diff --git a/scripts/install.sh b/scripts/install.sh
index fe71b1b..cdf931a 100644
--- a/scripts/install.sh
+++ b/scripts/install.sh
@@ -115,11 +115,18 @@ header() {
   clear
   printf "${BOLD}${BLUE}"
   cat << 'EOF'
-  ╔══════════════════════════════════════════════════════════╗
-  ║                       Some ASCII Art                     ║
-  ╠══════════════════════════════════════════════════════════╣
-  ║                  Installer  ·  Arch Linux                ║
-  ╚══════════════════════════════════════════════════════════╝
+  ╔══════════════════════════════════════════════════════════════════╗
+  ║          _   _             _____            _    _               ║
+  ║     /\  | | | |           |  __ \          | |  | |              ║
+  ║    /  \ | |_| | __ _ ___  | |  | | ___  ___| | _| |_ ___  _ __   ║
+  ║   / /\ \| __| |/ _` / __| | |  | |/ _ \/ __| |/ / __/ _ \| '_ \  ║
+  ║  / ____ \ |_| | (_| \__ \ | |__| |  __/\__ \   <| || (_) | |_) | ║
+  ║ /_/    \_\__|_|\__,_|___/ |_____/ \___||___/_|\_\\__\___/| .__/  ║
+  ║                                                          | |     ║
+  ║                                                          |_|     ║
+  ╠══════════════════════════════════════════════════════════════════╣
+  ║                     Installer  ·  Arch Linux                     ║
+  ╚══════════════════════════════════════════════════════════════════╝
 EOF
   printf "${RESET}\n"
 }
@@ -537,25 +544,63 @@ install_packages() {
 }
 
 # ─────────────────────────────────────────────────────────────────────────────
-#  STEP 9 — Stow dotfiles
+#  STEP 9 — Clone into ~/.atlas-dotfiles and stow
 # ─────────────────────────────────────────────────────────────────────────────
 stow_dotfiles() {
-  phase "Stowing dotfiles"
+  phase "Copying and stowing dotfiles"
 
-  step "Linking ${CONFIG_DIR} → ${HOME}"
+  # ~/.atlas-dotfiles is the permanent home of the repo. They can delete the original
+  # clone after installation without breaking anything.
+  local remote_url
+  remote_url=$(git -C "$REPO_DIR" remote get-url origin 2>/dev/null || true)
 
-  # The config/ dir IS the stow package (its contents mirror $HOME)
-  # We treat config/ as a single stow package named "config"
-  # stow will create symlinks in $HOME for everything inside config/
+  if [[ -z $remote_url ]]; then
+    die "Could not determine remote URL from $REPO_DIR (is origin set?)"
+  fi
 
-  # Backup any existing files that would conflict
+  step "Setting up ~/.atlas-dotfiles as the permanent repo"
+  info "Remote: $remote_url"
+
+  if [[ -d $DOTFILES_DIR/.git ]]; then
+    # Already a git repo — verify it points to the same remote
+    local existing_remote
+    existing_remote=$(git -C "$DOTFILES_DIR" remote get-url origin 2>/dev/null || true)
+    if [[ $existing_remote == $remote_url ]]; then
+      ok "~/.atlas-dotfiles already cloned from correct remote"
+      run_quiet "Pulling latest" git -C "$DOTFILES_DIR" pull --ff-only origin main
+    else
+      warn "~/.atlas-dotfiles exists but points to a different remote:"
+      warn "  existing: $existing_remote"
+      warn "  expected: $remote_url"
+      if confirm "Replace it with the correct repo?" y; then
+        rm -rf "$DOTFILES_DIR"
+        run_quiet "Cloning dotfiles" git clone "$remote_url" "$DOTFILES_DIR"
+      else
+        die "Aborted — ~/.atlas-dotfiles remote mismatch"
+      fi
+    fi
+  elif [[ -e $DOTFILES_DIR ]]; then
+    warn "~/.atlas-dotfiles exists but is not a git repo — moving to ~/.atlas-dotfiles.bak"
+    mv "$DOTFILES_DIR" "${DOTFILES_DIR}.bak"
+    run_quiet "Cloning dotfiles" git clone "$remote_url" "$DOTFILES_DIR"
+  else
+    run_quiet "Cloning dotfiles" git clone "$remote_url" "$DOTFILES_DIR"
+  fi
+
+  #TODO Checkout ?
+
+  ok "~/.atlas-dotfiles → $remote_url"
+
+  # Backup any real files that would conflict with stow links
+  local stow_config_dir="$DOTFILES_DIR/config"
   local conflicts=()
   while IFS= read -r link; do
-    local target="$HOME/${link#$CONFIG_DIR/}"
+    local rel="${link#$stow_config_dir/}"
+    local target="$HOME/$rel"
     if [[ -e $target && ! -L $target ]]; then
       conflicts+=("$target")
     fi
-  done < <(find "$CONFIG_DIR" -type f)
+  done < <(find "$stow_config_dir" -type f 2>/dev/null)
 
