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Specifically, the "CPPFLAGS" are for users only. We must never modify these flags to build a product. The appropriate system-internal flags are the "AM_CPPFLAGS". Moreover, the "LIBS" variable is an implementation detail that should not be directly modified by a particular build system. Inter-library link dependencies should be specified in the <library>_LDFLAGS. See, for instance, http://www.gnu.org/software/automake/manual/html_node/Libtool-Flags.html