"
+  if have "$cmd"; then
+    ok "$cmd"
+  else
+    warn "'$cmd' not found — $msg"
+  fi
+}
+
+warn_missing autotiling "install via pip: pip install --user autotiling"
+warn_missing eww        "install from https://github.com/elkowar/eww/releases"
+warn_missing wezterm    "install from https://wezfurlong.org/wezterm/install/linux.html"
+
+# ---------------------------------------------------------------------------
+# Starship
+# ---------------------------------------------------------------------------
+
+header "Starship"
+
+if have starship; then
+  ok "starship already installed"
+else
+  info "Installing Starship..."
+  curl -sS https://starship.rs/install.sh | sh
+fi
+
+# ---------------------------------------------------------------------------
+# npm global packages
+# ---------------------------------------------------------------------------
+
+header "npm global packages"
+
+if npm list -g --depth=0 @mariozechner/pi-coding-agent &>/dev/null; then
+  ok "@mariozechner/pi-coding-agent already installed"
+else
+  info "Installing @mariozechner/pi-coding-agent..."
+  npm install -g @mariozechner/pi-coding-agent
+fi
+
+# ---------------------------------------------------------------------------
+# pi extension dependencies
+# ---------------------------------------------------------------------------
+
+header "pi extension node_modules"
+
+for ext_dir in "$DOTFILES_DIR"/pi/.pi/agent/extensions/*/; do
+  [[ -f "$ext_dir/package.json" ]] || continue
+  ext_name="$(basename "$ext_dir")"
+
+  if [[ -d "$ext_dir/node_modules" ]]; then
+    ok "$ext_name (node_modules already present)"
+  else
+    info "Running npm install for $ext_name..."
+    npm install --prefix "$ext_dir" --ignore-scripts
+  fi
+done
+
+# ---------------------------------------------------------------------------
+# Fonts
+# ---------------------------------------------------------------------------
+
+header "Fonts"
+
+FONT_DIR="$HOME/.local/share/fonts/JetBrainsMono"
+if [[ -d "$FONT_DIR" ]]; then
+  ok "JetBrains Mono Nerd Font already installed"
+else
+  info "Installing JetBrains Mono Nerd Font..."
+  TMP="$(mktemp -d)"
+  curl -fLo "$TMP/JetBrainsMono.zip" \
+    "https://github.com/ryanoasis/nerd-fonts/releases/latest/download/JetBrainsMono.zip"
+  mkdir -p "$FONT_DIR"
+  unzip -q "$TMP/JetBrainsMono.zip" -d "$FONT_DIR"
+  rm -rf "$TMP"
+  fc-cache -f "$FONT_DIR"
+  ok "Font installed"
+fi
+
+# ---------------------------------------------------------------------------
+
+echo ""
+echo "All dependencies done. Run ./install-stow.sh to link configs."
diff --git a/install-stow.sh b/install-stow.sh
new file mode 100755
index 0000000..21f9a76
--- /dev/null
+++ b/install-stow.sh
@@ -0,0 +1,149 @@
+#!/usr/bin/env bash
+# install-stow.sh: Stow dotfile packages into $HOME with per-package prompts.
+# Packages that are already fully stowed are skipped automatically.
+# Run after install-deps.sh.
+
+set -euo pipefail
+
+DOTFILES_DIR="$(cd "$(dirname "$0")" && pwd)"
+
+# ---------------------------------------------------------------------------
+# Helpers
+# ---------------------------------------------------------------------------
+
+ok()     { echo "  ✓ $*"; }
+info()   { echo "  → $*"; }
+warn()   { echo "  ⚠ $*"; }
+header() { echo ""; echo "==> $*"; }
+
+# Ask yes/no. Returns 0 for yes, 1 for no.
