Move the include flags for files in the source tree from
configure.ac to Makefile.am where they belong.  Also use
AM_CPPFLAGS instead of CFLAGS/CXXFLAGS to make sure the
files in the build/source tree are always picked up first.

Also, remove the include/libsigrok sub-directory from the
search path, thereby making the <libsigrok/> prefix mandatory
when building libsigrok itself.  This matches the convention
already imposed on users of the library.