fix: Make the install script clone the repo instead of linking it and reflected changes into the updater

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."