Defining CPPFLAGS in Makefile.am causes problems if a user happens to already have CPPFLAGS set, as shown below. Using AM_CPPFLAGS instead achieves the same effect while gracefully handling the case where the user has CPPFLAGS set. A patch is attached to make this trivial change.
aarre@ganesha ~/src/ext/devtodo/trunk
$ ./autogen.sh
libtoolize
aclocal
automake
configure.in: installing `./install-sh'
configure.in: installing `./missing'
src/Makefile.am:11: CPPFLAGS was already defined in condition TRUE, which includes condition DEBUG ...
configure.in:9: ... `CPPFLAGS' previously defined here
src/Makefile.am: installing `./depcomp'
src/Makefile.am:11: `CPPFLAGS' is a user variable, you should not override it;
src/Makefile.am:11: use `AM_CPPFLAGS' instead.
src/Makefile.am:13: `CPPFLAGS' is a user variable, you should not override it;
src/Makefile.am:13: use `AM_CPPFLAGS' instead.
configure.in:88: required file `config.h.in' not found