Build $(PROJECT_BUILD_DIR)/autotools-stamps with normal Makefile rules

This patch will add a rule to top level Makefile to depend on the
$(PROJECT_BUILD_DIR)/autotools-stamps as a required directory. Hence it will be
generated if missing in stead of made when the $(PROJECT_BUILD_DIR)/.root rule
is triggered.

Signed-off-by: Hans-Christian Egtvedt <hans-christian.egtvedt@atmel.com>