   if (( ${#conflicts[@]} )); then
     warn "${#conflicts[@]} existing file(s) will be backed up (.bak):"
@@ -565,29 +610,9 @@ stow_dotfiles() {
     done
   fi
 
-  # Create DOTFILES_DIR as a symlink to CONFIG_DIR, or use CONFIG_DIR directly
-  # We symlink ~/.atlas-dotfiles → repo's config dir so stow state lives in the repo
-  if [[ -L $DOTFILES_DIR ]]; then
-    local existing_target; existing_target=$(readlink -f "$DOTFILES_DIR")
-    if [[ $existing_target != "$CONFIG_DIR" ]]; then
-      warn "~/.atlas-dotfiles already points elsewhere: $existing_target"
-      warn "Removing and re-linking to $CONFIG_DIR"
-      rm "$DOTFILES_DIR"
-      ln -s "$CONFIG_DIR" "$DOTFILES_DIR"
-    fi
-  elif [[ -d $DOTFILES_DIR ]]; then
-    warn "~/.atlas-dotfiles exists as a real directory. Renaming to ~/.atlas-dotfiles.bak"
-    mv "$DOTFILES_DIR" "${DOTFILES_DIR}.bak"
-    ln -s "$CONFIG_DIR" "$DOTFILES_DIR"
-  else
-    ln -s "$CONFIG_DIR" "$DOTFILES_DIR"
-  fi
-
-  ok "~/.atlas-dotfiles → $CONFIG_DIR"
-
-  # Now run stow from inside the repo's parent, treating config as the package
+  # Stow from ~/.atlas-dotfiles treating config/ as the stow package
   run_quiet "Stowing config" \
-    stow --dir="$REPO_DIR" --target="$HOME" --restow config
+    stow --dir="$DOTFILES_DIR" --target="$HOME" --restow config
 
   phase_done
 }
@@ -709,28 +734,37 @@ enable_services() {
 install_updater() {
   phase "Dotfiles updater"
 
-  local updater_src="$SCRIPTS_DIR/update.sh"
-  local updater_link="$HOME/.local/bin/atlas-update"
+  local updater_in_dotfiles="$DOTFILES_DIR/scripts/update.sh"
+  local updater_link="$HOME/.local/bin/dotfiles-update"
 
-  if [[ ! -f $updater_src ]]; then
-    warn "Updater not found at $updater_src — skipping"
+  if [[ ! -f $updater_in_dotfiles ]]; then
+    warn "update.sh not found in ~/.atlas-dotfiles/scripts/ — skipping"
+    info "Expected: $updater_in_dotfiles"
     phase_done
     return
   fi
 
+  chmod +x "$updater_in_dotfiles"
   mkdir -p "$HOME/.local/bin"
-  chmod +x "$updater_src"
 
-  # Create symlink (stow might also handle this if update.sh is in config/)
-  # Here we link directly so it's always in PATH regardless of stow layout
-  ln -sf "$updater_src" "$updater_link"
-  ok "atlas-update → $updater_src"
-  info "Run ${BOLD}atlas-update${RESET} any time to sync with upstream"
+  # Symlink into PATH — stow may also handle this if scripts/ is a stow pkg,
+  # but we do it explicitly here so it works regardless of stow layout.
+  ln -sf "$updater_in_dotfiles" "$updater_link"
+  ok "dotfiles-update → $updater_in_dotfiles"
+  info "Run ${BOLD}dotfiles-update${RESET} any time to sync with upstream"
 
