Fix setup stow flow

Commands/Setup/mod.just

@@ -11,7 +11,7 @@ base:
 
 # Stow shell files into $HOME.
 stow:
-    stow --dir='{{project_root}}' Zsh --target="$HOME"
+    bash '{{scripts_dir}}/setup.sh' --stow-only
 
 # Remove stowed shell files from $HOME.
 clean:

Justfile

@@ -4,6 +4,5 @@ mod bin "Commands/Bin"
 mod lang "Commands/Lang"
 mod setup "Commands/Setup"
 
-[default]
 help:
     just --list --list-submodules

Makefile

@@ -8,6 +8,4 @@ all: setup
 # Bootstrap entrypoint for first-run setup.
 # This intentionally keeps Make lightweight: base packages, then restow dotfiles.
 setup:
-	bash $(SCRIPTS_DIR)/base.sh
+	bash $(SCRIPTS_DIR)/setup.sh --bootstrap-only
-	stow --dir=. -D Zsh --target="$$HOME" 2>/dev/null || true
-	stow --dir=. Zsh --target="$$HOME"

Scripts/setup.sh

@@ -101,7 +101,26 @@ backup_conflicting_home_files() {
     fi
 }
 
-main() {
+stow_dotfiles() {
+    sync_repo_managed_secret_file
+    backup_conflicting_home_files
+
+    stow --dir="$REPO_ROOT" -D Zsh --target="$HOME" 2>/dev/null || true
+    stow --dir="$REPO_ROOT" Zsh --target="$HOME"
+}
+
+bootstrap_only() {
+    rm -f "$REBOOT_MARKER"
+
+    bash "$SCRIPT_DIR/base.sh"
+    handle_reboot_marker
+
+    stow_dotfiles
+
+    echo "Bootstrap setup completed."
+}
+
+full_setup() {
     rm -f "$REBOOT_MARKER"
 
     bash "$SCRIPT_DIR/base.sh"
@@ -116,13 +135,23 @@ main() {
     bash "$SCRIPT_DIR/r.sh"
     handle_reboot_marker
 
-    sync_repo_managed_secret_file
+    stow_dotfiles
-    backup_conflicting_home_files
-
-    stow --dir="$REPO_ROOT" -D Zsh --target="$HOME" 2>/dev/null || true
-    stow --dir="$REPO_ROOT" Zsh --target="$HOME"
 
     echo "Full setup completed."
 }
 
-main "$@"
+case "${1:-}" in
+    --bootstrap-only)
+        bootstrap_only
+        ;;
+    --stow-only)
+        stow_dotfiles
+        ;;
+    "")
+        full_setup
+        ;;
+    *)
+        echo "Usage: $0 [--bootstrap-only|--stow-only]"
+        exit 1
+        ;;
+esac