autogen.sh shouldn't run configure because it must be run from the source dir while configure should be run from the build dir, AND build dir might be different from the source dir. (really convenient when cross-compiling or when sharing source trees acrosse different platforms)
IMO it's o.k. to run configure. If you build HAL you need to run ./configure with your own options and at least autogen.sh is not part of the distributed package and you need configure to run make dist and distcheck.
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