+ask_yn() {
+  local prompt="$1"
+  while true; do
+    read -r -p "$prompt [y/N] " answer
+    case "${answer,,}" in
+      y|yes) return 0 ;;
+      n|no|"") return 1 ;;
+      *) echo "    Please answer y or n." ;;
+    esac
+  done
+}
+
+# ---------------------------------------------------------------------------
+# Check if a package is already fully stowed
+# (every file in the package has a correct symlink in $HOME)
+# ---------------------------------------------------------------------------
+
+is_stowed() {
+  local pkg="$1"
+  local pkg_dir="$DOTFILES_DIR/$pkg"
+  local all_ok=true
+
+  while IFS= read -r -d '' src; do
+    local rel="${src#$pkg_dir/}"
+    local target="$HOME/$rel"
+    # Must exist as a symlink pointing at this exact source
+    if [[ ! -L "$target" ]] || [[ "$(readlink -f "$target")" != "$(readlink -f "$src")" ]]; then
+      all_ok=false
+      break
+    fi
+  done < <(find "$pkg_dir" -type f -print0 2>/dev/null)
+
+  $all_ok
+}
+
+# List any real files (non-symlinks) that would be overwritten by stowing
+conflicts_for() {
+  local pkg="$1"
+  local pkg_dir="$DOTFILES_DIR/$pkg"
+  local conflicts=()
+
+  while IFS= read -r -d '' src; do
+    local rel="${src#$pkg_dir/}"
+    local target="$HOME/$rel"
+    if [[ -e "$target" ]] && [[ ! -L "$target" ]]; then
+      conflicts+=("$target")
+    fi
+  done < <(find "$pkg_dir" -type f -print0 2>/dev/null)
+
+  printf '%s\n' "${conflicts[@]}"
+}
+
+# ---------------------------------------------------------------------------
+# Collect packages (top-level dirs, skip hidden)
+# ---------------------------------------------------------------------------
+
+header "Stowing dotfile packages"
+
+PACKAGES=()
+for d in "$DOTFILES_DIR"/*/; do
+  pkg="$(basename "$d")"
+  [[ "$pkg" == .* ]] && continue
+  PACKAGES+=("$pkg")
+done
+
+STOWED=()
+SKIPPED=()
+
+for pkg in "${PACKAGES[@]}"; do
+  echo ""
+  echo "Package: $pkg"
+
+  if is_stowed "$pkg"; then
+    ok "already stowed — skipping"
+    STOWED+=("$pkg (already)")
+    continue
+  fi
+
+  # Show conflicts, if any
+  mapfile -t conflicts < <(conflicts_for "$pkg")
+  if [[ ${#conflicts[@]} -gt 0 ]]; then
+    warn "Stowing would overwrite these real files:"
+    for f in "${conflicts[@]}"; do
+      echo "      $f"
+    done
+    echo "    Back them up or delete them first, then re-run."
+  fi
+
+  if ask_yn "  Stow '$pkg'?"; then
+    stow --dir="$DOTFILES_DIR" --target="$HOME" --restow "$pkg"
+    ok "stowed"
+    STOWED+=("$pkg")
+  else
+    info "skipped"
+    SKIPPED+=("$pkg")
+  fi
+done
+
+# ---------------------------------------------------------------------------
+# Configure shell (after stowing zshrc)
+# ---------------------------------------------------------------------------
+
+header "Shell configuration"
+
+if [[ ! -f "$HOME/.zshrc" ]]; then
+  touch "$HOME/.zshrc"
+fi
+
+if ! grep -q 'eval "$(starship init zsh)"' "$HOME/.zshrc"; then
+  echo 'eval "$(starship init zsh)"' >> "$HOME/.zshrc"
+  ok "Added starship init to ~/.zshrc"
+else
+  ok "Starship already configured in ~/.zshrc"
+fi
+
+# ---------------------------------------------------------------------------
+# Summary
+# ---------------------------------------------------------------------------
+
+header "Summary"
+
+if [[ ${#STOWED[@]} -gt 0 ]]; then
+  echo "  Stowed:  ${STOWED[*]}"
+fi
+if [[ ${#SKIPPED[@]} -gt 0 ]]; then
+  echo "  Skipped: ${SKIPPED[*]}"
+fi
+
+echo ""
+echo "Done."
diff --git a/install.sh b/install.sh
deleted file mode 100755
index 23fa2b0..0000000
--- a/install.sh
+++ /dev/null
@@ -1,212 +0,0 @@
-#!/usr/bin/env bash
-# install.sh: Install dependencies and stow all packages.
