clean up makefile and separate general from qubes configs

Makefile

@@ -1,3 +1,20 @@
-.PHONY: apply
-apply:
-	stow --target=$${HOME} */
+QUBES_DIRS = qubes dom0
+ALL_DIRS = $(shell ls -d */ | sed 's#/##')
+GENERAL_DIRS = $(filter-out $(QUBES_DIRS), $(ALL_DIRS))
+
+.PHONY: all apply apply-general apply-qubes clean
+
+all: apply-general apply-qubes
+
+apply-general:
+	@echo "Applying general configurations..."
+	stow --target=$(HOME) $(GENERAL_DIRS)
+
+apply-qubes:
+	@echo "Applying Qubes configurations..."
+	stow --target=/ qubes
+
+clean:
+	@echo "Removing stowed configurations..."
+	stow -D --target=$(HOME) $(GENERAL_DIRS)
+	stow -D --target=/ qubes