-  # Save repo path into state so updater knows where it lives
-  mkdir -p "$STATE_DIR"
-  state_set "repo_dir" "$REPO_DIR"
-  state_set "last_commit" "$(git -C "$REPO_DIR" rev-parse HEAD)"
+  # Initialise state inside the permanent repo
+  local state_dir="$DOTFILES_DIR/.state"
+  mkdir -p "$state_dir"
+  # Point state file at the permanent repo, not the installer's location
+  grep -q "^repo_dir=" "$state_dir/update.state" 2>/dev/null ||     echo "repo_dir=$DOTFILES_DIR" >> "$state_dir/update.state"
+  # Stamp the current HEAD so the first `dotfiles-update` knows the baseline
+  local head; head=$(git -C "$DOTFILES_DIR" rev-parse HEAD)
+  if grep -q "^last_commit=" "$state_dir/update.state" 2>/dev/null; then
+    sed -i "s|^last_commit=.*|last_commit=${head}|" "$state_dir/update.state"
+  else
+    echo "last_commit=$head" >> "$state_dir/update.state"
+  fi
 
   phase_done
 }
@@ -744,7 +778,7 @@ finish() {
   cat << 'EOF'
   ╔══════════════════════════════════════════════════════════╗
   ║                                                          ║
-  ║     ✔  Installation complete!                           ║
+  ║     ✔  Installation complete!                            ║
   ║                                                          ║
   ╚══════════════════════════════════════════════════════════╝
 EOF
diff --git a/scripts/update.sh b/scripts/update.sh
index 4bfc37b..36c28bc 100644
--- a/scripts/update.sh
+++ b/scripts/update.sh
@@ -190,9 +190,13 @@ git_fetch_and_check() {
 
 # ── Conflict detection ────────────────────────────────────────────────────────
 collect_changed_files() {
-  # Files changed between old commit and new commit in the repo
+  # Files changed inside the config/ stow package between old and new commit.
+  # Strip the leading "config/" prefix so paths are relative to $HOME,
+  # matching what stow creates as symlink targets.
   git -C "$DOTFILES_DIR" diff --name-only "${OLD_HASH}" "${NEW_HASH}" \
-    | grep -v '^packages/' | grep -v '^\.' || true
+    | grep '^config/' \
+    | sed 's|^config/||' \
+    || true
 }
 
 handle_conflicts() {
@@ -292,33 +296,17 @@ apply_git_update() {
 # ── Stow ─────────────────────────────────────────────────────────────────────
 apply_stow() {
   section "Stowing dotfiles"
-  cd "$DOTFILES_DIR"
 
-  # Discover stow packages (top-level dirs, excluding hidden & packages/)
-  local stow_pkgs=()
-  while IFS= read -r d; do
-    local name
-    name=$(basename "$d")
-    [[ $name == packages ]] && continue
-    stow_pkgs+=("$name")
-  done < <(find "$DOTFILES_DIR" -mindepth 1 -maxdepth 1 -type d ! -name '.*' | sort)
-
-  if (( ${#stow_pkgs[@]} == 0 )); then
-    warn "No stow packages found in $DOTFILES_DIR"
-    return
+  local err_file; err_file=$(mktemp)
+  if stow --dir="$STOW_DIR" --target="$STOW_TARGET" --restow "$STOW_PKG"        2>"$err_file"; then
+    ok "stow: $STOW_PKG"
+  else
+    warn "stow: $STOW_PKG (errors below)"
+    while IFS= read -r line; do
+      echo "       ${DIM}${line}${RESET}"
+    done < "$err_file"
   fi
-
-  for pkg in "${stow_pkgs[@]}"; do
-    if stow --restow --target="$STOW_TARGET" "$pkg" 2>/tmp/stow_err; then
-      ok "stow: $pkg"
-    else
-      warn "stow: $pkg (see error below)"
-      while IFS= read -r line; do
-        echo "       ${DIM}${line}${RESET}"
-      done < /tmp/stow_err
-    fi
-  done
-  rm -f /tmp/stow_err
+  rm -f "$err_file"
 }
 
 # ── Package management ────────────────────────────────────────────────────────
@@ -493,7 +481,8 @@ process_aur_group() {
 # ── Entry point ───────────────────────────────────────────────────────────────
 main() {
   echo
-  echo "${BOLD}  Hyprland Dotfiles Updater${RESET}  ${DIM}(Arch Linux)${RESET}"
+  echo "${BOLD}  Atlas Desktop Updater${RESET}"
+  echo "${DIM}  Arch Linux${RESET}"
   echo "  ${DIM}Target: ${DOTFILES_DIR}${RESET}"
 
   [[ -d $DOTFILES_DIR/.git ]] || die "$DOTFILES_DIR is not a git repository."