-# Run this after cloning on a new machine.
-
-set -euo pipefail
-
-DOTFILES_DIR="$(cd "$(dirname "$0")" && pwd)"
-
-# ---------------------------------------------------------------------------
-# Detect Linux distribution
-# ---------------------------------------------------------------------------
-
-detect_distro() {
-  if [[ -f /etc/os-release ]]; then
-    . /etc/os-release
-    echo "$ID"
-  else
-    echo "unknown"
-  fi
-}
-
-DISTRO=$(detect_distro)
-
-# ---------------------------------------------------------------------------
-# Dependencies
-# ---------------------------------------------------------------------------
-
-COMMON_PACKAGES=(
-  stow
-  swayidle
-  mako
-  libnotify
-  fuzzel
-  wireplumber
-  brightnessctl
-  alsa-utils
-  wf-recorder
-  slurp
-  zenity
-  jq
-  firefox
-  zoxide
-)
-# On Arch-based systems, partial upgrades are unsupported — installing a
-# package that pulls in a newer library breaks packages built against the old
-# one.  The right fix is 'sudo pacman -Syu', but doing that over SSH risks
-# a dropped connection mid-kernel-upgrade.  So we just warn and let the user
-# decide.
-check_arch_updates() {
-  sudo pacman -Sy --noconfirm  # refresh databases only, no upgrade
-  local updates
-  updates=$(pacman -Qu 2>/dev/null | wc -l)
-  if [[ "$updates" -gt 0 ]]; then
-    echo ""
-    echo "WARNING: $updates system package(s) are out of date."
-    echo "  If pacman fails with dependency conflicts, run 'sudo pacman -Syu'"
-    echo "  locally (not over SSH, to avoid kernel upgrade risks), then re-run"
-    echo "  this script."
-    echo ""
-  fi
-}
-
-case "$DISTRO" in
-  endeavouros|arch)
-    # Keep distro-specific packages clearly listed
-    DISTRO_PACKAGES=(
-      pipewire-pulse  # Arch-specific
-      ffmpeg          # Available in official repos
-    )
-    PACKAGES=("${COMMON_PACKAGES[@]}" "${DISTRO_PACKAGES[@]}")
-    echo "Installing packages for Arch/EndeavourOS..."
-    sudo pacman -S --noconfirm "${PACKAGES[@]}"
-    ;;
-  fedora|fedora-asahi-remix)
-    DISTRO_PACKAGES=(
-      pipewire-utils  # Fedora's package name
-      ffmpeg          # Requires RPM Fusion
-    )
-    PACKAGES=("${COMMON_PACKAGES[@]}" "${DISTRO_PACKAGES[@]}")
-    echo "Installing packages for Fedora..."
-    sudo dnf install -y "${PACKAGES[@]}"
-    ;;
-  
-  *)
-    echo "ERROR: Unsupported distribution: $DISTRO"
-    exit 1
-    ;;
-esac   
-
-# ---------------------------------------------------------------------------
-# Packages not in Fedora repos - install manually if missing
-# ---------------------------------------------------------------------------
-
-warn_missing() {
-  local cmd="$1" msg="$2"
-  if ! command -v "$cmd" &>/dev/null; then
-    echo "WARNING: '$cmd' not found - $msg"
-  fi
-}
-
-warn_missing autotiling  "install via pip: pip install --user autotiling"
-warn_missing eww         "install from https://github.com/elkowar/eww/releases"
-warn_missing wezterm     "install from https://wezfurlong.org/wezterm/install/linux.html"
-
-# ---------------------------------------------------------------------------
-# Starship
-# ---------------------------------------------------------------------------
-
-if ! command -v starship &>/dev/null; then
-  echo ""
-  echo "Installing Starship..."
