Fix package.* files installation to work with new stage3's

The new (2015-02) stage3 tarballs use package.* directories instead of
files, causing the files to fail to be copied over.  This change instead
copies them to the directories, creating them if they don't already exist.

Makefile

@@ -173,10 +173,11 @@ endif
 	$(inroot) eselect profile set 1
 	cp configs/locale.gen $(CHROOT)/etc/locale.gen
 	$(inroot) locale-gen
-	mkdir -p $(CHROOT)/etc/portage
-ifdef PACKAGE_FILES
-	cp $(PACKAGE_FILES) $(CHROOT)/etc/portage/
-endif
+	for f in $(PACKAGE_FILES); do \
+		base=`basename $$f` ; \
+		mkdir -p $(CHROOT)/etc/portage/$$base; \
+		cp $$f $(CHROOT)/etc/portage/$$base/virtual-appliance-$$base; \
+	done
 	touch compile_options
 
 base_system: mounts compile_options