configure, make, etc. operations should be remove by "make maintainer-clean".
It occurs to me that perhaps it is desirable to split maintainer-clean (keep it as it is) and (say) bootstrap-clean after all. I can imagine, as a maintainer, wanting to rm everything *except* the bootstrap stuff -- especially if bootstrap needs a net connection to work. Also, it would make the standards.texi patch simpler :). Not sure, just occurred to me ...