-  curl -sS https://starship.rs/install.sh | sh
-else
-  echo ""
-  echo "Starship already installed, skipping."
-fi
-
-# ---------------------------------------------------------------------------
-# NPM packages
-# ---------------------------------------------------------------------------
-
-echo ""
-echo "Installing npm packages..."
-npm install -g @mariozechner/pi-coding-agent
-
-# ---------------------------------------------------------------------------
-# Fonts
-# ---------------------------------------------------------------------------
-
-FONT_DIR="$HOME/.local/share/fonts/JetBrainsMono"
-if [[ ! -d "$FONT_DIR" ]]; then
-  echo ""
-  echo "Installing JetBrains Mono Nerd Font..."
-  TMP="$(mktemp -d)"
-  curl -fLo "$TMP/JetBrainsMono.zip" \
-    "https://github.com/ryanoasis/nerd-fonts/releases/latest/download/JetBrainsMono.zip"
-  mkdir -p "$FONT_DIR"
-  unzip -q "$TMP/JetBrainsMono.zip" -d "$FONT_DIR"
-  rm -rf "$TMP"
-  fc-cache -f "$FONT_DIR"
-  echo "Font installed."
-else
-  echo "JetBrains Mono Nerd Font already installed, skipping."
-fi
-
-# ---------------------------------------------------------------------------
-# Stow all packages
-# ---------------------------------------------------------------------------
-
-echo ""
-echo "Stowing dotfiles..."
-
-# Check for conflicts before stowing
-CONFLICTS=()
-for PACKAGE in "$DOTFILES_DIR"/*/; do
-  PACKAGE="$(basename "$PACKAGE")"
-
-  # Skip hidden directories and .git
-  [[ "$PACKAGE" == .* ]] && continue
-
-  # Check if package has files that would conflict
-  while IFS= read -r -d '' dotfile; do
-    # Get the target path this would create
-    TARGET_PATH="${HOME}/${dotfile#$DOTFILES_DIR/$PACKAGE/}"
-
-    # If target exists and is NOT a symlink to the correct location, it's a conflict
-    if [[ -e "$TARGET_PATH" ]] && [[ ! -L "$TARGET_PATH" ]]; then
-      CONFLICTS+=("$PACKAGE (file: $TARGET_PATH)")
-    fi
-  done < <(find "$DOTFILES_DIR/$PACKAGE" -type f -print0 2>/dev/null || true)
-done
-
-if [[ ${#CONFLICTS[@]} -gt 0 ]]; then
-  echo "WARNING: Found conflicts with existing configs:"
-  for conflict in "${CONFLICTS[@]}"; do
-    echo "  ✗ $conflict"
-  done
-  echo ""
-fi
-
-# Stow all packages
-for PACKAGE in "$DOTFILES_DIR"/*/; do
-  PACKAGE="$(basename "$PACKAGE")"
-
-  # Skip hidden directories
-  [[ "$PACKAGE" == .* ]] && continue
-
-  echo "  $PACKAGE"
-  stow --dir="$DOTFILES_DIR" --target="$HOME" --restow "$PACKAGE"
-done
-
-# ---------------------------------------------------------------------------
-# Configure shell (after stowing)
-# ---------------------------------------------------------------------------
-
-echo ""
-echo "Configuring zsh..."
-
-# Ensure .zshrc exists (stow should have created it via symlink)
-if [[ ! -f "$HOME/.zshrc" ]]; then
-  touch "$HOME/.zshrc"
-fi
-
-# Ensure starship is initialized in .zshrc
-if ! grep -q 'eval "$(starship init zsh)"' "$HOME/.zshrc"; then
-  echo 'eval "$(starship init zsh)"' >> "$HOME/.zshrc"
-  echo "  Added starship initialization to ~/.zshrc"
-else
-  echo "  Starship already configured in ~/.zshrc"
-fi
-
-echo "Done."