Applied patch from Brian Foster <brian.foster@innova-card.com>:

make "make clean" remove the .root stamp, so that everything will
be reinstalled properly on a subsequent build. (bug id 4304)
Also remove new autotools-stamps directory.

Makefile

@@ -358,10 +358,10 @@ external-deps:
 #
 #############################################################
 clean: $(TARGETS_CLEAN)
-	rm -rf $(STAGING_DIR) $(TARGET_DIR) $(IMAGE)
+	rm -rf $(STAGING_DIR) $(TARGET_DIR) $(IMAGE) $(PROJECT_BUILD_DIR)/.root $(PROJECT_BUILD_DIR)/autotools-stamps
 
 dirclean: $(TARGETS_DIRCLEAN)
-	rm -rf $(STAGING_DIR) $(TARGET_DIR) $(IMAGE)
+	rm -rf $(STAGING_DIR) $(TARGET_DIR) $(IMAGE) $(PROJECT_BUILD_DIR)/.root $(PROJECT_BUILD_DIR)/autotools-stamps
 
 distclean:
 ifeq ($(DL_DIR),$(BASE_DIR)/dl)