Several variables are considered "user variables" by the GNU Standards.
This means that the user can pass these to their ./configure and make
invocations as they see fit.  These variables include CPPFLAGS, CFLAGS
and LDFLAGS.

This changeset pushes our use of these variables to the automake shadow
variables, AM_CPPFLAGS, AM_CFLAGS and AM_LDFLAGS, so that user variables
will no longer clobber flags required in order to build.